Two TMS K+ and water channel (conducts K+ (KD = 8 mM); blocked by Na+ (190 mM) (Renart et al., 2006) and tetrabutylammonium (Iwamoto et al., 2006)). Ion permeation occurs by ion-ion contacts in single file fashion through the selectivity filter (Köpfer et al. 2014). A narrow pore lined with four arrays of carbonyl groups is responsible for ion selectivity, whereas a conformational change of the four inner transmembrane helices (TMS2) is involved in gating (Baker et al. 2007). Two gates have been identified; one is located at the inner bundle crossing and is activated by H+ while the second gate is in the selectivity filter (Rauh et al. 2017). The C-terminal domain mediates pH modulation (Hirano et al., 2011; Pau et al., 2007). KcsA exhibits a global twisting motion upon gating (Shimizu et al., 2008). Activity is influenced by the phase of the lipid bilayer (Seeger et al. 2010), and occupancy of nonannular lipid binding sites increases the stability of the tetrameric complex (Triano et al. 2010). The open conformation of KcsA can disturb the bilayer integrity and catalyze the flipping of phospholipids (Nakao et al. 2014). This protein is identical to the KcsA orthologue (P0A333) in Streptomyces coelicolor. The stability of the pre domain in KcsA is stabilized by GCN4 (Yuchi et al. 2008). The potential role of pore hydration in channel gating has been evaluated (Blasic et al. 2015). Having multiple K+ ions bound simultaneously is required for selective K+ conduction, and a reduction in the number of bound K+ ions destroys the multi-ion selectivity mechanism utilized by K+ channels (Medovoy et al. 2016). The channel accomodates K+ and H2O molecules alternately in a K+-H2O-K+-H2O series through the channel (Kratochvil et al. 2016). Insertion of KcsA is spontaneous and directional as the cytosolic part of the protein does not translocate across the membrane barrier. Charged residues, not hydrophobic residues, are crucial for insertion of the unfolded protein into the membrane via electrostatic interactions between membrane and protein. A two-step mechanism was proposed. An initial electrostatic attraction between membrane and protein represents the first step prior to insertion of hydrophobic residues into the hydrocarbon core of the membrane (Altrichter et al. 2016). Bend, splay, and twist distinguish KcsA gate opening, filter opening, and filter-gate coupling, respectively (Mitchell and Leibler 2017). Details of the water permeability have been presented. Water flow through KcsA is halved by 200 mM K+ in the aqueous solution, which indicates an effective K+ dissociation constant in that range for a singly occupied channel. (Hoomann et al. 2013). A parameterized MARTINI program can be used to predict the hinging motions of the protein (Li et al. 2019). Activation of KcsA is initiated by proton binding to the pH gate upon an intracellular drop in pH which prompts a conformational switch, leading to a loss of affinity for potassium ions at the selectivity filter and therefore to channel inactivation (Rivera-Torres et al. 2016). An alteration in the conformational equilibrium of the intracellular K+-gate is one of the fundamental mechanisms underlying the dysfunctions of K+ channels caused by disease-related mutations (Iwahashi et al. 2020). Folding and misfolding of KcsA monomers during assembly and tetramerization has been examined (Song et al. 2021). The flexible C-terminus stabilizes KcsA tetramers at a neutral pH with decreased stabilization at acidic pH (Howarth and McDermott 2022).
Voltage-sensitive Na+ channel, NaV1.7 (Cox et al., 2006). The human orthologue, SCN3A or Nav1.3, when mutated causes cryptogenic pediatric partial epilepsy (Holland et al., 2008; Zaman et al. 2020). Batrachotoxin (BTX) is a steroidal alkaloid neurotoxin that activates NaV channels through interacting with transmembrane domain-I-segment 6 (IS6) of these channels. Ginsenoside inhibits BTX binding (Lee et al. 2008). VGSCs are heterotrimeric complexes consisting of a single pore-forming alpha subunit joined by two beta subunits, a noncovalently linked beta1 or beta3 and a covalently linked beta2 or beta4 subunit (Hull and Isom 2017). The binding mode and functional components of the analgesic-antitumour peptide from Buthus martensii Karsch to human voltage-gated sodium channel 1.7 have been characterized (Zhao et al. 2019). Dvorak et al. 2021 developed allosteric modulators of ion channels by targeting their PPI interfaces, particularly in the C-terminal domain of the Nav, with auxiliary proteins. Fenestrations are key functional regions of Nav that modulate drug binding, lipid binding, and influence gating behaviors (Gamal El-Din and Lenaeus 2022). Compartment-specific localizations and trafficking mechanisms for VGSCs are regulated separately to modulate membrane excitability in the brain (Liu et al. 2022).
Type 2 Na+ channel, SCN2A or NaV1.2, of 2,005 aas and 24 TMSs. Mutations give rise to epileptic encephalophathy, Ohtahara syndrome (Nakamura et al. 2013). They may also give rise to autism (ASD) (Tavassoli et al. 2014). This protein is orthologous to the rat Na+ channel, TC# 1.A.1.10.1 and very similar to the type 1 Na+ channel (1.A.1.10.7). NaV1.2 has a single pore-forming alpha-subunit and two transmembrane beta-subunits. Expressed primarily in the brain, NaV1.2 is critical for initiation and propagation of action potentials. Milliseconds after the pore opens, sodium influx is terminated by inactivation processes mediated by regulatory proteins including calmodulin (CaM). Both calcium-free (apo) CaM and calcium-saturated CaM bind tightly to an IQ motif in the C-terminal tail of the alpha-subunit. Thermodynamic studies and solution structure (2KXW) of a C-domain fragment of apo 13C,15N- CaM (CaMC) bound to an unlabeled peptide with the sequence of the rat NaV1.2 IQ motif showed that apo CaMC (a) was necessary and sufficient for binding, and (b) bound more favorably than calcium-saturated CaMC. CaMN apparently does not influence apo CaM binding to NaV1.2IQp (Mahling et al. 2017). The phenotypic spectrum of SCN2A-related epilepsy is broad, ranging from benign epilepsy in neonate and infancy to severe epileptic encephalopathy. Oxcarbazepine and valproate are the most effective drugs in epilepsy patients with SCN2A variants. Sodium channel blockers often worsen seizures in patients with seizure onset beyond 1 year of age. Abnormal brain MRI findings and de novo variations are often related to poor prognosis. Most SCN2A variants located in transmembrane regions were related to patients with developmental delay (Zeng et al. 2022).
Sodium channel Nav1.4-beta complex of 1820 and 209 aas, respectively. Voltage-gated sodium (Nav) channels initiate and propagate action potentials. Yan et al. 2017 presented the cryo-EM structure of EeNav1.4, the Nav channel from electric eel, in complex with the beta1 subunit at 4.0 Å resolution. The immunoglobulin domain of beta1 docks onto the extracellular L5I and L6IV loops of EeNav1.4 via extensive polar interactions, and the single transmembrane helix interacts with the third voltage-sensing domain (VSDIII). The VSDs exhibit ""up"" conformations, while the intracellular gate of the pore domain is kept open by a digitonin-like molecule. Structural comparison with closed NavPaS shows that the outward transfer of gating charges is coupled to the iris-like pore domain dilation through intricate force transmissions involving multiple channel segments. The IFM fast inactivation motif on the III-IV linker is plugged into the corner enclosed by the outer S4-S5 and inner S6 segments in repeats III and IV, suggesting a potential allosteric blocking mechanism for fast inactivation (Yan et al. 2017). The PDB# for the complex is 5XSY, and that for the two subunits are 5XSY_A and 5XSY_B. Domain 4 TMS 6 of Nav1.4 plays a key role in channel gating regulation, and is targeted by the neurotoxin, veratridine (VTD) (Niitsu et al. 2018).
Voltage-gated sodium channel of 1836 aas and 24 TMSs, PaFPC1. The 3-d structure has been determined (Shen et al. 2017). It mediates the voltage-dependent sodium ion permeability in excitable membranes.
Ca2+-regulated heart Na+ channel, Nav1.5, SCN5A or INa channel of 2016 aas. The COOH terminus functions in the control of channel inactivation and in pathologies caused by inherited mutations that disrupt it (Glaaser et al., 2006); regulated by ProTx-II Toxin (Smith et al. 2007), telethonin, the titin cap protein (167aas; secreted protein; O15273) (Mazzone et al., 2008), and the Mog1 protein, a central component of the channel complex (Wu et al., 2008). Nav1.5, the principal Na+ channel in the heart, possesses an ankyrin binding site, and direct interaction with ankyrin-G is required for the expression of Nav1.5 at the cardiomyocyte cell surface (Bennett and Healy, 2008; Lowe et al., 2008). Mutations cause type 3 long QT syndrome and type 1 Brugada syndrome, two distinct heritable arrhythmia syndromes (Mazzone et al., 2008; Kapplinger et al. 2010; Wang et al. 2015). SCN5A mutations causing arrhythmic dilated cardiomyopathy, commonly localized to the voltage-sensing mechanism, and giving rise to gating pore currents (currents that go through the voltage sensor) have been identified (McNair et al., 2011; Moreau et al., 2014). Patients with Brugada syndrome are prone to develop ventricular tachyarrhythmias that may lead to syncope, cardiac arrest or sudden cardiac death (Sheikh and Ranjan 2014) and (Kapplinger et al. 2015). Mutations causing disease have been identified (Qureshi et al. 2015). These give rise to arrhythias and cardiomyopathies (Moreau et al. 2015). Mutations that cause relative resistance to slow inactivation have been identified (Chancey et al. 2007). Green tea catechins are potential anti-arrhythmics because of the significant effect of Epigallocatechin-3-Gallate (E3G) on cardiac sodium channelopathies that display a hyperexcitability phenotype (Boukhabza et al. 2016). A mutatioin, R367G, causes the familial cardiac conductioin disease (Yu et al. 2017). The C-terminal domain of calmodulin (CaM) binds to an IQ motif in the C-terminal tail of the alpha-subunit of all NaV isoforms, and contributes to calcium-dependent pore-gating in some (Isbell et al. 2018). Ventricular fibrillation in patients with Brugada syndrome (BrS) is often initiated by premature ventricular contractions, and the presence of SCN5A mutations increases the risk upon exposure to sodium channel blockers in patients with or without baseline type-1 ECG (Amin et al. 2018). A mutation (R367G) is associated with familial cardiac conduction disease (Yu et al. 2017). Among ranolazine, flecainide, and mexiletine, only mexiletine restored inactivation kinetics of the currents of the mutant protein, A1656D (Kim et al. 2019). Epigallocatechin-3-gallate (EGCG) is protective against cardiovascular disorders due in part to its action on multiple molecular pathways and transmembrane proteins, including the cardiac Nav1.5 channels (Amarouch et al. 2020). An SCN1B variant affects both cardiac-type (NaV1.5) and brain-type (NaV1.1) sodium currents and contributes to complex concomitant brain and cardiac disorders (Martinez-Moreno et al. 2020). Mice null for Scn1b, which encodes NaV beta1 and beta1b subunits, have defects in neuronal development and excitability, spontaneous generalized seizures, cardiac arrhythmias, and early mortality (Martinez-Moreno et al., 2020; Martinez-Moreno et al. 2020). The structural basis of cytoplasmic NaV1.5 and NaV1.4 regulation has been reviewed (Nathan et al. 2021). Fibroblast growth factor 21 ameliorates NaV1.5 and Kir2.1 channel dysregulation in human AC16 cardiomyocytes (Li et al. 2021). The interaction of Nav1.5 with MOG1 (RANGRF), a Ran guanine nucleotide release factor and chaparone, provides a possible molecular mechanism for Brugada syndrome (Xiong et al. 2021). Arrhythmic phenotypes are a defining feature of dilated cardiomyopathy-associated SCN5A variants (Peters et al. 2021). A SCN5A genetic variant, Y739D, is associated with Brugada syndrome (Zaytseva et al. 2022). Melatonin treatment causes an increase of conduction via enhancement of sodium channel protein expression and increases of sodium current in the ventricular myocytes (Durkina et al. 2022). Quantification of Nav1.5 expression has been published (Adams et al. 2022).
The skeletal muscle Na+ channel, NaV1.4 of 1836 aas and 24 TMSs. Mutations in charged residues in the S4 segment cause hypokalemic periodic paralysis (HypoPP)) due to sustained sarcolemmal depolarization (Struyk and Cannon 2007; Sokolov et al., 2007; Groome et al. 2014). Also causes myotonia; regulated by calmodulin which binds to the C-terminus of Nav1.4 (Biswas et al., 2008). NaV1.4 gating pores are permeable to guanidine as well as Na+ and H+ (Sokolov et al., 2010). The R669H mutation allows transmembrane permeation of protons, but not larger cations, similar to the conductance displayed by histidine substitution at Shaker K+ channel S4 sites (Struyk and Cannon 2007). The mechanism of inactivation involves transient interactions between intracellular domains resulting in direct pore occlusion by the IFM motif and concomitant extracellular interactions with the beta1 subunit (Sánchez-Solano et al. 2016). Potassium-sensitive hypokalaemic and normokalaemic periodic paralysis are inherited skeletal muscle diseases in humans, characterized by episodes of flaccid muscle weakness. They are caused by single mutations in positively charged residues ('gating charges') in the S4 transmembrane segment of the voltage sensor of the voltage-gated sodium channel Nav1.4 or the calcium channel Cav1.1. Mutations of the outermost gating charges (R1 and R2) cause hypokalaemic periodic paralysis by creating a pathogenic gating pore in the voltage sensor through which cations leak in the resting state. Mutations of the third gating charge (R3) cause normokalaemic periodic paralysis owing to cation leak in both activated and inactivated states (Jiang et al. 2018). The neurotoxic cone snail peptide μ-GIIIA specifically blocks skeletal muscle voltage-gated sodium (NaV1.4) channels (Leipold et al. 2017). the cryo-electron microscopy structure of the human Nav1.4-β1 complex at 3.2-Å resolution. Accurate model building was made for the pore domain, the voltage-sensing domains, and the β1 subunit (Pan et al. 2018) provided insight into the molecular basis for Na+ permeation and kinetic asymmetry of the four repeats. Structural analysis of reported functional residues and disease mutations corroborates an allosteric blocking mechanism for fast inactivation of Nav channels. the S4-S5L of the DI, DII and DIII domains allosterically modulate the activation gate and stabilize its open state (Malak et al. 2020). The structural basis of cytoplasmic NaV1.5 and NaV1.4 regulation has been reviewed (Nathan et al. 2021). Mutations in SCN4A give rise to a variety of pathological conditions (Sun et al. 2021).
Voltage-sensitive Na+ channel, type 9, α-subunit, Nav1.7 or SCN9A (orthologous to 1.A.1.10.1). Loss of function, resulting from point mutations, results in a channelopathy called Congenital Insensitivity to Pain (CIP) (He et al. 2018), that causes the congenital inability to experience pain (Cregg et al., 2010; Kleopa, 2011). An S241T mutation causes inherited erythromelalgia IEM; erythermalgia, an autosomal dominant neuropathy characterized by burning pain in the extremities in response to mild warmth (due to altered gating) (Lampert et al., 2006; Drenth and Waxman, 2007). Gain-of-function mutations in the Na(v)1.7 channel lead to DRG neuron hyperexcitability associated with severe pain, whereas loss of the Na(v)1.7 channel in patients leads to indifference to pain (Dib-Hajj et al., 2007). Blocked by 1-benzazepin-2-one (Kd = 1.6 nM) (Williams et al., 2007). Mutations in the Nav1.7 Na channel α-subunit give rise to familial pain syndromes called chronic non-paoxysmal neuropathic pain (Catterall et al., 2008; Fischer and Waxman, 2010; Dabby et al. 2011 ). It interacts with the sodium channel beta3 (Scn3b), rather than the beta1 subunit, as well as the collapsing-response mediator protein (Crmp2) through which the analgesic drug lacosamide regulates Nav1.7 current (Kanellopoulos et al. 2018). The R1488 variant is totally inactive (He et al. 2018). Nav1.7 is inhibited by knottins (see TC# 8.B.19.2) (Agwa et al. 2018). Nav1.7 interacts with the following proteins: syn3b (TC# 8.a.17.1.2; the β3 subunit), Crmp2, Syt2 (Q8N9I0) and Tmed10 (P49755), and it also regulates opioid receptor efficacy (Kanellopoulos et al. 2018). Mutations in TRPA1 and Nav1.7 to insensitivity to pain-promoting algogens such as capsaicin, acid, and allyl isothiocyanate (AITC), have been documented (Eigenbrod et al. 2019). Nav1.7 is associated with endometrial cancer (Liu et al. 2019) and fever-associated seizures or epilepsy (FASE) (Ding et al. 2019). Nav1.7 and Nav1.8 peripheral nerve sodium channels are modulated by protein kinases A and C (Vijayaragavan et al. 2004).
Neuronal nonselective cation channel, NALCN (forms background leak conductance and controls neuronal excitability; Lu et al., 2007). It is also found in the pancreatic β-cell (Swayne et al. 2010). NALCN serves as a variable sensor that responds to calcium or sodium ion flux, depending on whether the total cellular current density is generated more from calcium-selective or sodium-selective channels (Senatore and Spafford 2013). It functions in a complex with Unc80 (3258 aas; Q8N2C7) and Unc79 (2635 aas; Q9P2D8) (Bramswig et al. 2018). Heterozygous de novo NALCN missense variants in the S5/S6 pore-forming segments lead to congenital contractures of the limbs and face, hypotonia, and developmental delay (Bramswig et al. 2018). Overexpression of the NALCN gene ablates allyl isothiocyanate-promoting pain reception by nociceptors (Eigenbrod et al. 2019).
The phosphoinositide (PI(3,5)P2)-activated Na+ two pore channel-2, TPC2, in endosomes and lysosomes (Wang et al. 2012). Previously thought, incorectly, according to Wang et al. 2012, to be a nicotinic acid adenine dinucleotide phosphate (NAADP)-dependent two pore Ca2+ channel. TPC2, like TPC1, has a 12 TMS topology (two channel units) (Hooper et al., 2011). The two domains of human TPCs can insert into the membrane independently (Churamani et al., 2012). Cang et al. (2013), showed that TPC1 and TPC2 together form an ATP-sensitive two-pore Na+ channel that senses the metabolic state of the cell. The channel complex detects nutrient status, becomes constitutively open upon nutrient removal, and controls the lysosome's membrane potential, pH stability, and amino acid homeostasis. Essential for Ebola virus (EBOV) host entry. Several inhibitors of TPC2 that act in the nM (tetrandrine) or μM (verapamil; Ned19) range block channel activity, prevent Ebola Virus from escaping cell vesicles and may be used to treat the disease (Sakurai et al. 2015). TPC2 may transport both Na+ and Ca2+ (Sakurai et al. 2015). Lipid-gated monovalent ion fluxes, mediated by TPC1 and TPC2 in mice, regulate endocytic traffic and support immune surveillance. This is in part achieved by catalyzing Na+ export from visicles derived from the plasma membrane by phagocytosis or pinocytosis, causing contraction and allowing the maintenance of a uniform cell volume (Freeman et al. 2020). This system is important for melanocyte function (Wiriyasermkul et al. 2020).
Muscle plasmalemma, voltage-gated, L-type dihydropyridine receptor Ca2+ channel, α-1 subunit (DHPR) (Ba2+ > Ca2+), Cav1.1, CACNA1S,CACH1 CDCN1, CACNL1A3 of 1873 aas in the human orthologue. Distinc voltage sensor domains control voltage sensitivity and kinetics of current activation (Tuluc et al. 2016). Rapid changes in the transmembrane potential are detected by the voltage-gated Ca2+ channel, dihydropyridine receptor (DHPR), embedded in the sarcolemma. DHPR transmits the contractile signal to another Ca2+ channel, the ryanodine receptor (RyR1), embedded in the membrane of the sarcoplasmic reticulum (SR), which releases a large amounts of Ca2+ from the SR that initiate muscle contraction (Shishmarev 2020).
The phosphoinositide (PI(3,5)P2)-activated Na+ two pore channel-1, TPC1 of endosomes and lysosomes (Wang et al. 2012). Previously thought, incorectly, according to Wang et al. (2012), to be an NAADP-activated two pore voltage-dependent calcium channel protein. However, Cang et al. (2013), showed that TPC1 and TPC2 (TC# 1.A.1.11.19) together form an ATP-sensitive two-pore Na+ channel that senses the metabolic state of the cell. The channel complex detects nutrient status, becomes constitutively open upon nutrient removal, and controls the lysosome's membrane potential, pH stability, and amino acid homeostasis. May be regulated by the HCLS-associated X-1 (HAX-1) protein (Lam et al. 2013). The cryoEM 3-D structure has been ellucidated (She et al. 2018). This voltage-dependent, phosphatidylinositol 3,5-bisphosphate (PtdIns(3,5)P2)-activated Na+ channel was solved in both the apo closed state and ligand-bound open state. The channel has a coin-slot-shaped ion pathway in the filter that defines the selectivity of mammalian TPCs. Only the voltage-sensing domain from the second 6-TMS domain confers voltage dependence while endolysosome-specific PtdIns(3,5)P2 binds to the first 6-TMS domain and activates the channel under conditions of depolarizing membrane potential. Structural comparisons between the apo and PtdIns(3,5)P2-bound structures show the interplay between voltage and ligand activation. These MmTPC1 structures reveal lipid binding and regulation in a 6-TMS voltage-gated channel (She et al. 2018).
Two pore Ca2+ > Na+, Li+ or K+ (non-selective for these three monovalen caions) channel protein of 733 aas and 12 TMSs, TPC1 (Guo et al. 2017). The crystal structure of this vacuolar two-pore channel, a homodimer, has been solved (Guo et al. 2015) (Kintzer and Stroud 2016). Activation requires both voltage and cytosolic Ca2+. Ca2+ binding to the cytosolic EF-hand domain triggers conformational changes coupled to the pair of pore-lining inner helices from the first 6-TMS domains, whereas membrane potential only activates the second voltage-sensing domain, the conformational changes of which are coupled to the pair of inner helices from the second 6-TMS domains. Luminal Ca2+ or Ba2+ modulates voltage activation by stabilizing the second voltage-sensing domain in the resting state and shift voltage activation towards more positive potentials. The basis for understanding ion permeation, channel activation, the location of voltage-sensing domains and regulatory ion-binding sites is partially explained by the 3-d structure (Kintzer and Stroud 2016). Only the second Shaker domain senses voltage (Jaślan et al. 2016). It has a selectivity filter that is passable by hydrated divalent cations (Demidchik et al. 2018). Dickinson et al. 2022 determined structures at different stages along its activation coordinate. These structures of activation intermediates, when compared with the resting-state structure, portray a mechanism in which the voltage-sensing domain undergoes dilation and in-membrane plane rotation about the gating charge-bearing helix, followed by charge translocation across the charge transfer seal. These structures, in concert with patch-clamp electrophysiology, showed that residues in the pore mouth sense inhibitory Ca2+ and are allosterically coupled to the voltage sensor. These conformational changes provide insight into the mechanism of voltage-sensor domain activation in which activation occurs vectorially over a series of elementary steps (Dickinson et al. 2022). Inhibition of the Akt/PKB kinase increases Nav1.6-mediated currents and neuronal excitability in CA1 hippocampal pyramidal neurons (Marosi et al. 2022).
Voltage-dependent P/Q-type Ca2+ channel subunit α1A, CACNA1A (CACH4; CACN3; CACNL1A4) of 2,505 aas. The CACNA1A gene is widely expressed throughout the CNS. The encoding protein is 90% identical to 1.A.1.11.8. Associated with four neurological phenotypes: familial and sporadic hemiplegic migraine type 1 (FHM1, SHM1), episodic ataxia type 2 (EA2), spinocerebellar ataxia type 6 (SCA6) and epileptic encephalopathy with nerve atrophy (Reinson et al. 2016). A gain of function mutation gave symptoms of congenital ataxia, abnormal eye movements and developmental delay with severe attacks of hemiplegic migraine (García Segarra et al. 2014). Mutations can cause F/SHM with high penitrance (Prontera et al. 2018). CACNA1A variants lead to a wide spectrum of neurological disorders including epileptic or non-epileptic paroxysmal events, cerebellar ataxia, and developmental delay. The variants are either gain of function GOF) or loss of function (LOF) mutations (Zhang et al. 2020). CACNA1A pathogenic variants have been linked to several neurological disorders including severe early onset developmental encephalopathies and cerebellar atrophy. Y1384 variants exhibit differential splice variant-specific effects on recovery from inactivation (Gandini et al. 2021). Patients with CACNA1A mutational variants located in the transmembrane region may be at high risk of status epilepticus (Niu et al. 2022).
Voltage-sensitive calcium channel (VSCC), CAV1.3, encoded by the CACNA1D gene, of 2161 aas and 24 TMSs (Singh et al. 2008). CaV1.3-R990H channels conduct omega-currents at hyperpolarizing potentials, but not upon membrane depolarization compared with wild-type channels (Monteleone et al. 2017). A CACNA1D de novo mutation causes a severe neurodevelopmental disorder (Hofer et al. 2020).
Pore-forming, alpha-1S subunit of the voltage-gated calcium channel, of 1873 aas and 24 TMSs, Cav1.1; CACNA1S; CACN1; CACH1; CACNL1A3, that gives rise to L-type calcium currents in skeletal muscle. Calcium channels containing the alpha-1S subunit play an important role in excitation-contraction coupling in skeletal muscle via their interaction with RYR1, which triggers Ca2+ release from the sarcplasmic reticulum and ultimately results in muscle contraction. Long-lasting (L-type) calcium channels belong to the 'high-voltage activated' (HVA) group (Jiang et al. 2018). The 3-d structure of a bacterial homologue has been solved (Jiang et al. 2018). Mutations in arginly residues in the TMS4 voltage lead to increased leak currently that may be responsible for hypokalaemic periodic paralysis (Kubota et al. 2020). Mutations in the voltage sensor domain of CaV1.1, the alpha1S subunit of the L-type calcium channel in skeletal muscle cause hypokalemic periodic paralysis (HypoPP), and these mutations give rise to gating pore currents (Wu et al. 2021).
The voltage-dependent L-type Ca2+ channel α-subunit-1C (L-type Cav1.2), CACNA1C (CACH2, CACN2, CACNL1A1, CCHL1A1) of 2221 aa. Mutations cause Timothy's syndrome, a disorder associated with autism (Splawski et al., 2006). The C-terminus of Cav1.2 encodes a transcription factor (Gomez-Ospina et al., 2006). Cav1.2 associates with the α-2, δ-1, β and γ subunits (Yang et al., 2011). The CRAC channel activator STIM1 binds and inhibits L-type voltage-gated calcium channel, Cav1.2 (Park et al., 2010). This channel appears to function as the molecular switch for synaptic transmission (Atlas 2013). Intramembrane signalling occurs with syntaxin 1A for catecholamine release in chromaffin cells (Bachnoff et al. 2013). miR-153 intron RNA is a negative regulator of both insulin and dopamine secretion through its effect on Cacna1c expression, suggesting that IA-2beta and miR-153 have opposite functional effects on the secretory pathway (Xu et al. 2015). Co-localizes with Syntaxin-1A in nano clusters at the plasma membrane (Sajman et al. 2017). It is a high voltage-activated Ca2+ channel in contrast to Cav3.3 which is a low voltage-activated Ca2+ channel (Sanchez-Sandoval et al. 2018). Nifedipine blocks and potentiates this and other L-type VIC Ca2+ channels (Wang et al. 2018). Cav1.2 is upregulated when STIM1 is deficient (Pascual-Caro et al. 2018). CaV1.2 regulates chondrogenesis during limb development (Atsuta et al. 2019). CACNA1C may be a prognostic predictor of survival in ovarian cancer (Chang and Dong 2021).
6TMS K+ channel (Munsey et al. 2002; Kuo et al., 2003). The kch gene, the only known potassium channel gene in E. coli, has the property to express both full-length Kch and its cytosolic domain (RCK) due to a methionine at position 240. The RCK domains form an octameric ring structure and regulate the gating of the potassium channels after having bound certain ligands. Several different gating ring structures have been reported for the soluble RCK domains. The octameric structure of Kch may be composed of two tetrameric full-length proteins through RCK interaction (Kuang et al. 2013). The RCK domains face the solution, and an RCK octameric gating ring arrangement does not form under certain conditions (Kuang et al. 2015).
2 TMS ( P-loop) Ca2+-gated K+ channel, MthK (see Jiang et al., 2002 for the crystal structure, and Parfenova et al., 2006 for mutations affecting open probability). For the studies of ion permeation and Ca2+ blockage, see Derebe et al., 2011. (structures: 3LDD_A and 2OGU_A.). Voltage-dependent K+ channels including MthK which lacks a canonical voltage sensor can undergo a gating process known as C-type inactivation, which involves entry into a nonconducting state through conformational changes near the channel's selectivity filter (Thomson and Rothberg, 2010). C-type inactivation may involve movements of transmembrane voltage sensor domains. In the absence of Ca2+, a single structure in a closed state was observed by cryoEM that was highly flexible with large rocking motions of the gating ring and bending of pore-lining helices (Fan et al. 2020). In Ca2+-bound conditions, several open-inactivated conformations were present with the different channel conformations being distinguished by rocking of the gating rings with respect to the transmembrane region. In all conformations displaying open channel pores, the N-terminus of one subunit of the channel tetramer sticks into the pore and plugs it. Deletion of this N terminus led to non-inactivating channels with structures of open states without a pore plug, indicating that this N-terminal peptide is responsible for a ball-and-chain inactivation mechanism (Fan et al. 2020). Lipid-protein interactions influence the conformational equilibrium between two states of the channel that differ according to whether a TMS has a kink. Two key residues in the kink region mediate crosstalk between two gates at the selectivity filter and the central cavity, respectively. Opening of one gate eventually leads to closure of the other (Gu and de Groot 2020). Activation of MthK is exquisitely regulated by temperature (Jiang et al. 2020).
Voltage-activated, Ca2+ channel blocker-inhibited, Na+ channel, NaChBac (Ren et al., 2001; Zhao et al., 2004; Nurani et al, 2008; Charalambous and Wallace, 2011). Arginine residues in the S4 segment play a role in voltage-sensing (Chahine et al. 2004). Transmembrane and extramembrane regions contribute to thermal stability (Powl et al., 2012). Deprotonation of arginines in S4 is involved in NaChBac gating (Paldi, 2012). Hinge-bending motions in the pore domain of NaChBac have been reported (Barber et al., 2012). The C-terminal coiled-coli stabilizes subunit interactions (Mio et al. 2010). Within the 4 TMS voltage sensor, coupling between residues in S1 and S4 determines its resting conformation (Paldi and Gurevitz 2010). The conserved asparagine was changed to aspartate, N225D, and this substitution shifted the voltage-dependence of inactivation by 25 mV to more hyperpolarized potentials. The mutant also displays greater thermostability (O'Reilly et al. 2017). Possibly, the side-chain amido group of asn225 forms one or more hydrogen bonds with different channel elements, and these interactions are important for normal channel function. The T1-tetramerization domain of Kv1.2 (TC# 1.A.1.2.10) rescues expression and preserves the function of a truncated form of the NaChBac sodium channel (D'Avanzo et al. 2022).
Voltage-gated Na+ channel, NavCh or NavAb. The 3d-structure is known (3ROW; Payandeh et al., 2011; 4MW3A-D; 4+ selectivity through partial dehydration of Na+ via its direct interaction with conserved glutamate side chains). The pore is preferentially occupied by two ions, which can switch between different configurations by crossing low free-energy barriers (Furini and Domene, 2012). Jiang et al. 2018 presented high-resolution structures of NavAb with the analogous gating-charge mutations that have similar functional effects as in the human channels that cause hypokalaemic and normokalaemic periodic paralysis. Wisedchaisri et al. 2019 presented a cryo-EM structure of the resting state and a complete voltage-dependent gating mechanism via the voltage sensor (VS). The S4 segment of the VS is drawn intracellularly, with three gating charges passing through the transmembrane electric field. This movement forms an elbow connecting S4 to the S4-S5 linker, tightens the collar around the S6 activation gate, and prevents its opening. This structure supports the classical "sliding helix" mechanism of voltage sensing and provides a complete gating mechanism for voltage sensor function, pore opening, and activation-gate closure based on high-resolution structures of a single sodium channel protein (Wisedchaisri et al. 2019).
(see also TC#s 1.A.1.10.4 and 1.A.1.11.32).
The transport reaction catalyzed by NavCh is:
Na+ (in) ⇌ Na+ (out)
Bacterial voltage-gated sodium channel, Nav. 3-d crystal structures of vaious conformations are known (4P_3A A-D; 4PA7_A-D; 4P9P_A-D. etc.) (McCusker et al. 2012). It has its internal cavity accessible to the cytoplasmic surface as a result of a bend/rotation about a central residue in the carboxy-terminal TMS that opens the gate to allow entry of hydrated sodium ions. The molecular dynamics of ion transport through the open conformation has been analyzed (Ulmschneider et al. 2013). The C-terminal four helix coiled coil bundle domain couples inactivation with channel opening, depedent on the negatively charged linker region (Bagnéris et al. 2013). A NaVSp1-specific S4-S5 linker peptide induced both an increase in NaVSp1 current density and a negative shift in the activation curve, consistent with the S4-S5 linker stabilizing the open state (Malak et al. 2020).
Tetrameric 6 TMS subunit Na+ channel protein, NaV. Two low resolution cyroEM structures revealed two conformations reconstituted in lipid bilayers (Tsai et al. 2013). Despite a voltage sensor arrangement identical with that in the activated form, Tsai et al. 2013 observed two distinct pore domain structures: a prominent form with a relatively open inner gate, and a closed inner-gate conformation similar to the first prokaryotic Nav structure. Structural differences, together with mutational and electrophysiological analyses, indicated that widening of the inner gate was dependent on interactions among the S4-S5 linker, the N-terminal part of S5 and its adjoining part in S6, and on interhelical repulsion by a negatively charged C-terminal region subsequent to S6 (Tsai et al. 2013).
6 TMS voltage-gated K+ channel, KCNQ2 or Kv7.2. Mutations cause benign familial neonatal convulsions (BNFC; epilepsy; Maljevic et al. 2016; Soldovieri et al. 2019). It forms homotetramers or heterotetramers with KCNQ3/Kv7.3) (Soldovieri et al., 2006; Uehara et al., 2008)). Like all other Kv7.2 channels, it is activated by phosphatidyl inositol-4,5-bisphosphate and hence can be regulated by various neurotransmitters and hormones (Telezhkin et al. 2013). Gating pore currents that go through the gating pores in TMSs1-4 (the voltage sensor) may give rise to peripheral nerve hyperexcitability (Moreau et al. 2014). Retigabine and ICA73, two anti-epileptic drugs, act via distinct mechanisms due to interactions with specific residues that underlie subtype specificity of KCNQ channel openers (Wang et al. 2016). A tight spatial and functional relationship between the DAT/GLT-1 transporters and the Kv7.2/7.3 potassium channel immediately readjusts the membrane potential of the neuron, probably to limit the neurotransmitter-mediated neuronal depolarization (Bartolomé-Martín et al. 2019). E-2-dodecenal from cilantro (Coriandrum sativum) is a potent activator and anticonvulsant that binds with an affinity of 60 nM to TMS5 in several KCNQ channels including KCNQ2 and 3 (Manville and Abbott 2019). The activities of Kv7 channels are modulated by polyunsaturated fatty acids (Larsson et al. 2020).
6 TMS voltage-gated K+ channel, KCNQ3 or Kv7.3. Mutations cause benign familial neonatal convulsions (BNFC; epilepsy; Maljevic et al. 2016). Forms homotetramers or heterotetramers with KCNQ2 (Soldovieri et al., 2006; Uehara et al., 2008). Retigabine and ICA73, two anti-epileptic drugs, act via distinct mechanisms due to interactions with specific residues that underlie subtype specificity of KCNQ channel openers (Wang et al. 2016). Gabapentin at low concentrations is a activator of KCNQ3, KCNQ2/3 and KCNQ5 but not KCNQ2 or KCNQ4 (Manville and Abbott 2018). At high concentrations it can be inhibitory. A tight spatial and functional relationship between the DAT/GLT-1 transporters and the Kv7.2/7.3 potassium channel immediately readjusts the membrane potential of the neuron, probably to limit the neurotransmitter-mediated neuronal depolarization (Bartolomé-Martín et al. 2019). E-2-dodecenal from cilantro (Coriandrum sativum) is a potent activator and anticonvulsant that binds with an affinity of 60 nM to TMS5 in several KCNQ channels including KCNQ2 and 3 (Manville and Abbott 2019). Pathogenic variants in KCNQ2 and KCNQ3, paralogous genes encoding Kv7.2 and Kv7.3 voltage-gated K+ channel subunits, are responsible for early-onset developmental/epileptic disorders characterized by heterogeneous clinical phenotypes ranging from benign familial neonatal epilepsy (BFNE) to early-onset developmental and epileptic encephalopathy (DEE). KCNQ2 variants account for the majority of pedigrees with BFNE, and KCNQ3 variants are responsible for a much smaller subgroup (Miceli et al. 2020). The M240R variant mainly affects the voltage sensitivity, in contrast to previously analyzed BFNE Kv7.3 variants that reduce current density (Miceli et al. 2020).
6 TMS cell volume sensitive, voltage-gated K+ channel, KCNQ4 or Kv7.4 (mutations cause DFNA2, an autosomal dominant form of progressive hearing loss) (forms homomers or heteromers with KCNQ3) (localized to the basal membrane of cochlear outer hair cells and in several nuclei of the central auditory pathway in the brainstem). Four splice variants form heterotetramers; each subunit has different voltage and calmodulin-sensitivities (Xu et al., 2007). Autosomal dominant mutant forms leading to progressive hearing loss (DFNA2) have been characterized (Kim et al. 2011). Phosphatidylinositol 4,5-bisphosphate (PIP2) and polyunsaturated fatty acids (PUFAs) impact ion channel function (Taylor and Sanders 2016). This channel may be present in mitochondria (Parrasia et al. 2019). Polyunsaturated fatty acids are modulators of KV7 channels (Larsson et al. 2020). The pathogenicity classification of KCNQ4 missense variants in clinical genetic testing has been described (Zheng et al. 2022).
K+ voltage-gated channel, LQT-like subfamily; Kv7.1; KvLQT1. KCNQ1 (regulated by KCNE peptides (TC# 8.A.58) affect voltage sensor equilibrium (Rocheleau and Kobertz, 2007). Almost 300 mutations of KCNQ1 have been identified in patients, and most are linked to the long QT syndrome (LQT1), some in the voltage sensor (Peroz et al., 2008; Eldstrom et al. 2010; Qureshi et al. 2013; Ikrar et al. 2008). KCNQ1-KCNE1 complexes may interact intermittently with the actin cytoskeleton via the C-terminal region (Mashanov et al., 2010). The stoichiometry of the KCNQ1 - KCNE1 complex is flexible, with up to four KCNE1 subunits associating with the four KCNQ1 subunits of the channel (Nakajo et al., 2010). A familial mutation in the voltage-sensor of the KCNQ1 channel results in a cardiac phenotype (Henrion et al., 2012). KCNQ1 regulates insulin secretion in the MIN6 beta-cell line (Yamagata et al., 2011; Gofman et al., 2012). Electrostatic interactions of S4 arginines with E1 and S2 contribute to gating movements of S4, but coupling requires the lipid phosphatidylinositol 4,5-bisphosphate (PIP2) as voltage-sensing domain activation failed to open the pore in the absence of PIP2 (Zaydman et al. 2013). The D242N mutation causes impaired action potential adaptation to exercise and an increase in heart rate. Moreover, the D242 amino acyl position is involved in the KCNE1-mediated regulation of the voltage-dependence of activation of the KV7.1 channel (Moreno et al. 2017). The KCNQ1 channel interacts with MinK (KCNE1) to cause pore constriction, generating the slow delayed rectifier (IKs) current in the heart (Jalily Hasani et al. 2018). KCNQ1 rescues TMC1 plasma membrane expression but not mechanosensitive channel activity (Harkcom et al. 2019). Activation of the neuronal Kv7/KCNQ/M-current represents an attractive therapeutic strategy for treatment of hyperexcitability-related neuropsychiatric disorders such as epilepsy, pain, and depression, and channel openers for treatment of antiepilepsy have been developed (Zhang et al. 2019). The relationship between mutation locations in KCNQ1, which is a major gene in long QT syndrome (LQTS), and phenotype has been analyzed and used for risk stratification (Yagi et al. 2018). The proximal C-terminal regions of KCNQ1 and KCNE1 participate in a physical and functional interaction during channel opening that is sensitive to perturbation (Chen et al. 2019). Retigabine analogs are activators of Kv7 channels (Ostacolo et al. 2020). People with borderline QTc prolongations were carriers of KCNQ1 mutations in TMSs 2 and 5, leading to haploinsufficiency, and they are potentially at risk of developing drug-induced arrhythmia (Gouas et al. 2004). Collision induced unfolding differentiates functional variants of the KCNQ1 voltage sensor domain (Fantin et al. 2020). The activated KCNQ1 channel promotes a fibrogenic response in hereditary gingival fibromatosis via clustering and activation of Ras (Gao et al. 2020). QT syndrome (LQTS) increases the risk of life-threatening arrhythmia in young individuals with structurally normal hearts. It may involve sixteen genes such as the KCNQ1, KCNH2, and SCN5A (Lin et al. 2020). The human KCNQ1 voltage sensing domain (VSD) has been studied in lipodisq nanoparticles by electron paramagnetic resonance (EPR) spectroscopy (Sahu et al. 2020).
The small conductance Ca2+-activated K+ channel, SkCa2, Sk2 or Kcnn2 (not inhibited by arachidonate) (activated by three small organic molecules, the 1-EBIO and N5309 channel enhancers and the DCEBIO channel modulation (Pedarzani et al., 2005)). It is inhibited by protonation of outer pore histidine residues (Goodchild et al., 2009). The same is true for SK3 (K(Ca) 2.3 (Q9UGI6)). Regulates endothelial vascular function (Sonkusare et al., 2012). Distinct subcellular mechanisms enhance the surface membrane expression by its interacting proteins, α-actinin 2 (TC# 8.A.66.1.3) and filamin A (TC# 8.A.66.1.4) (Zhang et al. 2016). SK channel activators can compensate for age-related changes of the autorhythmic functions of the cerebellum (Karelina et al. 2017). SK2 proteins are more abundant in Purkinje cells than in the ventricular myocytes of normal rabbit ventricles (Reher et al. 2017). Apamin inhibits and isoproterenol activates this and other SK (KCNN) channels, and activation by isoproterenol is sex-dependent (Chen et al. 2018). Diverse interactions between KCa and TRP channels integrate cytoplasmic Ca2+, oxidative, and electrical signaling affecting cardiovascular physiology and pathology (Behringer and Hakim 2019). This channel may be present in mitochondria (Parrasia et al. 2019). A non-neuronal hSK3 isoform has a dominant-negative effect on hSK3 currents (Wittekindt et al. 2004). Medicinal plant products can interact with SKCa (Rajabian et al. 2022).
The intermediate conductance, Ca2+-activated K+ channel, Kcnn4, SK4, Sk4, Smik, Ik1 hIK1, IKCa or KCa3.1, also called the Gardos channel, of 543 aas and 6 TMSs. It is inhibited by 1 μM arachidonate which binds in the pore (Hamilton et al., 2003)). Nucleoside diphosphate kinase B (NDPK-B) activates KCa3.1 via histidine phosphorylation, resulting in receptor-stimulated Ca2+ flux and T cell activation (Di et al., 2010). It regulates endothelial vascular function (Sonkusare et al., 2012). Tissue-specific expression of splice variants of the orthologous rat KCNN4 protein have been reported (Barmeyer et al. 2010). Residues involved in gating have been identified (Garneau et al. 2014). It is also present in the inner mitochondrial membrane where increases of mitochondrial matrix [Ca2+] cause mtKCa3.1 opening, thus linking inner membrane K+ permeability and transmembrane potential to Ca2+ signalling (De Marchi et al. 2009). KCa3.1 (IKCa) channels are expressed in CA1 hippocampal pyramidal cells and contribute to the slow afterhyperpolarization that regulates spike accommodation (Turner et al. 2016). SK channel activators can compensate for age-related changes of the autorhythmic functions of the cerebellum (Karelina et al. 2017). The activation mechanism has been revealed by the cryoEM structure of the SK4-calmodulin complex (Lee and MacKinnon 2018). It is responsible for hyperpolarization in some tumor cells (Lazzari-Dean et al. 2019). Mutations are linked to dehydrated hereditary stomatocytosis (xerocytosis) (Andolfo et al. 2015). This channel is present in mitochondria (Parrasia et al. 2019). KCNN4 promotes the progression of lung adenocarcinoma by activating the AKT and ERK signaling pathways (Xu et al. 2021). KCa3.1 channels in human microglia link extracellular ATP-evoked Ca2+ transients to changes in membrane conductance with an inflammation-dependent mechanism, and suggests that during brain inflammation, the KCa3.1-mediated microglial response to purinergic signaling may be reduced (Palomba et al. 2021).
The archaeal voltage-regulated K channel, KvAP (Ruta et al., 2003). X-ray and solution structures are available. The latter shows phospholipid interactions with the isolated voltage sensor domain (Butterwick and MacKinnon 2010; Li et al. 2014). The gating-charge arginine in TMS4 of the voltage sensor forms part of the helical hairpin "paddle", and it moves 15-20 Å through the membrane to open the pore (Ruta et al., 2005). The orientation and depth of insertion of the voltage-sensing S4 helix has been determined (Doherty et al., 2010). A synthetic S6 segment derived from the KvAP channel self-assembles, permeabilizes lipid vesicles, and exhibits ion channel activity in bilayer lipid membrane (Verma et al., 2011). Thus the gating mechanism combines structural rearrangements and electric-field remodeling ( Li et al. 2014). KvAP has been reconstituted in Giant Unilamellar Vesicles (GUVs) (Garten et al. 2015). TMS4 (S4) which senses voltage also promotes membrane insertion of the voltage-sensor domain (Mishima et al. 2016). KvAP has a configuration consistent with a water channel, possibly underlying the conductance of protons, and other cations, through voltage-sensor domains (Freites et al. 2006). The structural dynamics of the paddle motif loop in the activated conformation of the KvAP voltage sensor have been studied from biophysical standpoints (Das et al. 2019). The S4 alpha-helix, which is straight in the experimental crystal structure solved under depolarized conditions (Vm approximately 0), breaks into two segments when the cell membrane is hyperpolarized (Vm << 0) and reversibly forms a single straight helix following depolarization (Vm = 0) ((Bignucolo and Bernèche 2020). The outermost segment of S4 translates along the normal to the membrane, bringing new perspective to previously paradoxical accessibility experiments that were initially thought to imply the displacement of the whole VSD across the membrane. The breakage of S4 under (hyper)polarization could be a general feature of Kv channels with a non-swapped topology. The surface charge of the membrane does not significantly affect the topology and structural dynamics of the sensor loop in membranes (Das and Raghuraman 2021). The dynamic variability of the sensor loop is preserved in both zwitterionic (POPC) and anionic (POPC/POPG) lipid membranes. The lifetime distribution analysis for the NBD-labelled residues by the maximum entropy method (MEM) demonstrates that, in contrast to micelles, the membrane environment not only reduces the relative discrete population of sensor loop conformations, but also broadens the lifetime distribution peaks. The local curvature of cellular membranes acts as a driving force for the targeting of membrane-associated proteins to specific membrane domains, as well as a sorting mechanism for transmembrane proteins, as demonstrated for KvAP (Kluge et al. 2022).
|1.A.1.17.2||Voltage-gated K+ channel, Kv (Santos et al., 2008).||
Voltage-gated K+ channel, chain A, Shaker-related, Kv1.2 or KCNA2 (Crystal structure known, Long et al., 2007; Chen et al. 2010). It functions with the auxiliary subunit, Ivβ1.2; 8.A.5.1.1) (Peters et al. 2009). Delemotte et al. (2010) described the effects of sensor domain mutations on molecular dynamics of Kv1.2. The Sigma 1 receptor (Q99720; Sigma non-opioid intracellular receptor 1) interacts with Kv1.2 to shape neuronal and behavioral responses to cocaine (Kourrich et al. 2013). Amino acid substitutions cause Shaker to become heat-sensing (opens with increasing temperature as for TrpV1) or cold-sensing (opens with decreasing temperature as for TrpM8) (Chowdhury et al. 2014). The Shaker Kv channel was truncated after the 4th transmembrane helix S4 (Shaker-iVSD) which showed altered gating kinetics and formed a cation-selective ion channel with a strong preference for protons (Zhao and Blunck 2016). Direct axon-to-myelin linkage by abundant KV1/Cx29 (TC# 1.A.24.1.12) channel interactions in rodent axons supports the idea of an electrically active role for myelin in increasing both the saltatory conduction velocity and the maximal propagation frequency in mammalian myelinated axons (Rash et al. 2016). A cryoEM structure (3 - 4 Å resolution; paddle chimeric channel; closed form) in nanodiscs has been determined (Matthies et al. 2018). Possible gating mechanisms have been discussed (Kariev and Green 2018; Infield et al. 2018). Pathogenic variants in KCNA2, encoding the voltage-gated potassium channel Kv1.2, have been identified as the cause for an evolving spectrum of neurological disorders. Affected individuals show early-onset developmental and epileptic encephalopathy, intellectual disability, and movement disorders resulting from cerebellar dysfunction (Döring et al. 2021). In addition, individuals with a milder course of epilepsy, complicated hereditary spastic paraplegia, and episodic ataxia have been reported. Biophysical properties of a delayed rectifier K+ current can contribute to its role ingenerating spontaneous myogenic activity (Hu et al. 2021). The local curvature of cellular membranes acts as a driving force for the targeting of membrane-associated proteins to specific membrane domains, as well as a sorting mechanism for transmembrane proteins, as demonstrated for the chimeric channel, Kv1.2/2.1; KvChim induces a strong positive membrane curvature (Kluge et al. 2022).
Voltage-gated K+ channel, Kv1.1 or KCNA1. It is palmitoylated, modulating voltage sensing (Gubitosi-Klug et al. 2005). It is regulated by syntaxin (TC family 8.A.91) through dual action on channel surface expression and conductance (Feinshreiber et al., 2009). Defects cause episodic ataxia type 1 (EA1), an autosomal dominant K+ channelopathy accompanied by short attacks of cerebellar ataxia and dysarthria (D'Adamo et al. 2014; Yuan et al. 2020). Direct axon-to-myelin linkage by abundant KV1/Cx29 channel interactions in rodent axons supports the idea of an electrically active role for myelin in increasing both the saltatory conduction velocity and the maximal propagation frequency in mammalian myelinated axons (Rash et al. 2016). Kv1.1 is present in bull sperm where it is necessary for normal sperm progressive motility, per cent capacitated spermatozoa (B-pattern) and the acrosome reaction (Gupta et al. 2018). Gating induces large aqueous volumetric remodeling (Díaz-Franulic et al. 2018). Paulhus et al. 2020 have reviewed the pathology of mutants in this protein and showed that epilepsy or seizure-related variants tend to cluster in the S1/S2 transmembrane domains and in the pore region of Kv1.1, whereas EA1-associated variants occur along the whole length of the protein, but variants at the C-terminus are more likely to suffer from seizures and neurodevelopmental disorders (Yuan et al. 2020). Mutation in KCNA1 has been identified that impairs voltage sensitivity (Imbrici et al. 2021). Altering expression of the genes encoding Kv1.1, Piezo2, and TRPA1 regulate the response of mechanosensitive muscle nociceptors (Nagaraja et al. 2021).
The voltage-gated K+ channel subfamily D member 3, KCND3 or Kv4.3. Mutations cause spinocerebellar ataxia type 19 (Duarri et al. 2012). Positively charged residues in S4 contribute to channel inactivation and recovery (Skerritt and Campbell 2007). The crystal structure of Kv4.3 with its regulatory subunit, Kchip1, has been solved (2NZ0) (Wang et al. 2007).
Margatoxin-sensitive voltage-gated K+ channel, Kv1.3 (in plasma and mitochondrial membranes of T lymphocytes) (Szabò et al., 2005). Kv1.3 associates with the sequence similar (>80%) Kv1.5 protein in macrophage forming heteromers that like Kv1.3 homomers are r-margatoxin sensitive (Vicente et al., 2006). However, the heteromers have different biophysical and pharmacological properties. The Kv1.3 mitochondrial potassium channel is involved in apoptotic signalling in lymphocytes (Gulbins et al., 2010). Interactions between the C-terminus of Kv1.5 and Kvβ regulate pyridine nucleotide-dependent changes in channel gating (Tipparaju et al., 2012). Intracellular trafficking of the KV1.3 K+ channel is regulated by the pro-domain of a matrix metalloprotease (Nguyen et al. 2013). Direct binding of caveolin regulates Kv1 channels and allows association with lipid rafts (Pérez-Verdaguer et al. 2016). Addtionally, NavBeta1 interacts with the voltage sensing domain (VSD) of Kv1.3 through W172 in the transmembrane segment to modify the gating process (Kubota et al. 2017). During insertion of Kv1.3, the extended N-terminus of the second α-helix, S2, inside the ribosomal tunnel is converted into a helix in a transition that depends on the nascent peptide sequence at specific tunnel locations (Tu and Deutsch 2017). The microRNA, mmumiR449a, reduced the mRNA expression levels of transient receptor potential cation channel subfamily A member 1 (TRPA1), and calcium activated potassium channel subunit alpha1 (KCNMA1) and increased the level of transmembrane phosphatase with tension homology (TPTE) in the DRG cells (Lu et al. 2017). This channel is regulation by sterols (Balajthy et al. 2017). Loss of function causes atrial fibrillation, a rhythm disorder characterized by chaotic electrical activity of cardiac atria (Olson et al. 2006). The N-terminus and S1 of Kv1.5 can attract and coassemble with the rest of the channel (i.e. Frag(304-613)) to form a functional channel independently of the S1-S2 linkage (Lamothe et al. 2018). This channel may be present in mitochondria (Parrasia et al. 2019). Kv1.3 plays an essential role in the immune response mediated by leukocytes and is functional at both the plasma membrane and the inner mitochondrial membrane. Plasma membrane Kv1.3 mediates cellular activation and proliferation, whereas mitochondrial Kv1.3 participates in cell survival and apoptosis (Capera et al. 2022). Kv1.3 uses the TIM23 complex to translocate to the inner mitochondrial membrane. This mechanism is unconventional because the channel is a multimembrane spanning protein without a defined N-terminal presequence. Transmembrane domains cooperatively mediate Kv1.3 mitochondrial targeting involving the cytosolic HSP70/HSP90 chaperone complex as a key regulator of the process (Capera et al. 2022).
Voltage-gated K+ channel, Shaker. Shaker and Shab K+ channels are blocked by quinidine (Gomez-Lagunas, 2010). Also regulated by unsaturated fatty acids (Börjesson and Elinder, 2011). TMSs 3 and 4 comprise the voltage sensor paddle (Xu et al. 2013). Partially responsible for action potential repolarization during synaptic transmission (Ford and Davis 2014). Shaker K+ channels can be mutated in S4 to create an analogous "omega" pore (Held et al. 2018). The NMR structure of the isolated Shaker voltage-sensing domain in LPPG micelles has been reported (Chen et al. 2019). Substituting the first S4 arginine with a smaller amino acid opens a high-conductance pathway for solution cations in the Shaker K+ channel at rest. The cationic current does not flow through the central K+ pore and is influenced by mutation of a conserved residue in S2, suggesting that it flows through a protein pathway within the voltage-sensing domain (Tombola et al. 2005). The current can be carried by guanidinium ions, suggesting that this is the pathway for transmembrane arginine permeation. Tombola et al. 2005 proposed that when S4 moves, it ratchets between conformations in which one arginine after another occupies and occludes to ions in the narrowest part of this pathway. Specific resin acids activate and open voltage-gated channels dependent on its exact binding dynamics (Silverå Ejneby et al. 2021).
K+ voltage-gated ether-a-go-go-related channel, H-ERG (KCNH2; Erg; HErg; Erg1, Kv11.1) subunit Kv11.1 (long QT syndrome type 2) (Gong et al., 2006; Chartrand et al. 2010; McBride et al. 2013). Selective expression of HERG and Kv2 channels influences proliferation of uterine cancer cells (Suzuki and Takimoto 2004). H-ERG forms a heteromeric K+ channel regulating cardiac repolarization, neuronal firing frequency and neoplastic cell growth (Szabó et al., 2011). Oligomerization is due to N-terminal interactions between two splice variants, hERG1a and hERG1b (Phartiyal et al., 2007). Structure function relationships of ERG channel activation and inhibition have been reviewed (Durdagi et al., 2010). Interactions between the N-terminal domain and the transmembrane core modulate hERG K channel gating (Fernández-Trillo et al., 2011). The marine algal toxin azaspiracid is an open state blocker (Twiner et al., 2012). Verapamil blocks channel activity by binding to Y652 and F656 in TMS S6 (Duan et al. 2007). Hydrophobic interactions between the voltage sensor and the channel domain mediate inactivation (Perry et al. 2013), but voltage sensing by the S4 segment can be transduced to the channel gate in the absence of physical continuity between the two modules (Lörinczi et al. 2015). Mutations give rise to long QT syndrome (Osterbur et al. 2015). Polyphenols such as caffeic acid, phenylethyl ester (CAPE) and curcumin inhibit by modification of gating, not by blocking the pore (Choi et al. 2013). Potassium ions can inhibit tumorigenesis through inducing apoptosis of hepatoma cells by upregulating potassium ion transport channel proteins HERG and VDAC1 (Xia et al. 2016). Incorrectly folded hERG can be degraded by Bag1-stimulated Trc-8-dependent proteolysis (Hantouche et al. 2016). The S1 helix regulates channel activity. Thus, S1 region mutations reduce both the action potential repolarizing current passed by Kv11.1 channels in cardiac myocytes, as well as the current passed in response to premature depolarizations that normally helps protect against the formation of ectopic beats (Phan et al. 2017). Interactions of beta1 integrins with hERG1 channels in cancer cells stimulate distinct signaling pathways that depended on the conformational state of hERG1 (Becchetti et al. 2017). ERG1 is sensitive to the alkaloid, ginsenoside 20(S) Rg3 which alters the gating of hERG1 channels by interacting with and stabilizing the voltage sensor domain in an activated state (Gardner et al. 2017). Channels split at the S4-S5 linker, at the intracellular S2-S3 loop, and at the extracellular S3-S4 loop are fully functional channel proteins (de la Peña et al. 2018). IKr is the rapidly activating component of the delayed rectifier potassium current, the ion current largely responsible for the repolarization of the cardiac action potential. Inherited forms of long QT syndrome (LQTS) in humans are linked to functional modifications in the Kv11.1 (hERG) ion channel and potentially life threatening arrhythmias. hERG1b affects the generation of the cardiac Ikr and plays an important role in cardiac electrophysiology (Perissinotti et al. 2018). X-ray crystallography and cryoEM have revealed features of the "nonswapped" transmembrane architecture, an "intrinsic ligand," and small hydrophobic pockets off a pore cavity. Drug block and inactivation mechanisms are discussed (Robertson and Morais-Cabral 2019). It forms a complex with β-integrin (TC#9.B.87.1.25) and NHE1 (TC# 2.A.36.1.13) (Iorio et al. 2020). Cardiotoxicity is caused mainly by the inhibition of human ether-a-go-go related gene (hERG) channel protein which leads to a life-threatening condition known as cardiac arrhythmia and is due to probable collapse of the pore. (Koulgi et al. 2021). Transmembrane hERG channel currents have been measured based on solvent-free lipid bilayer microarrays (Miyata et al. 2021). A computational method for identifying an optimal combination of existing drugs to repair the action potentials of SQT1 ventricular myocytes has been published (Jæger et al. 2021). Ginsenoside Rg3 may be a promising cardioprotective agent against vandetanib-induced QT interval prolongation through targeting hERG channels (Zhang et al. 2021).
K+ voltage-gated channel, rEAG1; Kv10.1; rat ether a go-go channel 1 (962 aas). Blocked by Cs+, Ba2+ and quinidine (Schwarzer et al., 2008). Cysteines control the N- and C-linker-dependent gating of KCNH1 potassium channels (Sahoo et al., 2012). The 3-d structure has been determined at 3.8 Å resolution using single-particle cryo-EM with calmodulin bound. The structure suggests a novel mechanism of voltage-dependent gating. Calmodulin binding closes the potassium pore (Whicher and MacKinnon 2016). Eag1 has three intracellular domains: PAS, C-linker, and CNBHD. Whicher and MacKinnon 2019 demonstrated that the Eag1 intracellular domains are not required for voltage-dependent gating but likely interact with the VS to modulate gating. Specific interactions between the PAS, CNBHD, and VS domains modulate voltage-dependent gating, and VS movement destabilizes these interactions to promote channel opening. Mutations affecting these interactions render Eag1 insensitive to calmodulin inhibition (Whicher and MacKinnon 2019). The structure of the calmodulin insensitive mutant in a pre-open conformation suggests that channel opening may occur through a rotation of the intracellular domains, and calmodulin may prevent this rotation by stabilizing interactions between the VS and the other intracellular domains. Intracellular domains likely play a similar modulatory role in voltage-dependent gating of the related Kv11-12 channels. The human ortholog, EAG or EAG-1, is 989 aas long and is 95% identical to the rat protein. In ether-a-go-go K+ channels, voltage-dependent activation is modulated by ion binding to a site located in an extracellular-facing crevice between transmembrane segments S2 and S3 in the voltage sensor. Silverman et al. 2004 found that acidic residues, D278 in S2 and D327 in S3, are able to coordinate a variety of divalent cations, including Mg2+, Mn2+, and Ni2+, which have qualitatively similar functional effects, but different half-maximal effective concentrations. EAG (ether-a-go-go) voltage-dependent K+ channels with similarities and Differences in the structural organization and gating (Barros et al. 2020).
Cyclic nucleotide-binding, voltage-gated, Mg2+-dependent, CaMKII-regulated K+ channel, Eag. Eag recruits CASK (TC# 9.B.106.3.2) to the plasma membrane; forms a heterotetramer (Liu et al. 2010). Phosphorylation is catalyzed by CaMKII (TC# 8.A.104.1.11)
K+- and Na+-conducting NaK channel, NaK2K of 97 aas and 2 TMSs. The 3-D structure has been solved with Na+ and K+bound (Shi et al., 2006). It exhibits tight structural and dynamic coupling between the selectivity filter and the channel scaffold (Brettmann et al. 2015). A hydrophobic residue at the bottom of the selectivity filter, Phe92, appears in dual conformations. One of the two conformations of Phe92 restricts the diameter of the exit pore around the selectivity filter, limiting ion flow through the channel, while the other conformation of Phe92 provides a larger-diameter exit pore from the selectivity filter. Thus, Phe92 acts as a hydrophobic gate (Langan et al. 2020).
|1.A.1.23.2||Root nuclear envelope CASTOR: homomeric ion channel (preference of cations such as K+ over anions) (Charpentier et al., 2008) (62% identical to 1.A.1.23.1).||
The 6TMS bacterial cyclic nucleotide-regulated, voltage independent channel, MlotiK1 or MloK1 (Clayton et al., 2008). Gating involves large rearrangements of the cyclic nucleotide-binding domains (Mari et al., 2011). The electron crystalographic structure is available (PDB 4CHW) revealing ligand-induced structural changes (Schünke et al. 2011; Scherer et al. 2014; Kowal et al. 2014). Such changes may be lipid dependent (McCoy et al. 2014). High-speed atomic force microscopy has been used to measure millisecond to microsecond dynamics (Heath and Scheuring 2019).
Calcium-, magnesium- and voltage-activated K+ channel, Slo1 (Kcma1; KCNMA, KCNMA1), a BK channel, of 1236 aas and 6 N-terminal TMSs. Its activation dampens the excitatory events that elevate the cytosolic Ca2+ concentration and/or depolarize the cell membrane. It therefore contributes to repolarization of the membrane potential, and it plays a key role in controlling excitability in a number of systems. Ethanol and carbon monoxide-bound heme increase channel activation while heme inhibits channel activation (Tang et al. 2003). The molecular structures of the human Slo1 channel in complex with beta4 has been solved revealing four beta4 subunits, each containing two transmembrane helices, encircling Slo1, contacting it through helical interactions inside the membrane. On the extracellular side, beta4 forms a tetrameric crown over the pore. Structures with high and low Ca2+ concentrations show that identical gating conformations occur in the absence and presence of beta4, implying that beta4 serves to modulate the relative stabilities of 'pre-existing' conformations rather than creating new ones (Tao and MacKinnon 2019). BK channels show increased activities in Angelman syndrome due to genetic defects in the ubiquitin protein ligase E3A (UBE3A) gene (Sun et al. 2019). It is a large-conductance potassium (BK) channel that can be synergistically and independently activated by membrane voltage and intracellular Ca2+. The only covalent connection between the cytosolic Ca2+-sensing domain and the TM pore and voltage sensing domains is a 15-residue 'C-linker' which plays a direct role in mediating allosteric coupling between BK domains (Yazdani et al. 2020). Site specific deacylation by the alpha/beta acyl-hydrolase domain-containing protein 17A, ABHD17a (Q96GS6, 310 aas), controls BK channel splice variant activity (McClafferty et al. 2020). Compared with the structure of isolated hSlo1 Ca2+ sensing gating rings, two opposing subunits in hBK unfurled, resulting in a wider opening towards the transmembrane region of hBK. In the pore gate domain, two opposing subunits moved downwards relative to the two other subunits (Tonggu and Wang 2022).
Slo2.2 sodium-activated potassium channel subfamily T member 1 of 1217 aas and 6 putative N-terminal TMSs plus a P-loop. Cryo electron microscopic structures of the chicken orthologue at 4.5 Å resolution has been solved, revealing a large cytoplasmic gating ring in which resides the Na+-binding site and a transmembrane domain that closely resembles voltage-gated K+ channels (Hite et al. 2015).
K+ channel, AKT1; may form heteromeric channels with KC1 (TC # 1.A.1.4.9) (Geiger et al., 2009). Required for seed development and postgermination growth in low potassium (Pyo et al. 2010). Functions optimally with intermediate potassium concentrations (~1 mM) (Nieves-Cordones et al. 2014). In barley, it may play a role in drought resistance (Cai et al. 2019). HAK/KUP/KT8, GrAKT2.1 and GrAKT1.1 potassium channels may function in response to abiotic stress in Gossypium raimondii (Azeem et al. 2021). Plants obtain nutrients from the soil via transmembrane transporters and channels in their root hairs, from which ions radially transport in toward the xylem for distribution across the plant body. Dickinson et al. 2021 determined structures of the hyperpolarization-activated channel, AKT1, from Arabidopsis thaliana, which mediates K+ uptake from the soil into plant roots. The structures of AtAKT1, embedded in lipid nanodiscs, show that the channel undergoes a reduction of C4 to C2 symmetry, possibly to regulate its electrical activation.
The voltage-sensitive inward rectifying K+ channel, KAT1 (similar to 1.A.1.4.3; activated by protein 14-3-3 (AAF87262)) (Sottocornola et al., 2006). May also transport Na+ and Cs+ (Nakamura and Gaber, 2009). Forms heterotetrameric channels with KAT2 with a stoichiometry of 2:2 (Lebaudy et al., 2010). The pH-sensor is built of a sensory cloud rather than of single key amino acids (Gonzalez et al., 2011). The transmembrane core region of KAT1 is important for its activity in S. cerevisiae, and this involves not only the pore region but also parts of its voltage-sensor domain (Saito et al. 2017). Electromechanical coupling and gating polarity in KAT1 displays a depolarized voltage sensor, which interacts with a closed pore domain directly via two interfaces and indirectly via an intercalated phospholipid. Direct interaction between the sensor and the C-linker hairpin in the adjacent pore subunit is the primary determinant of gating polarity (Clark et al. 2020). Possibly an inward motion of the S4 sensor helix of 5-7 Å underlies a direct-coupling mechanism, driving a conformational reorientation of the C-linker and ultimately opening the activation gate formed by the S6 intracellular bundle. KAT1, and presumably other hyperpolarization-gated plant CNBD channels, can open from an S4-down VSD conformation homologous to the divalent/proton-inhibited conformation of EAG family K+ channels (Zhou et al. 2021).
Orthologue K+/Na+ pacemaker channel, Hcn4 (Scicchitano et al., 2012). Hyperpolarization-activated cyclic nucleotide-regulated HCN channels underlie the Na+-K+ permeable IH pacemaker current. As with other voltage-gated members of the 6-transmembrane KV channel superfamily, opening of HCN channels involves dilation of a helical bundle formed by the intracellular ends of S6, but this is promoted by inward, not outward, displacement of S4. Direct agonist binding to a ring of cyclic nucleotide-binding sites, one of which lies immediately distal to each S6 helix, imparts cAMP sensitivity to HCN channel opening. At depolarized potentials, HCN channels are further modulated by intracellular Mg2+ which blocks the open channel pore and blunts the inhibitory effect of outward K+ flux. Lyashchenko et al. 2014 showed that cAMP binding to the gating ring enhances not only channel opening but also the kinetics of Mg2+ block. Mutations in HCN4 cause sick sinus and the Brugada syndrome, cardiac abnormalities. HCN4 is associated with famiial sinus bradycardia (Boulton et al. 2017). Activation of Hcn4 by cAMP has been reviewed (Porro et al. 2020). The HCN1-4 channel family is responsible for the hyperpolarization-activated cation current If/Ih that controls automaticity in cardiac and neuronal pacemaker cells. Saponaro et al. 2021 presented cryo-EM structures of HCN4 in the presence or absence of bound cAMP, displaying the pore domain in closed and open conformations. Analysis of cAMP-bound and -unbound structures shed light on how ligand-induced transitions in the channel cytosolic portion mediate the effect of cAMP on channel gating and highlighted the regulatory role of a Mg2+ coordination site formed between the C-linker and the S4-S5 linker. Comparison of open/closed pore states shows that the cytosolic gate opens through concerted movements of the S5 and S6 transmembrane helices. Furthermore, in combination with molecular dynamics analyses, the open pore structures provide insights into the mechanisms of K+/Na+ permeation (Saponaro et al. 2021).
Hyperpolarization-activated cyclic nucleotide-gated (HCN) inward current carrying cationic channel, I(f), (HCN2/HCN4) (Ye and Nerbonne, 2009). Functional interactions between the HCN2 TM region and C-terminal region govern multiple CNB fold-mediated mechanisms, implying that the molecular mechanisms of autoinhibition, open-state trapping, and Quick-Activation include participation of TM region structures (Page et al. 2020). Rhythmic activity in pacemaker cells, as in the sino-atrial node in the heart, depends on the activation of HCN channels. As in depolarization-activated K+ channels, the fourth transmembrane segment S4 functions as the voltage sensor in hyperpolarization-activated HCN channels (Wu et al. 2021). S4 in HCN channels moves in two steps in response to hyperpolarizations, and the second S4 step correlates with gate opening (Wu et al. 2021).
Cyclic nucleotide-gated cation channel α3 (CNGA3 or CNG3); photoreceptor cGMP-gated channel α-subunit. Also possibly expressed in inner ear cell cells where it binds to an intracellular C-terminal domain of EMILIN1 (Selvakumar et al., 2012). Elastic network model analysis of the CNGA3 channel supports a modular model of allosteric gating, according to which protein domains are quasi-independent: they can move independently but are coupled to each other allosterically (Gofman et al. 2014). An intact S4 is required for proper protein folding and/or assembly involving two glycosylation sites in the endoplasmic reticulum membrane (Faillace et al. 2004). It may function with CNGB3 (TC# 1.A.1.5.37; Q9NQW8; 809 aas and 6 TMSs).
|1.A.1.5.14||Probable cyclic nucleotide-gated ion channel 6 (AtCNGC6) (Cyclic nucleotide- and calmodulin-regulated ion channel 6)||
Cyclic nucleotide-gated K+channel of 430 aas, probably with 6 TMSs in a 2 + 2 + 1 + P-loop + 1 TMS arrangement. The channel is activated by cAMP, not by cGMP, and is highly specific for K+ over Na+. It has a C-terminal hydrophilic cAMP-binding domain linked to the 6 TMS channel domain (Brams et al. 2014). An SthK C-linker domain is essential for coupling cyclic nucleotide binding to channel opening (Evans et al. 2020). An agonist-dependent conformational change in which residues of the B'-helix displayed outward movement with respect to the symmetry axis of the channel in the presence of cAMP was observed, but not with the partial agonist, cGMP. This conformational rearrangement was observed both in detergent-solubilized SthK and in channels reconstituted into lipid nanodiscs. In addition to outward movement of the B'-helix, channel activation involves upward translation of the cytoplasmic domain with formation of state-dependent interactions between the C-linker and the transmembrane domain (Evans et al. 2020).
Hyperpolarization-activated and cyclic nucleotide-gated K+ channel, HCN (bCNG-1) (PNa+/PK+ ≈ 0.3). The human orthologue (O88703) is 863 aas in length and also catalyzes mixed monovalent cation currents K+:Na+= 4:1 (Lyashchenko and Tibbs et al., 2008). Biel et al. (2009) presented a detailed review of hyperpolarization-activated cation-channels. They are inhibited by nicotine and epibatidine which bind to the inner pore (Griguoli et al., 2010). They control cardiac and neuronal rhythmicity. HCN channels contain cyclic nucleotide-binding domains (CNBDs) in their C-terminal regions, linked to the pore-forming transmembrane segment with a C-linker. The C-linker couples the conformational changes caused by the direct binding of cyclic nucleotides to the HCN pore opening. Cyclic dinucleotides antagonize the effect of cyclic nucleotides in HCN4 but not in HCN2 channels. Interaction of the C-linker/CNBD with other parts of the channel appears to be necessary for cyclic-dinucleotide binding in HCN4 channels (Hayoz et al. 2017).
TAX-4 cyclic nucleotide-gated cation channel A (CNGA) of 733 aas (Wojtyniak et al. 2013). Li et al. 2017 determined the 3.5 Å resolution single-particle electron cryo-microscopy structure in the cyclic guanosine monophosphate (cGMP)-bound open state. The channel has an unusual voltage-sensor-like domain, accounting for its deficient voltage dependence. A carboxy-terminal linker connecting S6 and the cyclic-nucleotide-binding domain interacts directly with both the voltage sensor-like domain and the pore domain, forming a gating ring that couples conformational changes triggered by cyclic nucleotide binding to the gate. The selectivity filter is lined by the carboxylate side chain of a functionally important glutamate and three rings of backbone carbonyls (Li et al. 2017).
spHCN1 is a pacemaker hyperpolarization-activated cyclic nucleotide-gated (HCN) non-selective cation channel of 767 aas and 6 TMSs that opens due to inward movement of the positive charges in the fourth TMS (S4). This channel is similar to a COOH-terminal-deleted HCN1 channel, suggesting that the main functional differences between spHCN and HCN1 channels are due to differences in their COOH termini (Vemana et al. 2004). These channels open after only two S4s have moved, and S4 motion is rate limiting during voltage activation of spHCN channels (Bruening-Wright et al. 2007). HCN channels regulate electrical activity in the heart and brain. Distinct from mammalian isoforms, the sea urchin (spHCN) channel exhibits strong voltage-dependent inactivation in the absence of cAMP (Idikuda et al. 2018). The voltage sensor undergoes a large downward motion during hyperpolarization (Dai et al. 2019). Sea urchin HCN1 and 2 (TC# 1.A.1.5.33) (spHCN) channels undergo inactivation with hyperpolarization which occurs only in the absence of cyclic nucleotide (Dai et al. 2021). Removing cAMP produces a largely rigid-body rotation of the C-linker relative to the transmembrane domain, bringing the A' helix of the C-linker in close proximity to the voltage-sensing S4 helix. In addition, rotation of the C-linker is elicited by hyperpolarization minus cAMP. Thus, in contrast to electromechanical coupling for channel activation - the A' helix serves to couple the S4-helix movement for channel inactivation, which is likely a conserved mechanism for CNBD-family channels (Dai et al. 2021).
Multi-domain cation channel with a C-terminal cyclic nucleotide-binding domain; of 465 aas and 6 TMS, LliK. Cyclic nucleotide-gated (CNG) and hyperpolarization-activated cyclic nucleotide-regulated (HCN) channels play roles in phototransduction, olfaction, and cardiac pace making. James et al. 2017 used cryoEM to determine the structure of the intact LliK CNG channel. A short S4-S5 linker connects voltage-sensing and pore domains to produce a non-domain-swapped transmembrane architecture. The conformation of the LliK structure may represent a functional state of this channel family not seen before (James et al. 2017).
HCN1 is a hyperpolarization-activated cyclic nucleotide-gated (HCN) channel of 890 aas and 6 TMSs that opens due to inward movement of the positive charges in the fourth transmembrane domain (S4). These channels open after only two S4s have moved, and S4 motion is rate limiting during voltage activation of spHCN channels (Bruening-Wright et al. 2007). HCN1 exhibits weak selectivity for potassium over sodium ions. It's structure (3.5 Å resolution) is known (Lee and MacKinnon 2017). It contributes to the native pacemaker currents in heart and neurons. It may also mediate responses to sour stimuli. It is inhibited by Cs+, zatebradine, capsazepine and ZD7288 (Gill et al. 2004). HCN1 mutational variants include epileptic encephalopathy and common generalized epilepsy. HCN1 has a pivotal function in brain development and control of neuronal excitability (Marini et al. 2018). The interaction with filamin A seems to contribute to localizing HCN1 channels to specific neuronal areas and to modulating channel activity (Gravante et al. 2004). The HCN domain is required for HCN channel cell-surface expression, and it couples voltage- and cAMP-dependent gating mechanisms (Wang et al. 2020). Changes in the local S4 environment provide a voltage-sensing mechanism for mammalian hyperpolarization-activated HCN channels (Bell et al. 2004).
The cyclic ABP-gated K+ channel, SthK of 430 aas and 6 TMSs in a 2 + 2 + 1 + P-loop +1 TMS arrangement. This channel and others have been studied by high-speed atomic force microscopy (HS-AFM) which has made it possible to characterized the conformational dynamics of single unlabeled transmembrane channels and transporters (Heath and Scheuring 2019).
TWIK-1 (KCNK1, HOHO1, KCNO1) inward rectifier K+ channel (Enyedi and Czirják, 2010) expressed in the distal nephron segments (Orias et al. 1997). Lipid tails from both the upper and lower leaflets can partially penetrate into the pore (Aryal et al. 2015). The lipid tails do not sterically occlude the pore, but there is an inverse correlation between the presence of water within the hydrophobic barrier and the number of lipids tails within the lining of the pore (Aryal et al. 2015).
TREK-1 (KCNK2) K+ channel subunit (Regulated by group 1 metabotropic glutamate receptors and by diacylglycerols and phosphatidic acids) (Chemin et al., 2003). TREK-1, TREK-2 and TRAAK are all regulated by lysophosphatidic acid, converting these mechano-gated, pH voltage-sensitive channels into leak conductances (Chemin et al., 2005). The mammalian K2P2.1 potassium channel (TREK-1, KCNK2) is highly expressed in excitable tissues, where it plays a key role in the cellular mechanisms of neuroprotection, anaesthesia, pain perception and depression (Cohen et at., 2008). Alternative translation initiation in rat brain yields K2P2.1 potassium channels permeable to sodium (Thomas et al. 2008). The crystal structure of the human 2-pore domain K+ channel, K2P1 has been solved (Miller and Long, 2012). Multiple modalities converge on a common gate to control K2P channel function (Bagriantsev et al., 2011). TREK-1 mediates fast and slow glutamate release in astrocytes upon GPCR activation (Woo et al. 2012). It is a mechanosensitive K+ channel, present in rat bladder myocytes, which is activated by swelling and arachidonic acid (Fukasaku et al. 2016). The M2-hinges of TREK-1 and TREK-2 channels control their macroscopic current, subcellular localization and gating (Zhuo et al. 2017). The human ortholog has acc # O95069 and has an additional N-terminal 15 aas. BL-1249, a compound from the fenamate class of nonsteroidal anti-inflammatory drugs, is known to activate K2P2.1(TREK-1), the founding member of the thermo- and mechanosensitive TREK subfamily (Pope et al. 2018). Spadin and arachidonic acid, are known to suppress and activate TREK-1 channels, respectively (Pappa et al. 2020).
pH-dependent, voltage-insensitive, background potassium channel protein involved in maintaining the membrane potential, KCNK9, K2P9.1 or TASK3 (TASK-3) of 374 aas (Huang et al. 2011). Terbinafine is a selective activator of TASK3 (Wright et al. 2017). The response of the tandem pore potassium channel TASK-3 to voltage involves gating at the cytoplasmic mouth (Ashmole et al., 2009). TASK-3 is involved in several physiological and pathological processes including sleep/wake control, cognition and epilepsy (Tian et al. 2019). N-(2-((4-nitro-2-(trifluoromethyl)phenyl)amino)ethyl)benzamide (NPBA) is an activator (Tian et al. 2019). KCC2 regulates neuronal excitability and hippocampal activity via interaction with Task-3 channels (Goutierre et al. 2019). A biguanide compound, CHET3, is a highly selective allosteric activator, and TASK-3 is a druggable target for treating pain (Liao et al. 2019). This channel may be present in mitochondria (Parrasia et al. 2019).
KCNK3 K+ channel (TASK1, OAT1, TBAK1) (the K+ leak conductance). TASK1 and 3 may play roles in nontumorigenic primary hyperaldosteronism (Davies et al., 2008). KCNK3/9/15 expression limits membrane depolarization and depolarization-induced secretion at least in part by maintaining intracellular K+ (Huang et al. 2011). TWIK-related acid-sensitive potassium (TASK) channels, members of the two pore domain potassium (K2P) channel family, are found in neurons, cardiomyocytes and vascular smooth muscle cells, where they are involved in the regulation of heart rate, pulmonary artery tone, sleep/wake cycles and responses to volatile anaesthetics (Rödström et al. 2020). K2P channels regulate the resting membrane potential, providing background K+ currents controlled by numerous physiological stimuli. Unlike other K2P channels, TASK channels are able to bind inhibitors with high affinity, exceptional selectivity and very slow compound washout rates. In general, potassium channels have an intramembrane vestibule with a selectivity filter situated above and a gate with four parallel helices located below, but the K2P channels studied so far all lack a lower gate. Rödström et al. 2020 presented the X-ray crystal structure of TASK-1, and showed that it contains a lower gate designated 'X-gate', created by interaction of the two crossed C-terminal M4 transmembrane helices at the vestibule entrance. This structure is formed by six residues ((243)VLRFMT(248)) that are essential for responses to volatile anaesthetics, neurotransmitters and G-protein-coupled receptors. Mutations within the X-gate and the surrounding regions affect both the channel-open probability and the activation of the channel by anaesthetics. Structures of TASK-1 bound to two high-affinity inhibitors showed that both compounds bind below the selectivity filter and are trapped in the vestibule by the X-gate, which explains their exceptionally low washout rates (Rödström et al. 2020).
Neuronal 2-P (4 TMS) domain K+ membrane tension-gated channel, TRAAK (stimulated by arachidonic acid and polyunsaturated fatty acids (Fink et al., 1998). The crystal structures of conductive and nonconductive human K2P TRAAK K+ channel has been solved (Brohawn et al., 2012; Brohawn et al. 2014). Regulated by mechanical deformation of the membrane and temperature as well as polyunsaturated fatty acids (Brohawn et al., 2012). Multiple modalities converge on a common gate to control K2P channel function (Bagriantsev et al., 2011). In the non-conductive state, a lipid acyl chain accesses the channel cavity through a 5 Å-wide lateral opening in the membrane inner leaflet and physically blocks ion passage. In the conductive state, rotation of transmembrane helix 4 about a central hinge seals the intramembrane opening, preventing lipid block of the cavity and permitting ion entry. Additional rotation of a membrane interacting TM2-TM3 segment, unique to mechanosensitive K2Ps, against TM4 may further stabilize the conductive conformation. Comparison of the structures provodes a biophysical explanation for TRAAK mechanosensitivity--an expansion in cross-sectional area up to 2.7 nm2 in the conductive state is expected to create a membrane-tension-dependent energy difference between conformations that promotes force activation (Brohawn et al. 2014). TM helix straightening and buckling may underlie channel activation (Lolicato et al. 2014). A lipid chain blocks the conducting path in the closed state (Rasmussen 2016).
Outward rectifying mechanosensitive 2-P (4 TMS) domain K+ channel, TREK-2 (KCNKA; KCNK10; K2P10). Activated by membrane stretch, acidic pH, arachidonic acid and unsaturated fatty acids. Dong et al. 2015 described crystal structures of the human TREK-2 channel (up to 3.4 angstrom resolution) in two conformations and in complex with norfluoxetine, the active metabolite of fluoxetine (Prozac) and a state-dependent blocker of TREK channels. Norfluoxetine binds within intramembrane fenestrations found in only one of these two conformations. Channel activation by arachidonic acid and mechanical stretch involves conversion between these states through movement of the pore-lining helices. This provides an explanation for TREK channel mechanosensitivity, regulation by diverse stimuli, and possible off-target effects of the serotonin reuptake inhibitor Prozac (Dong et al. 2015). The unique gating properties of TREK-2 and the mechanisms by which extracellular and intracellular stimuli harness pore gating allosterically have been studied (Zhuo et al. 2016). TREK-2 moves from the """"down"""" to """"up"""" conformation in direct response to membrane stretch. Aryal et al. 2017 showed how state-dependent interactions with lipids affect the movement of TREK-2, and how stretch influences both the inner pore and selectivity filter. They also demonstrated why direct pore block by lipid tails does not represent theprincipal mechanism of mechanogating (Aryal et al. 2017). The M2-hinges of TREK-1 and TREK-2 channels control their macroscopic current, subcellular localization and gating (Zhuo et al. 2017). TREK-2 responds to a diverse range of stimuli. Two states, termed """"up"""" and """"down,"""" are known from x-ray structural crystallographic studies and have been suggested to differ in conductance. Brennecke and de Groot 2018 found that the down state is less conductive than the up state. The introduction of membrane stretch in the simulations shifts the state of the channel toward an up configuration. Membrane pressure changes the conformation of the transmembrane helices directly and consequently also influences the channel conductance (Brennecke and de Groot 2018). 3-d structures are known (PDB 4XDJ_!-D. Phosphatidyl-(3,5)-bisphosphate (PI(3,5)P2) activates (Kirsch et al. 2018).
AMPA-selective glutamate ionotropic channel receptor (GIC; AMPAR), kainate-subtype, GluR-K1; GluR1; GluR-A; GluA1; Gria1 of 906 aas (preferentially monovalent cation selective). A mature complex contains GluR1, TARPs, and PSD-95 (Fukata et al. 2005). The receptor contributes to amygdala-dependent emotional learning and fear conditioning (Humeau et al., 2007). Transmembrane AMPAR regulatory protein (TARP) gamma-7 (TC#8.A.16.2.5) selectively enhances the synaptic expression of Ca2+-permeable (CP-AMPARs) and suppresses calcium-impermeable (CI-AMPAR) activities (Studniarczyk et al. 2013). Thus, TARPs modulate the pharmacology and gating of AMPA-type glutamate receptors (Soto et al. 2014). TARPs interact with the N-terminal domain of the AMPAR and control channel gating; residues in the receptor and the TARP involved in this interaction have been identified (Cais et al. 2014). The auxilary protein, Shisa9 or CKAMP44 (UniProt acc# B4DS77), has a C-terminal PDZ domain that allows interaction with scaffolding proteins and AMPA glutamate receptors (Karataeva et al. 2014). The transmembrane domain alone can tetramerize (Gan et al. 2016). The most potent and well-tolerated AMPA receptor inhibitors, used to treat epilepsy, act via a noncompetitive mechanism. The crystal structures of the rat AMPA-subtype GluA2 receptor in complex with three noncompetitive inhibitors have been solved. The inhibitors bind to a binding site, completely conserved between rat and human, at the interface between the ion channel and linkers connecting it to the ligand-binding domains (Yelshanskaya et al. 2016). The endogenous neuropeptide, cyclopropylglycine, at a physiological concentration of 1 μM, enhances the transmembrane AMPA currents in rat cerebellar Purkinje cells (Gudasheva et al. 2016). The energetics of glutamate binding have been estimated (Yu and Lau 2017). The TMEM108 protein (Q6UXF1 of 575 aas and 2 TMSs, N- and C-terminal, is required for surface expression of AMPA receptors (Jiao et al. 2017). CERC-611 is a selective antagonist of AMPA receptors containing transmembrane AMPA receptor regulatory protein (TARP; TC# 8.A.16) gamma-8 (Witkin et al. 2017). Drug effects, regulatory protein modulators and positive allosteric modulators have been reviewed (Fu et al. 2019). Herguedas et al. 2019 presented a cryo-EM structure of the heteromeric GluA1/2 receptor associated with two transmembrane AMPAR regulatory protein (TARP) gamma8 auxiliary subunits, the principal AMPAR complex at hippocampal synapses. The native heterotetrameric AMPA-R adopts various conformations, which reflect a variable separation of the two dimeric extracellular amino-terminal domains; members of the stargazin/TARP family of transmembrane proteins co-purify with AMPA-Rs and contribute to the density representing the transmembrane region of the complex. Glutamate and cyclothiazide altered the conformational equilibrium of the channel complex, suggesting that desensitization is related to separation of the N-terminal domains (Nakagawa et al. 2005). Positive allosteric modulators (PAMs) of AMPA receptors boost cognitive performance in clinical studies, and mibampator and BIIB104 discriminate between AMPARs complexed with distinct TARPs, and particularly those with lower stargazin/gamma2 efficacy such as BIIB104 (Ishii et al. 2020). Yelshanskaya et al. 2020 identified trans-4-butylcyclohexane carboxylic acid (4-BCCA) binding sites in the transmembrane domain of AMPA receptors, at the lateral portals formed by TMSs M1-M4. At this binding site, 4-BCCA is very dynamic, assumes multiple poses and can enter the ion channel pore. Cannabidiol inhibits febrile seizure by modulating AMPA receptor kinetics through its interaction with the N-terminal domain of GluA1/GluA2 (Yu et al. 2020). Inhibition of AMPA receptors (AMPARs, e.g., TC# 1.A.10.1.1) containing transmembrane AMPAR regulatory protein gamma-8 (TC# 8.A.61.1.10) with JNJ-55511118 (TC#8.A.179.1.1) shows preclinical efficacy in reducing chronic repetitive alcohol self-administration (Hoffman et al. 2021). Mechanisms underlying TARP modulation of the GluA1/2-gamma8 AMPA receptor have been studied (Herguedas et al. 2022).
The homo- and heteromeric glutamate receptor, GLR3.3/3.4 (Desensitized in 3 patterns: (1) by Glu alone; (2) by Ala, Cys, Glu or Gly; (3) by Ala, Cys, Glu, Gly, Ser or Asn (Stephens et al., 2008). A regulatory mechanism underlies Ca2+ homeostasis by sorting and activation of AtGLRs by AtCNIHs (see for example, 8.A.61.1.9) (Wudick et al. 2018). May be responsible in part for Cd2+ uptake (Chen et al. 2018). GLR3.3 and GLC3.6 (TC# 1.A.10.1.24) (but not GLR3.4) play different roles in nervous system-like signaling in plant defense by a mechanism that differs substantially from that in animals (Toyota et al. 2018).
GriK2; GluK2; GluR6 glutamate receptor, ionotropic kainate 2. The 3-d structure is known (2XXY_A). The domain organization and function have been analyzed by Das et al. (2010). Two auxiliary subunits, Neto1 and Neto2 (Neuropilin and tolloid-like proteins) alter the trafficking, channel kinetics and pharmacology of the receptors (Howe 2014). They reduce inward rectification without altering calcium permeability (Fisher and Mott 2012). Interactions between the pore helix (M2) and adjacent segments of the transmembrane inner (M3) and outer (M1) helices may be involved in gating (Lopez et al. 2013). Mutations in the human GRIK2 (GLUR6) cause moderate-to-severe nonsyndromic autosomal recessive mental retardation (Motazacker et al. 2007). Kainate receptors regulate KCC2 (TC# 1.A.10.1.11) expression in the hippocampus (Pressey et al. 2017). GluR6, carrying the pore loop plus adjacent transmembrane domains of the prokaryotic, glutamate-gated, K+-selective GluR0 (TC# 1.A.10.2.1), adopted several electrophysiological properties of the donor pore upon pore transplantation (Hoffmann et al. 2006). Clustered mutations in the GRIK2 kainate receptor subunit gene underlie diverse neurodevelopmental disorders (Stolz et al. 2021). Concanavalin A modulation of kainate receptor function is mediated by a shift in the conformation of the kainate receptor toward a tightly packed extracellular domain (Gonzalez et al. 2021).
The NMDA receptor. The crystal structure of the N-terminal domains (GluN1 and GluN2) have been determined (PDB#3QEL; Talukder and Wollmuth, 2011). The ligand-specific deactivation time courses of GluN1/GluN2D NMDA receptors have been measured (Vance et al., 2011). NMDA receptors are Hebbian-like coincidence detectors, requiring binding of glycine and glutamate in combination with the relief of voltage-dependent magnesium block to open an ion conductive pore. Lee et al. 2014 presented X-ray structures of the Xenopus laevis GluN1-GluN2B NMDA receptor with the allosteric inhibitor, Ro25-6981, partial agonists and the ion channel blocker, MK-801. Receptor subunits are arranged in a 1-2-1-2 fashion, demonstrating extensive interactions between the amino-terminal and ligand-binding domains. The 3-TMS transmembrane domains harbour a closed-blocked ion channel, a pyramidal central vestibule lined by residues implicated in binding ion channel blockers and magnesium, and a approximately twofold symmetric arrangement of ion channel pore loops. GRIN2D mediates developmental and epileptic encephalopathy (XiangWei et al. 2019).
Glu2 AMPA receptor (GluR-2; GluR2-flop; CX614; GluA2). The 3-d structure is known at 3.6 Å resolution. It shows a 4-fold axis of symmetry in the transmembrane domain, and a 2-fold axis of symmetry overall, although it is a homotetramer (Sobolevsky et al. 2009). A structure showing an agoniar-bound form of the rat GluA2 receptor revealed conformational changes that occur during gating (Yelshanskaya et al. 2014). GluR2 interacts directly with β3 integrin (Pozo et al., 2012). In general, integrin receptors form macromolelcular complexes with ion channels (Becchetti et al. 2010). TARPS are required for AMP receptor function and trafficking, but seven other auxiliary subunits have also been identified (Sumioka 2013). For example, AMPA receptors are regulated by S-SCAM through TARPs (Danielson et al. 2012). The C-terminal domains of various TARPs (TC#8.A.16.2) play direct roles in the regulation of GluRs (Sager et al. 2011). Whole-genome analyses have linked multiple TARP loci to childhood epilepsy, schizophrenia and bipolar disorders (Kato et al. 2010). Thus, TARPs emerge as vital components of excitatory synapses that participate both in signal transduction and in neuropsychiatric disorders. The architecture of a fully occupied GluR2-TARP complex has been illucidated by cryoEM, showing the homomeric GluA2 AMPA receptor saturated with TARP Υ2 subunits, showing how the TARPs are arranged with four-fold symmetry around the ion channel domain, making extensive interactions with the M1, M2 and M4 TMSs (Zhao et al. 2016). The binding mode and sites for prototypical negative allosteric modulators at the GluA2 AMPA receptor revealing new details of the molecular basis of molulator binding and mechanisms of action (Stenum-Berg et al. 2019). Drug effects, regulatory protein modulators and positive allosteric modulators have been reviewed (Fu et al. 2019). TARP γ2 converts the desensitized state to the high-conductance state which exhibits tighter coupling between subunits in the extracellular parts of the receptor (Carrillo et al. 2020).
Glutamate receptor 4, GIC, AMPA-subtype, GluR4, GRIA4 or GluR-D (preferentially monovalent cation selective). Binding of the excitatory neurotransmitter, L-glutamate, induces a conformation change, leading to the opening of the cation channel, thereby converting the chemical signal to an electrical impulse. The receptor then desensitizes rapidly and enters a transient inactive state, characterized by the presence of bound agonist. In the presence of CACNG4, CACNG7 or CACNG8, GluR4 shows resensitization characterized by a delayed accumulation of current flux upon continued application of glutamate (Gill et al. 2008; Birdsey-Benson et al. 2010). De novo variants in GRIA4 lead to intellectual disability with or without seizures, gait abnormalities, problems of social behavior, and other variable features (Martin et al. 2017).
Heteromeric ionotropic NMDA receptor (NMDAR) consisting of two subunits, GluN1 (938 aas) and GluN2A (1464 aas). Positions of the Mg2+ and Ca2+ ions in the ion channel divalent cation binding site have been proposed, and differences in the structural and dynamic behavior of the channel proteins in the presence of Mg2+ or Ca2+ have been analyzed (Mesbahi-Vasey et al. 2017). GRIN variants in receptor M2 channel pore-forming loop are associated with neurological diseases (Li et al. 2019). Disease-associated variants have revealed mechanistic aspect of the NMDA receptor (Amin et al. 2021). Cross-subunit interactions that stabilize open states mediate gating in NMDA receptors (Iacobucci et al. 2021). The gating mechanism and a modulatory niche of human GluN1-GluN2A NMDA receptors have been reported (Wang et al. 2021). GluN2A and GluN2B NMDA receptors apparently use distinct allosteric routes (Tian et al. 2021). A negative allosteric modulatory site in the GluN1 M4 determines the efficiency of neurosteroid modulation (Langer et al. 2021). Excitatory signaling mediated by NMDAR is critical for brain development and function, as well as for neurological diseases and disorders. Channel blockers of NMDARs can be used for treating depression, Alzheimer's disease, and epilepsy. Chou et al. 2022 monitored the binding of three clinically important channel blockers: phencyclidine, ketamine, and memantine in GluN1-2B NMDARs at local resolutions of 2.5-3.5 Å around the binding site. The channel blockers form interactions with pore-lining residues, which control mostly off-speeds but not on-speeds (Chou et al. 2022). NMDAR channel blockers include MK-801, phencyclidine, ketamine, and the Alzheimer's disease drug memantine, can bind and unbind only when the NMDAR channel is open. NMDAR channel blockers can enter the channel through two routes: the well-known hydrophilic path from extracellular solution to channel through the open channel gate, and also a hydrophobic path from plasma membrane to channel through a gated fenestration (Wilcox et al. 2022). Pregnane-based steroids are positive NMDA receptor modulators that may compensate for the effect of loss-of-function disease-associated GRIN mutations (Kysilov et al. 2022).
AMPA glutamate receptor 3 (GluR3, GluA3. GRIA3. LLUR3. GLURC) (non-selective monovalent cation channel and Ca2+ channel) (Ayalon et al., 2005; Midgett et al., 2012). Regulated by AMPA receptor regulatory proteins (TARPs) including stargazin and CNIH auxiliary subunits (Kim et al., 2010; Straub and Tomita, 2011; Jackson and Nicoll, 2011; Bats et al., 2012; Rigby et al. 2015). The domain architecture of a calcium-permeable AMPA receptor in a ligand-free conformation has been solved (Midgett et al., 2012). The TARP, stargazin, is elevated in the somatosensory cortex of Genetic Absence Epilepsy Rats (Kennard et al. 2011). TARPs alter the conformation of pore-forming subunits and thereby affect antagonist interactions (Cokić and Stein 2008). The structural basis of AMPAR regulation by TARP gamma2, or stargazin (STZ) involves variable interaction stoichiometries of the AMPAR-TARP complex, with one or two TARP molecules binding one tetrameric AMPAR (Twomey et al. 2016). The ion channel extracellular collar plays a role in gating and represents a hub for powerful allosteric modulation of AMPA receptor function (Yelshanskaya et al. 2017). The A653T mutation stabilizes the closed configuration of the channel and affects duration of sleep and awake periods in both humans and mice (Davies et al. 2017). The tetramer exhibits 4 distinct conductase leves due to independent subunit activation. Perampanel is an anticonvulsant drug that regulates gating (Yuan et al. 2019).
The homomeric cation channel/glutamate receptor/kainate 1, GluR5, GluK1, GRIK1 of 918 aas and (weakly responsive to glutamate) (expressed in the developing nervous system) (Bettler et al., 1990). The 3-d structures of the protein have been determined with agonists and antagonists. The agonist, domoic acid, stabilizes the ligand-binding core of the iGluR5 complex in a conformation that is 11 degrees more open than the conformation observed when the full agonist, (S)-glutamate, is bound (Hald et al. 2007). Kainate receptors regulate KCC2 expression in the hippocampus (Pressey et al. 2017). GluR5/ERK signaling is regulated by the phosphorylation and function of the glycine receptor alpha1ins subunit (TC# 9.A.14.3.4) in the spinal dorsal horn of mice (Zhang et al. 2019). The human ortholog is 918 aas long and 97% identical to the rat homolog. (-)-Arctigenin and a series of new analogues are AMPA and kainate receptor antagonists of human homomeric GluA1 and GluK2 receptors (Rečnik et al. 2021).
The heteromeric monovalent cation/Ca2+ channel/glutamate (NMDA) receptor NMDAR1/NMDAR2A/NMDAR2B/NMDAR2C) (Monyer et al., 1992). Note: NR2B is the same as NR3, GluN2A, GRIN2A or subunit epsilon (Schüler et al., 2008). Mediates voltage- and Mg2+-dependent control of Na+ and Ca2+ permeability (Yang et al., 2010). Mutations in the subunit, GRIN1, a 1464 aa protein, identified in patients with early-onset epileptic encephalopathy and profound developmental delay, are located in the transmembrane domain and the linker region between the ligand-binding and transmembrane domains (Yuan et al. 2014; Ohba et al. 2015). Karakas and Furukawa 2014 determined the crystal structure of the heterotetrameric GluN1-GluN2B NMDA receptor ion channel at 4 Å resolution. The receptor is arranged as a dimer of GluN1-GluN2B heterodimers with the twofold symmetry axis running through the entire molecule composed of an amino terminal domain, a ligand-binding domain, and a transmembrane domain. The GluN2 subunit regulates synaptic trafficking of AMPA in the neonatal mouse brain (Hamada et al. 2014). GRIN1 and GRIN2A mutations are associated with severe intellectual disability with cortical visual impairment, epilepsy and oculomotor and movement disorders being discriminating phenotypic features (Lemke et al. 2016; Chen et al. 2017).The cryoEM structure of a triheteromeric receptor including GluN1 (glycine binding), GluN2A and GluN2B (both glutamate binding) has been solved with and without a GluN2B allosteric antagonist, Ro 25-6981 (Lü et al. 2017). Ogden et al. 2017 implicated the pre-M1 region in gating, providing insight into how different subunits contribute to gating, and suggesting that mutations in the pre-M1 helix, such as those that cause epilepsy and developmental delays, can compromise neuronal health. The severity of GRIN2A (Glu2A)-related disorders can be predicted based on the positions of the mutations in the encoding gene (Strehlow et al. 2019). Knock-in mice expressing an ethanol-resistant GluN2A NMDA receptor subunit show altered responses to ethanol (Zamudio et al. 2019). Results of McDaniel et al. 2020 revealed the role of the pre-M1 helix in channel gating, implicated the surrounding amino acid environment in this mechanism, and suggested unique subunit-specific contributions of pre-M1 helices to GluN1 and GluN2 gating. The human ortholog is 998.5% identical. An autism-associated mutation in GluN2B prevents NMDA receptor trafficking and interferes with dendrite growth (Sceniak et al. 2019). The binding of calcium-calmodulin to the C-terminus of GluN1 has long range allosteric effects on the extracellular segments of the receptor that may contribute to the calcium-dependent inactivation (Bhatia et al. 2020). GluN1 interacts with PCDH7 (O60245) to regulate dendritic spine morphology and synaptic function (Wang et al. 2020).
Glutamate-gated ionotropic K+ channel receptor, GluR0 (5TMSs). X-ray structures are available (PDB: 1IIT) (Lee et al. 2005; Lee et al. 2008) GluR6 (TC# 1.A.10.1.11), carrying the pore loop plus adjacent transmembrane domains of this prokaryotic, glutamate-gated, K+-selective GluR0, adopted several electrophysiological properties of the donor pore upon pore transplantation (Hoffmann et al. 2006).
The mixed lineage kinase domain-like (MLKL) protein of 471 aas and 5 TMSs; forms Mg2+-selective channels in the presence of Na+ and K+ (Xia et al. 2016).
The Transmembrane and coiled-coil domains protein 1 (TMCO1, TMCC4, PNAS-10, PNAS-136, UNQ155) of 188 aas and 3 TMSs. It is an ER transmembrane protein that actively prevents Ca2+ stores from overfilling, acting as a "Cacium Load-activated Calcium channel" or ""CLAC"" channel. TMCO1 undergoes reversible homotetramerization in response to ER Ca2+ overloading and disassembly upon Ca2+ depletion to form a Ca2+-selective ion channel as demonstrated in liposomes (Wang et al. 2016). TMCO1 knockout mice reproduce the main clinical features of human cerebrofaciothoracic (CFT) dysplasia spectrum, a developmental disorder linked to TMCO1 dysfunction, and exhibit severe mishandling of ER Ca2+ in cells (Alanay et al. 2014). Thus, TMCO1 provides a protective mechanism to prevent overfilling of ER stores with calcium ions (Wang et al. 2016). It regulates Ca2+ stores in granulosa cells (Sun et al. 2018). TMCO1-mediated Ca2+ leak underlies osteoblast functions via CaMKII signaling (Li et al. 2019). The TMCO1 gene is a tumor suppressor in urinary bladder urothelial carcinomas (UBUC). TMCO1 dysregulates cell-cycle progression via suppression of the AKT pathway, and S60 of the TMCO1 protein is crucial for its tumor-suppressor roles (Li et al. 2017). Batchelor-Regan et al. 2021 published a short review about the clinical and scientific advances made with TMCO1. Ca2+ homeostasis maintained by TMCO1 underlies corpus callosum development via ERK signaling (Yang et al. 2022).
Pore-forming Hemoglobin-α of 142 aas (Morrill and Kostellow 2016).
Pore-forming hemoglobin-β of 147 aas (Morrill and Kostellow 2016).
Pore-forming myoglobin of 154 aas (Morrill and Kostellow 2016).
Pore-forming neuroglobin of 151 aas (Morrill and Kostellow 2016).
Pore-forming cytoglobin of 154 aas (Morrill and Kostellow 2016).
Fibroblast growth factor 2, FGF2, of 288 aas. Forms oligomeric pores in the plasma membrane, and these are involved in its secretion to the external medium where it exerts its action (La Venuta et al. 2016; see family description). The ATP1A1 (TC# 3.A.3.1.1) serves as the receptor for membrane insertion (Zacherl et al. 2015).
Fibroblast growth factor 23, FGF23 of 251 aas. Functions through FGF receptor 4 to regulate the level of the calcium/inorganic cation channel, TrpC6 or TRP6 (TC# 1.A.4.1.5) (Smith et al. 2017).
Interleukin-1 alpha, IL1α or IL1A, of 271 aas and 0 TMSs. Regulates gap junctional communication in Sertoli cells, which is critical for sertoli cell barrier/blood-testis barrier (BTB) restructuring (Chojnacka et al. 2016).
Interleukin 1β, IL1β, IL1beta, IL1B, IL1F2, of 269 aas. Its release depends on its insertion into the membrane with the formation of a transmembrane pore (Martín-Sánchez et al. 2016). IL-1beta is generated by macrophages upon activation of intracellular NLRP3 (NOD-like, leucine rich repeat domains, and pyrin domain-containing protein 3), part of the functional NLRP3 inflammasome complex that detects pathogenic microorganisms and stressors, while neutrophils are enhanced by increasing levels of IL-1beta (Yaqinuddin and Kashir 2020).
Ammonia transporter and regulatory sensor, AmtB (Blauwkamp and Ninfa, 2003; Khademi et al., 2004). It has a cleavable N-terminal signal peptide, and while Amt proteins in Gram-negative bacteria appear to utilize a signal peptide, the homologous proteins in Gram-positive organisms do not (Thornton et al. 2006).
|1.A.11.1.6||Trimeric ammonia channel protein, Amt-1 (391 aas)||
|1.A.11.3.2||High-affinity ammonia transporter and sensor, Mep2 (also an NH4+ sensor) (Javelle et al., 2003a; Rutherford et al., 2008) (has a pair of conserved his/his residues; mutation to his/glu as in Mep1 leads to uncoupling of transport and sensor functions (Boeckstaens et al., 2008))||
|1.A.11.3.5||The Mep2 ammonium transporter 60% identical to the S. cerevisiae Mep2 (1.A.11.3.2). (Distinct residues mediate transport and signaling; Dabas et al., 2009).||
Rhesus (Rh) type C glycoprotein NH3/NH4+ transporter, RhCG (also called tumor-related protein DRC2) (Bakouh et al., 2004; Worrell et al., 2007). Zidi-Yahiaoui et al. (2009) have described characteristics of the pore/vestibule. The structure is known to 2.1 Å resolution (Gruswitz et al., 2010). Each monomer contains 12 transmembrane helices, one more than in the bacterial homologs. Reconstituted into proteoliposomes, RhCG conducts NH3 to raise the internal pH. Models of the erythrocyte Rh complex based on the RhCG structure suggest that the erythrocytic Rh complex is composed of stochastically assembled heterotrimers of RhAG, RhD, and RhCE (Gruswitz et al., 2010). Rh proteins also transport CO2 (Michenkova et al. 2021).
The RH50 NH3 channel (most like human Rh proteins TC# 1.A.11.4.1 and 2; 36-38% identity) (Cherif-Zahar et al., 2007). The Rh CO2 channel protein (3-D structure ± CO2 available) (3B9Z_A; 3B9Y_A) (Li et al., 2007; Lupo et al., 2007) (also transports methyl ammonia) (Weidinger et al., 2007).
The OTOP3 protopn channel protein of 681 aas and 12 TMSs. The cryo-EM structure along with functional characteristics have been described (Chen et al. 2019). XtOTOP3 forms a homodimer with each subunit containing 12 transmembrane helices that can be divided into two structurally homologous halves; each half assembles as an alpha-helical barrel that could serve as a proton conduction pore.
Kidney metal (Mg2+) transporter, Cyclin (CNN) M2 isoform CRA_b (CNNM2). Defects cause hypomagnesemia. It has an extracellular N-terminus, an N-terminal TMS, a hydrophilic domain followed by 4 TMSs, another hydrophilic domain, and an intracellular C-terminus (de Baaij et al., 2012). CNNM2a forms heterodimers with the smaller isoform CNNM2b. The human splice variant 1 of CNNM2 (ACDP2; Q9H8M5) is a Mg2+ transporter (Brandao et al. 2012). The Bateman module is involved in AMP binding and Mg2+ sensing, and their binding causes a conformational change in the CBS module, transmitted to the transmembrane domain (Corral-Rodríguez et al. 2014). It may be able to transport divalent metal cations, Mg2+, Co2+, Mn2+, Sr2+, Ba2+, Cu2+, Fe2+ and monvalent cation, Na+. In prokaryotes, homologs are CorB/C.
Metal transporter CNNM3 (Ancient conserved domain-containing protein 3) (mACDP3) (Cyclin-M3) of 713 aas and probably 5 TMSs with one N-terminal, and four together in the first half of the protein (Chen et al. 2018). See the family description for the domain order of the CNNM proteins.
Metal transporter CNNM3 (Ancient conserved domain-containing protein 3) (Cyclin-M3). As of 2018, the function of this protein as a Mg2+ transporter is under debate (Schäffers et al. 2018).
Metal transporter CNNM4 (Ancient conserved domain-containing protein 4) (Cyclin-M4). As of 2018, the function of this protein as a Mg2+ transporter was under debate (Schäffers et al. 2018).
Putative Mg2+ exporter of 875 aas and 5 TMSs, CNNM2 or ACDP2 (Chen et al. 2018). The bacterial CorC is involved in resistance to antibiotic exposure and to the survival of pathogenic microorganisms in their host environments. CorC possesses a cytoplasmic region containing the (regulatory ?) ATP-binding site (Huang et al. 2021). An inhibitor, IGN95a, targets the ATP-binding site and blocks both ATP binding and Mg2+ export. The cytoplasmic domain structure in complex with IGN95a was determined (Huang et al. 2021). With ATP bound to the cytoplasmic domain, the conformational equilibrium of CorC shifts toward the inward-facing state of the transmembrane domain (Huang et al. 2021). These considerations suggest that CorC may be an ATP-driven Mg2+ efflux porter, and if so, the family belongs in TC sub-class, 3.A. CorC homologs may be able to export Mg2+, Co2+, Mn2+, Sr2+, Ba2+, Cu2+ and Fe2+.
Cyclotide, kalata-B1, kB1. Targets membranes in a process that depends on lipid interactions; hemolytic; can disrupt HIV membranes (Henriques et al., 2011).
The Varv peptide A/Kalata-B1
Nuclear chloride channel-27, NCC27 or CLIC1 (Br- > Cl- > I-) (241 aas). CLIC1 has two charged residues, K37 and R29, in its single TMS which are important for the biophysical properties of the channel (Averaimo et al. 2013). A putative Lys37-Trp35 cation-pi interaction stabilizes the active dimeric form of the CLIC1 TMS in membranes (Peter et al. 2013). This channel may play a role in cancer (Peretti et al. 2014). A positively charged motif at the C-terminus of the single TMS enhances membrane partitioning and insertion via electrostatic contacts. It also functions as an electrostatic plug to anchor the TMS in membranes and is involved in orientating the TMS with respect to the cis and trans faces of the membrane (Peter et al. 2014). The CLIC1 protein accumulates in the circulating monocyte membrane during neurodegeneration (Carlini et al. 2020). The involvement of CLIC1 protein functions in physiological and in pathological conditions has been reviewed (Cianci and Verduci 2021).
The Janus protein, CLIC2. The 3-D structure of its water soluble form has been determined at 1.8 Å resolution (Cromer et al., 2007). CLIC2 interacts with the skeletal ryanodine receptor (RyR1) and modulates its channel activity (Meng et al., 2009).
Chloride intracellular channel protein 4, CLIC4. Regulates the histamine H3 receptor (Maeda et al., 2008)) Discriminates poorly between anions and cations (Singh and Ashley, 2007). 76% identical to CLIC5; it may play a role in cancer (Peretti et al. 2014). CLIC5 was the first mitochondrial chloride channel to be identified in the inner mitochondrial membrane, while CLIC4 is located predominantly in the outer mitochondrial membrane. Gururaja Rao et al. 2020 discussed the intracellular chloride channels, their roles in pathologies, such as cardiovascular, cancer, and neurodegenerative diseases, and developments concerning their usage as theraputic targets in humans.
Intracellular Cl- channel-3 (CLIC3). The 3-d structure is known (3FY7). This protein is associated with pregnancy disorders (Murthi et al., 2012).
|1.A.12.2.1||The plant Cl- intracellular channel protein DHAR1 (glutathione dehydrogenase/dehydroascorbate reductase) (Elter et al., 2007)||
Putative Glutathione S-transferase. Pore formation has not been demonstrated in prokaryotes.
Ca+2-activated Cl- channel, or Chloride Channel Accessory 1 (CLCA1 or CACC1), of 914 aas. CLCA1 may play a role in inflammatory airway diseases (Sala-Rabanal et al. 2015). It is thought to play a role in Cl- secretion in the intestine (A. Quach, personal communication).
The 7 TMS proton-sensitive Ca2+ leak channel, YetJ. The activity and high resolution 3-d structure have been determined (Chang et al. 2014). BsYetJ in lipid nanodiscs is structurally different from those crystallized in detergents. Li et al. 2020 showed that the BsYetJ conformation is pH-sensitive in the apo state (lacking calcium), whereas in a calcium-containing solution it is stuck in an intermediate state, inert to pH changes. Only when the transmembrane calcium gradient is established can the calcium-release activity of holo-BsYetJ occur and be mediated by pH-dependent conformational changes, suggesting a dual gating mechanism. Conformational substates involved in the process and a key residue, D171, relevant to the gating of calcium were identified. Thus, BsYetJ/TMBIM6 is a pH-dependent, voltage-gated calcium channel (Li et al. 2020).
NS channel protein-1 or Sec62 protein of 399aas and 2 TMSs. Efficient secretion of small proteins in mammalian cells relies on Sec62-dependent posttranslational translocation (Lakkaraju et al. 2012).
Formate uptake/efflux permease, FocA. It catalyzes bidirectional transport, has a pentameric aquaporin-like (TC# 1.A.8) structure, and may function by a channel-type mechanism (Falke et al., 2009; Wang et al. 2009). The structure at 2.25 Å resolution has been determined (Wang et al., 2009). The protein is encoded in an operon with pyruvate-formate lyase, PflB. A pyruvate:formate antiport mechanism has been suggested (Moraes and Reithmeier 2012). The C-terminal 6 aas are required for formate transport, but not for homopentamer formation (Hunger et al. 2017). The N-terminus of FocA interacts with PflB, and this interaction is essential for optimal formate translocation (Doberenz et al. 2014). In fact, the GREs, TdcE and PflB, interact with the FNT channel protein, probably to control formate translocation by FocA (Falke et al. 2016). The lipophilic constrictions of FocA mainly act as barriers to isolate the central histidine from the aqueous bulk, preventing protonation via proton wires. Thus, an FNT transport model is supported in which the central histidine is uncharged, and weak acid substrate anion protonation occurs in the vestibule regions of the transporter before passing the constrictions (Schmidt and Beitz 2021). An interplay between the conserved pore residues Thr-91 and His-209 controls formate translocation through the FocA channel (Kammel et al. 2022). T91 is essential for formate permeation in both directions; however, it is particularly important to allow anion efflux. H209 is essential for formate uptake by FocA, strongly suggesting that protonation-deprotonation of this residue plays a role in formate uptake. These observations substantiate the premise that efflux and influx of formate by FocA are mechanistically distinct processes that are controlled by the interplay between T91 and H209 (Kammel et al. 2022).
Nitrite uptake/efflux channel (Jia et al. 2009).
Hydrosulfide (hydrogen sulfide; HS-), Fnt3 (Hsc) channel. Also probably transports chloride, formate and nitrite. The 3-d crystal structure (2.2Å resolution in the closed state) is known (PDB# 3TE2) (Czyzewski and Wang, 2012). The Fnt3 gene is linked to the asrABC operon encoding the sulfite (SO32-) reductase that gives HS- as the product (Czyzewski and Wang 2012).
TMEM16 of 735 aas and 10 TMSs. Operates as a Ca2+-activated lipid scramblase (Wang et al. 2018). Each subunit of the homodimer contains a hydrophilic membrane-traversing cavity that is exposed to the lipid bilayer as a potential site of catalysis. This cavity harbours a conserved Ca2+-binding site, located within the hydrophobic core of the membrane. Mutations of residues involved in Ca2+ coordination affect both lipid scrambling in N. haematococca TMEM16 and ion conduction in the Cl- channel of TMEM16A. The structure reveals the general architecture of the family and its mode of Ca2+ activation (Brunner et al. 2014). While the cytoplasmic portion of the protein is important for function, it does not appear to regulate scramblase activity via a detectable conformational change (Andra et al. 2018). Dynamic modulation of the lipid translocation groove generates a conductive ion channel in Ca2+-bound nhTMEM16 (Khelashvili et al. 2019) (see family description). Permeation of potassium ions through the lipid scrambling path of nhTMEM16 has been documented (Cheng et al. 2022).
TMem16A or Anoctamin-1 (Ano1) Ca2+-activated anion (Cl-) channel of 960 aas and 10 TMSs. Its structure has been solved by cryoEM (Paulino et al. 2017). The protein shows a similar organization to the fungal nhTMEM16, except for changes at the site of catalysis. There, the conformation of transmembrane helices, constituting a membrane-spanning furrow that provides a path for lipids in scramblases, is replaced to form an enclosed aqueous pore that is largely shielded from the membrane (Paulino et al. 2017). It thus provides a pathway for anions such as Cl-. During activation, the binding of Ca2+ to a site located within the transmembrane domain, in the vicinity of the pore, alters the electrostatic properties of the ion conduction path and triggers a conformational rearrangement of an α-helix that comes into physical contact with the bound ligand, and thereby directly couples ligand binding and pore opening (Paulino et al. 2017). The E143A mutant showed reduced sensitivity to Ca2+ but not to high temperatures, whereas the E705V mutant exhibited reduced sensitivity to both Ca2+ and noxious heat (Choi et al. 2018). Loss of TMEM16A resulted in reduced nephron number and, subsequently, albuminuria and tubular damage (Schenk et al. 2018). mAno1 expression is regulated via alternative promoters, and its transcriptional variation results in variation of the N-terminal sequence of the Ano1 protein due to alternative translation initiation sites (Kamikawa et al. 2018). The Ca2+ gating mechanism of TMEM16A, involving a Ca2+-sensing element close to the anion pore, alters conduction and substrate selection. De Jesús-Pérez et al. 2022 studied the gating-permeant anion relationship using mouse TMEM16A, showing that the apparent Ca2+ sensitivity increases with highly permeant anions and SCN- mole fractions, likely by stabilizing bound Ca2+. Conversely, mutations in crucial gating elements, including the Ca2+-binding site 1,TMS 6, and the hydrophobic gate, impaired anion permeability and selectivity. Thus, there is a reciprocal rationship between gating and selectivity (De Jesús-Pérez et al. 2022).
Anoctamin-10 or TMEM16K of 660 aas and 9 or 10 TMSs. In the presence of Ca2+, TMEM16K directly binds Ca2+ to form a stable complex (Ishihara et al. 2016). In the absence of Ca2+, TMEM16K and TMEM16F (TC# 1.A.17.1.4) aggregate, suggesting that their structures are stabilized by Ca2+. Mutagenesis of acidic residues in TMEM16K's cytoplasmic and transmembrane regions identified five residues that are critical for binding Ca2+. These residues are well conserved between TMEM16F and 16K, and point mutations of these residues in TMEM16F reduced its ability to support Ca2+-dependent phospholipid scrambling (Ishihara et al. 2016). Phosphatidyl serine in the ER of mammalian cells is predominantly localized to the cytoplasmic leaflet, but TMEM16K directly or indirectly mediates Ca2+-dependent phospholipid scrambling (Tsuji et al. 2019). Ano10 plays roles in cell division, migration, apoptosis, cell signalling, and developmental processes (Chrysanthou et al. 2022).
Anoctamin-8, Ano8 or TMEM16H, of 1232 aas and 9 TMSs. It tethers the endoplasmic reticulum and plasma membrane for assembly of Ca2+ signaling complexes at the ER/PM compartment (Jha et al. 2019). ANO8 is a key tether in the formation of the ER/PM junctions that are essential for STIM1-STIM1 interaction and STIM1-Orai1 interaction and channel activation at a ER/PM PI(4,5)P2-rich compartment. Moreover, ANO8 assembles all core Ca2+ signaling proteins: Orai1, PMCA, STIM1, IP3 receptors, and SERCA2 at the ER/PM junctions to mediate a novel form of Orai1 channel inactivation by markedly facilitating SERCA2-mediated Ca2+ influx into the ER. This controls the efficiency of receptor-stimulated Ca2+ signaling, Ca2+ oscillations, and the duration of Orai1 activity to prevent Ca2+ toxicity (Jha et al. 2019).
The non-rectifying, plasma membrane, calcium-permeable, stress-gated, cation channel 1 (CSC1) of 771 aas (Hou et al. 2014). Activated by hyperosmotic shock. Permeable to Ca2+, K+ and Na+. Inactivation or closure is Ca2+-dependent. The N-terminal region contains 3 TMSs, the first of which may be a cleavable signal peptide., and the C-terminal region contains 6 TMSs corresponding to the DUF221 domain. Arabidopsis contains at least 15 CSCs ((Hou et al. 2014). Some plant homologues are transcriptionally upregulated in response to vaious abiotic and biotic stresses involving mechanical perturbation (Kiyosue et al. 1994).
OSCA1.2 of 772 aas and 11 TMSs. It is a dimer containing eleven TMSs per subunit, similar to other TMEM16 proteins. Jojoa Cruz et al. 2018 located the ion permeation pathway within each subunit by demonstrating that a conserved acidic residue is a determinant of channel conductance. Molecular dynamics simulations revealed membrane interactions, suggesting a role of lipids in gating. The high resolution structure of this hyperosmolality-gated calcium-permeable channel has been determined (Liu et al. 2018). It contains 11 TMSs and forms a homodimer. The pore-lining residues were clearly identified. Its cytosolic domain contains an RNA recognition motif and two unique long helices. The linker between these two helices forms an anchor in the lipid bilayer and may be essential to osmosensing. Genome-wide analyses of OSCA gene family members in Vigna radiata have revealed their involvement in the osmotic response (Yin et al. 2021).
Dimeric OSCA1.2 of 766 aas and 11 TMSs. The 3-D structure has been determined (K. Maity et al., PNAS, in press). This protein is 69% identical to the A. thaliana ortholog (TC# 1.A.17.5.10). It is a putative early stress-responsive osmolality-sensing ion channel protein. A model has been proposed by which it may mediate hyperosmolality-sensing and consequent gating of ion transport. It has a cytosolic domain structurally related to RNA recognition proteins that includes helical arms paralell to the plane of the membrane. They may sense lateral tension in the inner leaflet, caused by changes in turgor pressure, allowing gating of the channel via coupling of the two domains.
Tic110 channel protein. The x-ray structure (4.2Å resolution) of Tic110B and C from Cyanidioschyzon merolae is known (Tsai et al., 2013). The C-terminal half of Tic110 posesses a rod-shaped helix-repeat structure that is too flattened and elongated to be a channel. The structure is most similar to the HEAT-repeat motif that functions as scaffolds for protein-protein interactions (Tsai et al., 2013).
Matrix protein, M2, an acid activated drug-sensitive proton channel. Transport involves binding to the four His-37s and transfer to water molecules on the inside of the channel (Acharya et al., 2010). Functional properties and structure are known (Hong and Degrado 2012). The cytoplasmic tail facilitates proton conduction (Liao et al. 2015). It is a dimer of dimers (Andreas et al. 2015). The four TMSs flanking the channel lumen alone seem to determine the proton conduction mechanism (Liang et al. 2016). His-37 forms a planar tetrad in the configuration of the bundle accepting and translocating the incoming protons from the N terminal side, exterior of the virus, to the C terminal side, inside the virus (Kalita and Fischer 2017). The cholesterol binding site in M2 that mediates membrane scission in a cholesterol-dependent manner to cause virus budding and release has been identified (Elkins et al. 2017).Transport-related conformational changes coupled to water and H+ movements have been studied (Mandala et al. 2018). The L46P mutant confers a novel allosteric mechanism of resistance towards the influenza A virus M2 S31N proton channel blockers (Musharrafieh et al. 2019). The C-terminal domain of M2 may serve as a sensor that regulates how M2 participates in critical events in the viral infection cycle (Kim et al. 2019). The M2 proton channel protein self-assembles into tetramers that retain the ability to bind to the drug amantadine, and the effects of phospholipid acyl chain length and cholesterol on the peptide association were investigated. Association of the helices depends on the thickness of the bilayer and cholesterol levels present in the phospholipid bilayer. The most favorable folding occurred when there was a good match between the width of the apolar region of the bilayer and the hydrophobic length of the transmembrane helix with tighter association upon inclusion of cholesterol in the lipid bilayer (Cristian et al. 2003).
G-protein-activated inward rectifying K+ channel, Kir3.2, KATP2, KCNJ6, KCNJ7 or GIRK2 of 423 aas and 2 TMSs (Inanobe et al., 2011; Yokogawa et al. 2011). Mutations cause the Keppen-Lubinsky syndrome (Gao et al. 2022). It functions in electrical signaling in neurons and muscle cells (Weng et al. 2021), being important in regulating heart rate and neuronal excitability. It is activated by binding of the βγ-subunit complex to the cytoplasmic pore gate (Yokogawa et al. 2011). Chen et al. 2017 found that GIRK channels are activated by Ivermectin (IVM). Cholesterol binds to and upregulates GIRK channels (GIRK2 and 4), and the binding sites have been determined (Rosenhouse-Dantsker 2018). An inherited gain-of-function mutation in the human GIRK3.4 causes familial human sinus node dysfunction (SND). The increased activity of GIRK channels likely leads to a sustained hyperpolarization of pacemaker cells and thereby reduces heart rate (Kuß et al. 2019). GIRK2 channels are abundantly expressed in the heart and require that phosphatidylinositol bisphosphate (PIP2) is present so that intracellular channel-gating regulators such as Gbetagamma (Gβγ) and Na+ ions maintain the channel-open state. Li et al. 2019 determined how each regulator uses channel domain movements to control gate transitions. Na+ controls the cytosolic gate of the channel through an anti-clockwise rotation, whereas Gβγ stabilizes the transmembrane gate in the open state through a rocking movement of the cytosolic domain. Both effects altered the way by which the channel interacts with PIP2 and thereby stabilizes the open states of the respective gates (Li et al. 2019). The protein plays a role in heart atrial fibrillation-valvular heart disease (VHD) (Zhao et al. 2021). Measurements of ligand binding and channel current have been made (Usher et al. 2021). CryoEM structures of GIRK2 in the presence and absence of the cholesterol analog cholesteryl hemisuccinate (CHS) and phosphatidylinositol 4,5-bisphosphate (PIP2) reveal that CHS binds near PIP2 in lipid-facing hydrophobic pockets of the transmembrane domain, suggesting that CHS stabilizes the PIP2 interaction with the channel to promote engagement of the cytoplasmic domain with the transmembrane region (Mathiharan et al. 2021).
KCNJ11 or Kir6.2 or KATP of 390 aas; 96% identical to the rat homologue, TC# 1.A.2.1.7. Congenital hyperinsulinism (CHI) is characterized by persistent insulin secretion despite severe hypoglycemia. Mutations in the pancreatic ATP-sensitive K+ (K(ATP)) channel proteins sulfonylurea receptor 1 (SUR1) and Kir6.2, encoded by ABCC8 and KCNJ11, respectively, is the most common cause of the disease. Many mutations in SUR1 render the channel unable to traffic to the cell surface, thereby reducing channel function. Many studies have shown that for some SUR1 trafficking mutants, the defects could be corrected by treating cells with sulfonylureas or diazoxide (Yan et al. 2007). Inward rectifier potassium channels are characterized by a greater tendency to allow potassium to flow into the cell rather than out of it. Their voltage dependence is regulated by the concentration of extracellular potassium; as external potassium is raised, the voltage range of the channel opening shifts to more positive voltages. The inward rectification is mainly due to the blockage of outward current by internal magnesium (Tammaro and Ashcroft 2007). Kir6.2 is an ATP-sensitive potassium (KATP) channel coupling cell metabolism to electrical activity by regulating K+ fluxes across the plasma membrane. Channel closure is facilitated by ATP, which binds to the pore-forming subunit (Kir6.2). Conversely, channel opening is potentiated by phosphoinositol bisphosphate (PIP2), which binds to Kir6.2 and reduces channel inhibition by ATP. The PIP2 binding site has been identified (Haider et al. 2007). KATP channels are metabolic sensors that couple cell energetics to membrane excitability. In pancreatic beta-cells, channels formed by SUR1 and Kir6.2 regulate insulin secretion and are the targets of antidiabetic sulfonylureas. Martin et al. 2017 used cryo-EM to elucidate the structural basis of channel assembly and gating. The structure, determined in the presence of ATP and the sulfonylurea, glibenclamide, at ~6 Å resolution, revealed a closed Kir6.2 tetrameric core with four peripheral SUR1s, each anchored to a Kir6.2 by its N-terminal transmembrane domain (TMD0). Intricate interactions between TMD0, the loop following TMD0, and Kir6.2 near the proposed PIP2 binding site, and where ATP density is observed, suggest that SUR1 may contribute to ATP and PIP2 binding to enhance Kir6.2 sensitivity to both. The SUR1-ABC core is found in an unusual inward-facing conformation whereby the two nucleotide binding domains are misaligned along a two-fold symmetry axis, revealing a possible mechanism by which glibenclamide inhibits channel activity (Martin et al. 2017). a cryo-EM structure of a hamster SUR1/rat Kir6.2 channel bound to a high-affinity sulfonylurea drug glibenclamide and ATP has been solved at 3.63 Å resolution. The structure shows that glibenclamide is lodged in the transmembrane bundle of the SUR1-ABC core connected to the first nucleotide binding domain near the inner leaflet of the lipid bilayer (Martin et al. 2017). The activation of K(ATP) channels contributes to the shortening of action potential duration but is not the primary cause of extracellular K+ accumulation during early myocardial ischemia (Saito et al. 2005). KATP binds nucleotides (Usher et al. 2021). Mitochondrial KATP channels stabilize intracellular Ca2+ during hypoxia in retinal horizontal cells of goldfish (Carassius auratus) (Country and Jonz 2021). Medicinal plant products can interact with KATP (Rajabian et al. 2022). Remodeling of excitation-contraction coupling in transgenic mice expressing ATP-insensitive sarcolemmal KATP channels has been observed (Flagg et al. 2004). Thus, a compensatory increase in I(Ca) counteracts a mild activation of ATP-insensitive K(ATP) channels.
Inward rectifier potassium channel 4, KCNJ4, IRK3 or 4, of 445 aas. Its voltage dependence is regulated by the concentration of extracellular potassium; as external potassium is raised, the voltage range of the channel opening shifts to more positive voltages. The inward rectification is mainly due to the blockage of outward current by internal magnesium, and it can be blocked by extracellular barium and cesium. It may play a role in the control of polyamine-mediated channel gating and in the blocking by intracellular magnesium. Overexpression of KCNJ4 correlates with cancer progression and nfavorable prognosis in lung adenocarcinoma (Wu and Yu 2019).
G-protein enhanced inward rectifier K channel 2, IRK1, IRK2, KCNJ2, KCNJ5, Kir2.1 (Andersen-Tawil Syndrome (ATS-1) protein; the V302M mutation causing the syndrome, alters the G-loop cytoplasmic K conduction pathway) (Bendahhou et al., 2003; Ma et al., 2007). (Blocked by chloroquine which binds in the cytoplasmic pore domain (Rodriguez-Menchaca et al., 2008)). Forms heteromultimers with Kir3.1 and Kir3.4 (Ishihara et al., 2009). A C-terminal domain is critical for the sensitivity of Kir2.1 to cholesterol (Epshtein et al., 2009). Flecainide increases Kir2.1 currents by interacting with cysteine 311, decreasing the polyamine-induced rectification (Caballero et al., 2010). The inhibitory cholesterol binding site has been identified (Fürst et al. 2014). Polyamines and Mg2+ block ion flux synergistically (Huang and Kuo 2016). Long polyamines serve a dual role as both blockers and coactivators (with PIP2) of Kir2.1 channels (Xie et al. 2005). Cytoplasmic domain structures of Kir2.1 and Kir3.1 show sites for modulating gating and rectification (Pegan et al. 2005). Loss-of-function mutations are a rare cause of long QT syndrome (Fodstad et al. 2004). Fibroblast growth factor 21 ameliorates NaV1.5 and Kir2.1 channel dysregulation in human AC16 cardiomyocytes (Li et al. 2021). The trafficking of Kir2.1 and its role in development have been reviewed (Hager et al. 2021). Cholesterol-induced suppression of Kir2 channels is mediated by decoupling at the inter-subunit interfaces (Barbera et al. 2022).
Kidney/pancreas/muscle ATP-senstive, ER/Golgi K+ channel, KATP or ROMK (Kir6.2) (Boim et al., 1995) (three alternatively spliced isoforms are called ROMK1-3). Involved in congenital hyperinsulinism (Lin et al., 2008). Regulated by Ankyrin-B (Li et al., 2010). ATP activates ATP-sensitive potassium channels composed of mutant sulfonylurea receptor 1 (SUR1) and Kir6.2 with diminished PIP2 sensitivity (Pratt and Shyng, 2011). This channel protects the myocardium from hypertrophy induced by pressure-overloading (Alvin et al., 2011). Domain organization studies show which domains in Sur and Kir6.2 interact (Wang et al. 2012). KATP channels consisting of Kir6.2 and SUR1 couple cell metabolism to membrane excitability and regulate insulin secretion in pancreatic beta cells, and mutations in the former protein can compensate for mutations in the latter (Zhou et al. 2013). Mutations cause inactivation of channel function by disrupting PIP2-dependent gating (Bushman et al. 2013). Thus, these proteins comprise part of the glucose sensing mechanism (Rufino et al. 2013). A single point mutation can confer voltage sensitivity (Kurata et al. 2010). Its involvement in type II diabetes has been reviewed by Bonfanti et al. 2015. KATP channels (Kir6.2/SUR1) in the brain and endocrine
pancreas couple metabolic status to the membrane potential. In beta-cells, increases in
cytosolic [ATP/ADP] inhibit KATP channel activity, leading to membrane depolarization and
exocytosis of insulin granules. Mutations in ABCC8 (SUR1) or KCNJ11 (Kir6.2) can result in gain or
loss of channel activity and cause neonatal diabetes (ND) or congenital hyperinsulinism (CHI),
respectively. Nucleotide binding without hydrolysis switches SUR1 to stimulatory conformations. Increased affinity for ATP gives rise to ND while decreased affinty gives rise to CHI (Ortiz and Bryan 2015). Kir6.2 can associate with either SUR1 (TC# 3.A.1.208.4) or SUR2A (TC# 3.A.1.208.23) to form heteroctamers, leading to different locations and consequences (Principalli et al. 2015). IATP channels and Ca2+ influx play roles in purinergic vasotoxicity and cell death (Shibata et al. 2018).
Prokaryotic K+-selective Kir channel KirBac1.1 (selectivity: K+ = Rb+ = Cs+ >> Li+, Na+ or NMGM) (Enkvetchakul et al., 2004), inward rectifying (Cheng et al., 2009). Closure of the Kir1.1 pH gate results from steric occlusion of the permeation path by the convergence of four leucines (or phenylalanines) at the cytoplasmic apex of the inner transmembrane helices. In the open state, K+ crosses the pH gate together with its hydration shell (Sackin et al. 2005). An inhibitory cholesterol binding site has been identified (Fürst et al. 2014). Conformational changes associated with an open activation gate have been identified, and these suggest an allosteric pathway that ties the selectivity filter to the activation gate through interactions between both transmembrane helices, the turret, the selectivity filter loop, and the pore helix. Specific residues involved in this conformational exchange that are highly conserved among human Kir channels have also been identified (Amani et al. 2020). Anionic lipids, especially cardiolipin, initiate a concerted rotation of the cytoplasmic domain subunits. This action buries ionic side chains away from the bulk water, while allowing water greater access to the K+ conduction pathway (Borcik et al. 2020). Kv1.5 channels are regulated by PKC-mediated endocytic degradation (Du et al. 2021). Pore-forming TMSs control ion selectivity and the selectivity filter conformation in the KirBac1.1 channel (Matamoros and Nichols 2021).
The KirBac3.1 K+ channel (a dimer of dimers with gating visualized by atomic force microscopy (Jaroslawski et al., 2007) (regulated by binding lipids, G-proteins, nucleotides, and ions (H+, Ca2+, and Mg2+)). The 3-D structure is available (1XL6_A). The inhibitory cholesterol binding site has been identified (Fürst et al. 2014). The constricted opening in this, and presumably other, Kir channels does not impede potassium conduction (Black et al. 2020). The structural and dynamic properties of a KirBac3.1 mutant revealed the function of a highly conserved tryptophan in the transmembrane domain (Fagnen et al. 2021).
Inward rectifier potassium channel
BNip3 channel-forming protein (Bocharov et al., 2007). It is an apoptosis-inducing protein that can overcome BCL2 suppression and may play a role in repartitioning calcium between the two major intracellular calcium stores in association with BCL2 (Ghavami et al. 2010). It is also involved in mitochondrial quality control via its interaction with SPATA18/MIEAP: in response to mitochondrial damage, it participates in mitochondrial protein catabolic process (also named MALM) leading to the degradation of damaged proteins inside mitochondria. The physical interaction of SPATA18/MIEAP, BNIP3 and BNIP3L/NIX at the mitochondrial outer membrane regulates the opening of a pore in the mitochondrial double membrane in order to mediate the translocation of lysosomal proteins from the cytoplasm to the mitochondrial matrix (Nakamura et al. 2012). Platinum-based combination chemotherapy triggers cancer cell death through induction of BNIP3 and ROS, but not autophagy (Chung et al. 2020).
Apoptosis regulator Bcl-X(L) of 233 aas. Also called Bcl2-like protein 1, isoform 1. Membrane insertion of the soluble form has been characterized (Vargas-Uribe et al. 2013). The cytosolic domain of Bcl-2 forms small pores in the mitochondrial outer membrane (Peng et al. 2009).
Bcl-2 apoptosis regulator of 239 aas and 2 TMSs. It suppresses apoptosis in a variety of cell systems including factor-dependent lymphohematopoietic and neural cells. It regulates cell death by controlling the mitochondrial membrane permeability and appears to function in a feedback loop system with caspases. It inhibits caspase activity either by preventing the release of cytochrome c from the mitochondria and/or by binding to the apoptosis-activating factor (APAF-1), and it may attenuate inflammation by impairing NLRP1-inflammasome activation, hence CASP1 activation and IL1B release (Bruey et al. 2007).
|1.A.21.1.12||The Cell Death (CED-9) protein (Siskind et al., 2008)||
The mitochondrial apoptosis-inducing channel-forming protein, BAX. The C-terminal helix mediates membrane binding and pore formation (Garg et al. 2012). BAX pores are large enough to allow cytochrome c release and it activates the mitochondrial permeabilty transition pore; both play a role in programmed cell death, but the latter is quantitatively more important (Gómez-Crisóstomo et al. 2013). Bax functions like a holin when expressed in bacteria (Pang et al. 2011). Bax (and likely Bak) dimers assemble into oligomers with an even number of molecules that fully or partially delineate pores of different sizes to permeabilize the mitochondrial outer membrane (MOM) during apoptosis (Cosentino and García-Sáez 2016). The membrane domain of Bax interacts with other members of the Bcl-2 family to form hetero-oligomers (Andreu-Fernández et al. 2017). Uren et al. 2017 reviewed how clusters of dimers and their lipid-mediated interactions provide a molecular explanation for the heterogeneous assemblies of Bak and Bax observed during apoptosis. After BAK/BAX activation and cytochrome c loss, the mitochondrial network breaks down, and large BAK/BAX pores appear in the outer membrane. These macropores allow the inner membrane an outlet through which it herniated, carrying with it mitochondrial matrix components including the mitochondrial genome (McArthur et al. 2018). The core/dimerization domain of Bax and Bak is water exposed with only helices 4 and 5 in membrane contact, whereas the piercing/latch domain is in peripheral membrane contact, with helix 9 being transmembrane (Bleicken et al. 2018). The mechanism of the membrane disruption and pore-formation by the BAX C-terminal TMS has been investigated (Jiang and Zhang 2019). Bax membrane permeabilization results from oligomerization of transmembrane monomers (Annis et al. 2005). Bax localization and apoptotic activity are conformationally controled by Pro168 (Schinzel et al. 2004).
The mitochondrial apoptosis-inducing channel-forming protein, BAK. 3-D structures are known (2IMT_A). Functions like a holin when expressed in bacteria (Pang et al. 2011). Formation of the apoptotic pore involves a flexible C-terminal domain (Iyer et al. 2015). Bax (and likely Bak) dimers assemble into oligomers with an even number of molecules that fully or partially delineate pores of different sizes to permeabilize the mitochondrial outer membrane (MOM) during apoptosis (Cosentino and García-Sáez 2016). BAK is a C-tail-anchored mitochondrial outer membrane protein (Setoguchi et al. 2006). BAK plays a role in peroxisomal permeability, similar to mitochondrial outer membrane permeabilization (Hosoi et al. 2017). Uren et al. 2017 reviewed how clusters of dimers and their lipid-mediated interactions provide a molecular explanation for the heterogeneous assemblies of Bak and Bax observed during apoptosis. After BAK/BAX activation and cytochrome c loss, the mitochondrial network breaks down, and large BAK/BAX pores appear in the outer membrane. These macropores allow the inner membrane an outlet through which it herniates, carrying with it mitochondrial matrix components including the mitochondrial genome (McArthur et al. 2018). A high-resolution analysis of the conformational transition of pro-apoptotic Bak at the lipid membrane has been published (Sperl et al. 2021).
Pro-survival Bcl-w protein. Binds the BH3-only protein Bop to inhibit Bop-induced apoptosis (Zhang et al. 2012). The structure is known (PDB# 1MK3).
Pore-forming Bcl-2-related ovarian killer protein, Bok (BokL, Bcl2L9) of 212 aas and 2 or more predicted TMSs. It is an apoptosis regulator that functions through different apoptotic signaling pathways (Einsele-Scholz et al. 2016, Yakovlev et al. 2004, Jääskeläinen et al. 2010). The transmembrane-domain contributes to the pro-apoptotic function and interactions of Bok with other proteins (Stehle et al. 2018). Bok binds to a largely disordered loop in the coupling domain of type 1 inositol 1,4,5-trisphosphate receptors, and high affinity binding is mediated by multivalent interactions (Szczesniak et al. 2021).
Large mechanosensitive ion channel: MscL, with a subunit size of 136 aas with 2 TMSs; it catalyzes efflux of ions (slightly cation selective), osmolytes and small proteins. Residues in the putative primary gate are present in the first TMS (Levin and Blount 2004). Protein-lipid interactions are important for gating, dependent on TMS tilting (Iscla et al., 2011b). The carboxyl-terminal cytoplasmic helices assemble into a pentameric bundle that resembles cartilage oligomeric matrix protein, and these are required for the selective formation of the pentamer (Ando et al. 2015). Lysophospholipids can increase the size of particles that can be transported (Foo et al. 2015). 500 - 700 channels are needed for 80% survival follwing a large changes in osmotic pressure, a number of channels similar to that found in wild type E. coli cells (Chure et al. 2018). its activation threshold decreases with membrane thickness; the membrane-thickness-dependent MscL opening mainly arises from structural changes in MscL to match the altered membrane thickness by stretching (Katsuta et al. 2018). MscL can provide a route for antibiotic entry into the E. coli cell, and agonists are available to facilitate their entry (Wray et al. 2020; Zhao et al. 2020). MscL has been used to design a synthetic mechanosensitive signaling pathway in compartmentalized artificial cells (Hindley et al. 2019). Available information at the ultrastructural level on lipids tightly bound to transport proteins and the impact of altered bulk membrane lipid composition has been reviewed (Stieger et al. 2021). Competition between hydrophobic mismatch and tension may result in opening tension for MscL (Wiggins and Phillips 2004).
Large conductance mechanosensitive channel protein, MscL, of 101 aas and 2 TMSs. When the membrane is stretched, MscL responds to the increase of membrane tension and opens a nonselective pore to about 30 A wide, exhibiting a large unitary conductance of approximately 3 nS. The structures of this archaeal MscL, trapped in the closed and expanded intermediate states, has been solved (Li et al. 2015). The comparative analysis of these two new structures reveals significant conformational rearrangements in the different domains of MscL. The large changes observed in the tilt angles of the two transmembrane helices (TMS1 and TMS2) fit well with the helix-pivoting model. Meanwhile, the periplasmic loop region transforms from a folded structure, containing an omega-shaped loop and a short beta-hairpin, to an extended and partly disordered conformation during channel expansion. Moreover, a significant rotating and sliding of the N-terminal helix (N-helix) is coupled to the tilting movements of TMS1 and TMS2. The dynamic relationships between the N-helix and TMS1/TMS2 suggest that the N-helix serves as a membrane-anchored stopper that limits the tilts of TM1 and TM2 in the gating process (Li et al. 2015). Residues I21-T30 in TMS 1 constitute the hydrophobic gate, and the packing of aromatic rings of F23 in each subunit of Ma-MscL is critical to the hydrophobic gate (Zhang et al. 2021). Hydrophilic substitutions of the other functionally important residues, A22 and G26, modulate channel gating by attenuating the hydrophobicity of the F23 constriction.
Large mechanosensitive ion channel of 151 aas and 2 TMSs. The 3-D structure is known, and it may reflect a nearly closed rather than fully closed state. Modeling support a clockwise rotation of the pore-forming first TMS promotes gating (Bartlett et al. 2004).
Major MscS channel protein, YggB. Seven residues, mostly hydrophobic, in the first and second transmembrane helices are lipid-sensing residues (Malcolm et al., 2011). X-ray structures are available (Lai et al. 2013). The cytoplasmic cage domain senses macromolecular crowding (Rowe et al. 2014). A gating mechanism has been proposed (Malcolm et al. 2015). The thermodynamics of K+ leak have been studied (Koprowski et al. 2015). In the MscS crystal structure (PDB 2OAU ), a narrow, hydrophobic opening is visible in the crystal structure, and a vapor lock, created by hydrophobic seals consisting of L105 and L109, is the barrier to water and ions (Rasmussen et al. 2015). The voltage dependence of inactivation occurs independently of the positive charges of R46, R54, and R74 (Nomura et al. 2016). The closed-to-open transition may involve rotation and tilt of the pore-lining helices (Edwards et al. 2005).
Mitochondrial mechanosensitive ion channel protein 1, MscS-like channel, MSL1, of 497 aas and 5 TMSs. As the sole member of the Arabidopsis MSL family, localized in the mitochondrial inner membrane, MSL1 is essential for maintaining the normal membrane potential of mitochondria. Li et al. 2020 reported a cryoelectron microscopy (cryo-EM) structure of AtMSL1 at 3.3 Å. The overall architecture of AtMSL1 is similar to MscS, but the transmembrane domain of AtMSL1 is larger. Structural differences are observed in both the transmembrane and the matrix domain, and the carboxyl-terminus of AtMSL1 is more flexible while the beta-barrel structure observed in MscS is absent. The side portals in AtMSL1 are significantly smaller, and enlarging the size of the portal by mutagenesis can increase the channel conductance (Li et al. 2020).
Connexin 43 (gap junction α-1 protein), CX43 encoded by the GJA1 gene (transports ATP, ADP and AMP better than CX32 does; Goldberg et al., 2002). Hemichannels mediate efflux of glutathione, glutamate and other amino acids as well as ATP (Stridh et al., 2008; Kang et al., 2008). CX43 has a half life of ~3 h due to ubiquitination and lysosomal and proteasomal degradation (Leithe and Rivedal, 2007). Cx43 and Cx46 regulate each other's expression and turnover in a reciprocal manner in addition to their conventional roles as gap junction proteins in lens cells (Banerjee et al., 2011). A mutant form of Connexin 43 causes Oculodentodigital dysplasia (Gabriel et al., 2011). Suppressing the function of Cx43 promotes expression of wound healing-associated genes and hibitits scarring (Tarzemany et al. 2015). Channel conductance and size selectivity are largely determined by pore diameter, whereas charge selectivity results from the amino-terminal domains; transitions between fully open and (multiple) closed states involves global changes in structure of the pore-forming domains (Ek Vitorín et al. 2016). The human Cx43 orthologue is almost identical to the rat protein. It may mediate resistance against the parkinsonian toxin, 1-methyl-4-phenylpyridine (MPP+) which induces apoptosis in neuroblastoma cells by modulating mitochondrial apoptosis (Kim et al. 2016). Dopamine neurons may be the target of MPP+ and play a role in Parkinson's disease. In humans, Cx43 plays roles in the development of the central nervous system and in the progression of glioma (Wang et al. 2017). It interacts with and is regulated by many proteins including NOV (CCN3, IGFBP9; P48745) (Giepmans 2006). Cx43 plays roles in intercellular communication mediated by extracellular vesicles, tunnelling nanotubes and gap junctions (Ribeiro-Rodrigues et al. 2017). Phosphorylation of Cx43 leads to astrocytic coupling and apoptosis, and ultimately, to vascular regeneration in retinal ischemia. Paxillin (Pxn; 591 aas; P49023), a cytoskeletal protein involved in focal adhesion, leads to changes in connexin 43 by direct protein-protein binding, thereby influencing osteocyte gap junction elongation (Zhang et al. 2018). Regulation of Cx43 abundance involves transcriptional/post-transcriptional and translational/post-translational mechanisms that are modulated by an interplay between TGF-beta isoforms and PGE2, IL-1beta, TNF-alpha and IFN-gamma (Cheng et al. 2018). In the developing fetal human kidney, cytoplasmic expression of Cx36 was localized to nephrons in different developmental stages, glomerular vessels and collecting ducts, and of Cx43 was localized to the endothelium of glomerular and peritubular vessels, as well as to the epithelium of the proximal tubules (Ráduly et al. 2019). Mutations in the gap junction protein α1 (GPA1) gene cause oculodentodigital dysplasia (Pace et al. 2019). Expression of connexin 43 is elevated in atypical fibroxanthoma cells (Fernandez-Flores et al. 2020). Astrocytic connexin43 channels are candidate targets in epilepsy treatment (Walrave et al. 2020). Cx43 plays roles in physiological functions such as regulating cell growth, differentiation, and maintaining tissue homeostasis (Sha et al. 2020). Amyloid-beta (TC# 1.C.50) regulates connexin 43 trafficking in cultured primary astrocytes (Maulik et al. 2020). Gap junction protein Cx43 plays a role in regulating cellular function and paracrine effects of smooth muscle progenitor cells (Tien (田婷怡) et al. 2021). A serine residues in the connexin43 carboxyl tail is important for B-cell antigen receptor-mediated spreading of B-lymphocytes (Pournia et al. 2020). Connexin 43 plays an antagonistic role in the development of primary bone tumors as a tumor suppressor and also as a tumor promoter (Talbot et al. 2020). Retinal astrocytes abundantly express Cx43 that forms gap junction (GJ) channels and unopposed hemichannels, and Cx43 is upregulated in retinal injuries. Astrocytic Cx43 plays a role in retinal ganglion cell (RGC) loss associated with injury (Toychiev et al. 2021). Screens for inhibitors of Cx43 hemichannel function have revealed several candidates (Soleilhac et al. 2021). The dodecameric channel is formed by the end-to-end docking of two hexameric connexons, each comprised of 24 transmembrane alpha-helices (Cheng et al. 2019). Cx43 appears to be involved in the tumorigenesis of most pituitary adenomas and have a potential therapeutic value for pituitary tumor therapy (Nunes et al. 2022).
Connexin36, connexin delta2, Cxδ2, GJD2, Cx36 of 321 aas and 4 TMSs. In the developing fetal kidney, cytoplasmic expression of Cx36 is localized to nephrons in different developmental stages, glomerular vessels and collecting ducts. Cx43 is localized to the endothelium of glomerular and peritubular vessels, as well as to the epithelium of the proximal tubules (Ráduly et al. 2019). A reciprocal relationship between Cx36 and seizure-associated neuronal hyperactivityhas been obseerved; thus, Cx36 deficiency contributes to region-specific susceptibility to neuronal hyperactivity, while neuronal hyperactivity-induced downregulation of Cx36 may increase the risk of future epileptic events (Brunal et al. 2020).
Heteromeric connexin (Cx)32/Cx26; (CxB2, GJβ2, GJB2) (transports cAMP, cGMP and all inositol phosphates with 1-4 esterified phosphate groups (homomeric Cx26(β2) or homomeric Cx32 do not transport the inositol phosphates as well) (Ayad et al., 2006). The GJB2 gene encodes connexin 26, the protein involved in cell-cell attachment in many tissues. GJB2 mutations cause autosomal recessive (DFNB1) and sometimes dominant (DFNA3) non-syndromic sensorineural hearing loss as well as various skin disease phenotypes (Iossa et al., 2011; Tian et al. 2022). TMS1 regulates oligomerization and function (Jara et al., 2012). The carboxyl tail pg Cx32 regulates gap junction assembly (Katoch et al. 2015). In Cx46, neutralization of negative charges or addition of positive charge in the Cx26 equivalent region reduced the slow gate voltage dependence. In Cx50 the addition of a glutamate in the same region decreased the voltage dependence and the neutralization of a negative charge increased it. Thus, the charges at the end of TMS1 are part of the slow gate voltage sensor in Cxs. The fact that Cx42, which has no charge in this region, still presents voltage dependent slow gating suggests that charges still unidentified also contribute to the slow gate voltage sensitivity (Pinto et al. 2016). Syndromic deafness mutations at Asn14 alter the open stability of Cx26 hemichannels (Sanchez et al. 2016). The Leu89Pro substitution in the second TMS of CX32 disrupts the trafficking of the protein, inhibiting the assembly of CX32 gap junctions, which in turn may result in peripheral neuropathy (Da et al. 2016). Cx26 mutants that promote cell death or exert transdominant effects on other connexins in keratinocytes lead to skin diseases and hearing loss, whereas mutants having reduced channel function without aberrant effects on coexpressed connexins cause only hearing loss (Press et al. 2017). When challenged by a field of 0.06 V/nm, the Cx26 hemichannel relaxed toward a novel configuration characterized by a widened pore and an increased bending of the second TMS at the level of the conserved Pro87. A point mutation that inhibited such a transition impeded hemichannel opening in electrophysiology and dye uptake experiments. Thus, the Cx26 hemichannel uses a global degree of freedom to transit between different configuration states, which may be shared among all connexins (Zonta et al. 2018). A group of human mutations within the N-terminal (NT) domain of connexin 26 hemichannels produce aberrant channel activity, which gives rise to deafness and skin disorders, including keratitis-ichthyosis-deafness (KID) syndrome. Structural and functional studies indicate that the NT domain of connexin hemichannels is folded into the pore, where it plays important roles in permeability and gating. The mutation, N14K disrupts cytosolic intersubunit interactions and promotes channel opening (Valdez Capuccino et al. 2018). A missense mutation in the Connexin 26 gene is associated with hereditary autosomal recessive sensorineural deafness (Leshinsky-Silver et al. 2005, Zytsar et al. 2020). Cx26 hemichannels mediate the passage of contents between the cytoplasm and extracellular space. To generate hemichannels, the mutation N176Y was introduced into the second extracellular loop of Cx26. The cryoEM structure of the hexameric hemichannel in lipid bilayer nanodiscs displays an open pore and a 4-helix bundle transmembrane design that is nearly identical to dodecameric GJCs. In contrast to the high resolution of the transmembrane alpha-helices, the extracellular loops are less well resolved. The conformational flexibility of the extracellular loops may be essential to facilitate surveillance of hemichannels in apposed cells to identify compatible Cx isoforms that enable intercellular docking (Khan et al. 2021). A rare variant c.516G>C (p.Trp172Cys) in the GJB2 (connexin 26) gene is associated with nonsyndromic hearing loss (Maslova et al. 2021). Keratitis-ichthyosis-deafness (KID) syndrome is caused by mutations in the GJB2 gene (Asgari et al. 2020). An increase in the partial pressure of carbon dioxide (PCO2) has been shown to cause Cx26 gap junctions to close. Cryo-EM was used to determine the structure of human Cx26 gap junctions under increasing levels of PCO2. Brotherton et al. 2022 showed a correlation between the level of PCO2 and the size of the aperture of the pore, governed by the N-terminal helices that line the pore. Thus, CO2 alone is sufficient to cause conformational changes in the protein. Analysis of the conformational states showed that movements at the N-terminus are linked to both subunit rotation and flexing of the transmembrane helices (Brotherton et al. 2022). Cysteine residues in the C-terminal tail of connexin32 regulate its trafficking (Ray and Mehta 2021).
Connexin 30 complex (connexin30.2/connexin31.3 (CX30.2/CX31.3)). Also called connexinΥ3/GJC3/GJε1; 279 aas, encoded by the GJB6 (13q12) gene (Cascella et al. 2016)). ATP is released from cells that stably expressed CX30.2 in a medium with low calcium, suggesting a hemichannel-based function. Liang et al. (2011) suggested that it shares functional properties with pannexin hemichannels rather than gap junction channels. Defects cause nonsyndromic hypoacusia (hearing loss) due to partial loss of channel activity (Su et al. 2012; Su et al. 2013; Cascella et al. 2016). Cx30, but not Cx43, hemichannels close upon protein kinase C activation, showing that connexin hemichannels display not only isoform-specific permeability profiles but also isoform-specific regulation by PKC (Alstrom et al. 2015). The W77S mutant has a dominant negative effect on the formation and function of the gap junction and is probably responsible for hearing loss (Wong et al. 2017). Mutations in Cs30 rescue hearing and reveal roles for gap junctions in cochlear amplification (Lukashkina et al. 2017). The cryo-EM structure of the human Cx31.3/GJC3 connexin hemichannel has been solved (Lee et al. 2020). Cx31.3)/GJC3 hemichannels in the presence and absence of calcium ions and with a hearing-loss mutation R15G were solved at 2.3-, 2.5- and 2.6-Å resolutions, respectively. Compared with available structures of GJICh in the open conformation, the Cx31.3 hemichannel shows substantial structural changes of highly conserved regions in the connexin family, including opening of calcium ion-binding tunnels, reorganization of salt-bridge networks, exposure of lipid-binding sites, and collocation of amino-terminal helices at the cytoplasmic entrance. The hemichannel has a pore with a diameter of ~8 Å and selectively transports chloride ions (Lee et al. 2020).
Connexin45 (Cx45; Cx-45; Gap Junction protein γ1; GJγ1; Gjc1; Gja7; CxG1) of 396 aas and 4 TMSs (Kopanic et al. 2015).
Innexin-6 protein, Inx-6 or Opu-6, of 389 aas and 4 TMSs. A single INX-6 gap junction channel consists of 16 subunits, a hexadecamer, in contrast to chordate connexin channels, which consist of 12 subunits. The channel pore diameters at the cytoplasmic entrance and extracellular gap region are larger than those of connexin26 (Oshima et al. 2016). Nevertheless, the arrangements of the transmembrane helices and extracellular loops of the INX-6 monomer are highly similar to those of connexin-26 (Cx26). The INX-6 gap junction channel comprises hexadecameric subunits but reveals an N-terminal pore funnel consistent with Cx26. The helix-rich cytoplasmic loop and C-terminus are intercalated through an octameric hemichannel, forming a dome-like entrance that interacts with N-terminal loops in the pore (Oshima et al. 2016).
Pannexin-1 (PANX1) has been reported to form functional, single membrane, cell surface channels (Penuela et al., 2007). Pannexin1 is part of the pore forming unit of the P2X(7) receptor death complex (Locovei et al., 2007). It can catalyze ATP release from cells (Huang and Roper, 2010) and promote ATP signalling in mice (Suadicani et al. 2012). It also promotes acetaminophen liver toxicity by allowing it to enter the cell (Maes et al. 2016). Pannexin1 and pannexin2 channels show quaternary similarities to connexons but different oligomerization numbers (Ambrosi et al., 2010). Pannexin 1 constitutes the large conductance cation channel of cardiac myocytes (Kienitz et al., 2011). Pannexin 1 (Px1, Panx1) and pannexin 2 (Px2, Panx2) underlie channel function in neurons and contribute to ischemic brain damage (Bargiotas et al., 2011). Single cysteines in the extracellular and transmembrane regions modulate pannexin 1 channel function (Bunse et al., 2011). Spreading depression triggers migraine headaches by activating neuronal pannexin1 (panx1) channels (Karatas et al. 2013). The channel in the mouse orthologue opens upon apoptosis (Spagnol et al. 2014). Transports ATP out of the cell since L-carbenoxolone (a Panx1 channel blocker) inhibits ATP release from the nasal mucosa, but flufenamic acid (a connexin channel blocker) and gadolinium (a stretch-activated channel blocker) do not (Ohbuchi et al. 2014). CALHM1 (TC#1.N.1.1.1) and PANX1 both play roles in ATP release and downstream ciliary beat frequency modulation following a mechanical stimulus in airway epithelial cells (Workman et al. 2017). Pannexin1 may play a role in the pathogenesis of liver disease (Willebrords et al. 2018). Inhibition of pannexin1 channel opening may provide a novel approach for the treatment of drug (acetaminophen-induced)-induced hepatotoxicity (Maes et al. 2017). Pannexin-1 is necessary for capillary tube formation on Matrigel and for VEGF-C-induced invasion. It is highly expressed in HDLECs and is required for in vitro lymphangiogenesis (Boucher et al. 2018). cryo-EM structure of a pannexin 1 reveals unique motifs for ion selection and inhibition. The cryo-EM structure of a pannexin 1 revealed unique motifs for ion selection and inhibition (Michalski et al. 2020). In another study, Deng et al. 2020 obtained near-atomic-resolution structures of human and frog PANX1 determined by cryo-EM that revealed a heptameric channel architecture. Compatible with ATP permeation, the transmembrane pore and cytoplasmic vestibule were exceptionally wide. An extracellular tryptophan ring located at the outer pore created a constriction site, potentially functioning as a molecular sieve that restricts the sizes of permeable substrates. Pannexin 1 channels in renin-expressing cells influence renin secretion and homeostasis (DeLalio et al. 2020). Structures of human pannexin 1 have revealed ion pathways and mechanism of gating (Ruan et al. 2020). PANX1 is critical for functions such as blood pressure regulation, apoptotic cell clearance and human oocyte development. Ruan et al. 2020 presented several structures of human PANX1 in a heptameric assembly at resolutions of up to 2.8 Å, including an apo state, a caspase-7-cleaved state and a carbenoxolone-bound state. A gating mechanism was revealed that involves two ion-conducting pathways. Under normal cellular conditions, the intracellular entry of the wide main pore is physically plugged by the C-terminal tail. Small anions are conducted through narrow tunnels in the intracellular domain. These tunnels connect to the main pore and are gated by a long linker between the N-terminal helix and the first transmembrane helix. During apoptosis, the C-terminal tail is cleaved by caspase, allowing the release of ATP through the main pore. A carbenoxolone (a channel blocker)-binding site is embraced by W74 in the extracellular entrance. A gap-junction-like structure was observed as expected (Yen and Saier 2007; Chou et al. 2017). Navis et al. 2020 provided a review of the literature on Panx1 structural biology and known pharmacological agents that target it. The R217H mutation perturbs the conformational flexibility of the C-terminus, leading to channel dysfunction (Purohit and Bera 2021). Panx1 plays decisive roles in multiple physiological and pathological settings, including oxygen delivery to tissues, mucociliary clearance in airways, sepsis, neuropathic pain, and epilepsy. It exerts some of these roles in the context of purinergic signaling by providing a transmembrane pathway for ATP, but Panx1 can also act as a highly selective membrane channel for chloride ions without ATP permeability (Mim et al. 2021). Pannexin 1 regulates skeletal muscle regeneration by promoting bleb-based myoblast migration and fusion through a lipid based signaling mechanism (Suarez-Berumen et al. 2021). Pannexin-1 activation by phosphorylation is crucial for platelet aggregation and thrombus formation (Metz and Elvers 2022).
The volume-regulated Anion Channel, VRAC, or volume-sensitive outward rectifying anion channel, VSOR. It is also called the SWELL1 protein. It consists of the leucine-rich repeat-containing protein 8A, with an N-terminal pannexin-like domain, LRRC8A, together with other LRRC8 subunits (B, C, D and E). The first two TMSs of the 4 TMS LRRC8 proteins appear as DUF3733 in CDD (Abascal and Zardoya, 2012). The C-terminal soluble domain shows sequence similarity to the heme-binding protein, Shv, and pollen-specific leucine-rich repeat extension-like proteins (3.A.20.1.1). The volume-regulated anion channel, VRAC, has LRRC8A as a VRAC component. It forms heteromers with other LRRC8 membrane proteins (Voss et al. 2014). Genomic disruption of LRRC8A ablated VRAC currents. Cells with disruption of all five LRRC8 genes required LRRC8A cotransfection with other LRRC8 isoforms to reconstitute VRAC currents. The isoform combination determined the VRAC inactivation kinetics. Taurine flux and regulatory volume decrease also depended on LRRC8 proteins. Thus, VRAC defines a class of anion channels, suggesting that VRAC is identical to the volume-sensitive organic osmolyte/anion channel VSOAC, and explains the heterogeneity of native VRAC currents (Voss et al. 2014). Point mutations in two amino-acyl residues (Lys98 and Asp100 in LRRC8A and equivalent residues in LRRC8C and -E) upon charge reversal, alter the kinetics and voltage-dependence of inactivation (Ullrich et al. 2016). Using cryo-electron microscopy and X-ray crystallography, Deneka et al. 2018 and Kasuya et al. 2018 determined the structures of a homomeric channel of the obligatory subunit LRRC8A. This protein conducts ions and has properties in common with endogenous heteromeric channels. Its modular structure consists of a transmembrane pore domain followed by a cytoplasmic leucine-rich repeat domain. The transmembrane domain, which is structurally related to connexins, is wide towards the cytoplasm but constricted on the outside by a structural unit that acts as a selectivity filter. An excess of basic residues in the filter and throughout the pore attracts anions by electrostatic interaction (Deneka et al. 2018). The structure shows a hexameric assembly, and the transmembrane region features a topology similar to gap junction channels. The LRR region, with 15 leucine-rich repeats, forms a long, twisted arc. The channel pore is located along the central axis and constricted on the extracellular side, where highly conserved polar and charged residues at the tip of the extracellular helix contribute to the permeability to anions and other osmolytes. Two structural populations were identified, corresponding to compact and relaxed conformations. Comparing the two conformations suggests that the LRR region is flexible and mobile with rigid-body motions, which might be implicated in structural transitions on pore opening (Kasuya et al. 2018). VRAC is inhibited by Tamoxifen and Mefloquine (Lee et al. 2017). The intracellular loop connecting TMSs 2 and 3 of LRRC8A and the first extracellular loop connecting transmembrane domains 1 and 2 of LRRC8C, LRRC8D, or LRRC8E are essential for VRAC activity (Yamada and Strange 2018). The N termini of the LRRC8 subunits may line the cytoplasmic portion of the VRAC pore, possibly by folding back into the ion permeation pathway (Zhou et al. 2018). On the adipocyte plasma membrane, the SWELL1-/LRRC8 channel complex activates in response to increases in adipocyte volume in the context of obesity. SWELL1 is required for insulin-PI3K-AKT2 signalling to regulate adipocyte growth and systemic glycaemia (Gunasekar et al. 2019).
The Mg2+ transporter, MgtE. The crystal structure of the N-terminal hydrophilic domain has been determined to 2.3 Å resolution (Hattori et al., 2007) (>50% identical to 9.A.19.1.1), while the C-terminal transmembrane domain has been determined at 2.2 Å resolution (Takeda et al. 2014). The structure reveals a homoldimer with the channel at the interface of the two subunits. There's a plug at the cytoplasmic face. It can bind Mg2+, Mn2+ and Ca2+.
The sterol (dexamethasone, aldosterone) and low NaCl diet-inducible FXYD domain-containing ion transport regulator 4 precursor (Channel inducing factor, CHIF). It is an IsK-like MinK homologue (Attali et al., 1995). It regulates the Na+,K+-ATPase and the KCNQ1 channel protein as well as other ICNQ channels, opening them at all membrane potentials (Jespersen et al. 2006). CHIF as an indirect modulator of several different ion transport mechanisms, consistent with regulation of the Na+-K+-ATPase as the common denominator (Goldschmidt et al. 2004).
Phospholemman, FXYD1 or PLM of 92 aas and 1 TMS. See 1.A.27.1.1 for details for the dog ortholog. Palmitoylation affects the regulation of cardiac electrophysiology, by modifying the sodium-calcium exchanger, phospholemman and the cardiac sodium pump, as well as the voltage-gated sodium channel (Essandoh et al. 2020). Palmitoylation of PLM inhibits the Na+ K+-ATPase while phosphorylation reverses this inhibition. The conserved FXYD motif is found in this protein at residues 29-32 (Cheung et al. 2013).
γ-subunit (proteolipid) of Na+,K+-ATPase, FXYD2. Also functions as a cation-selective channel (Sha et al. 2008).
THe urea transporter channel protein of 337 aas and 11 TMSs in an apparent 6 + 5 TMS arrangement. The 3-d structure (2.3 Å resolution) is available (Levin et al., 2009). Urea binding and flux as well as dimethylurea (DMU) transport have been modeled (Zhang et al. 2017).
Urea transporter 1 or UT-B1 (Solute carrier family 14 member 1; Urea transporter of the erythrocyte) (Bagnasco 2006). A phenylphthalazine compound, PU1424, is a potent UT-B inhibitor, inhibiting human and mouse UT-B-mediated urea transport with IC50 values of 0.02 and 0.69 mumol/L, respectively, and exerted 100% UT-B inhibition at high concentrations (Ran et al. 2016). Another potent inhibitor is the thienopyridine, CB-20 (5-ethyl-2-methyl-3-amino-6-methylthieno[2,3-b]pyridine-2,5-dicarboxylate) (Li et al. 2019). UT-B catalyzes transmembrane water transport which can be ued as a reporter system (Schilling et al. 2016). Knocking out both UT1 and UT2 increases urine output 3.5-fold and lowers urine osmolarity (Jiang et al. 2016). The double knockout also lowered blood pressure and promoted maturation of the male reproductive system. Thus, functional deficiency of all UTs causes a urea-selective urine-concentrating defect with few physiological abnormalities in extrarenal organs (Jiang et al. 2016). UT-B may be related to the occurrence of melanoma and play a role in tumor development (Liu et al. 2018).
Proton-gated urea transport channel (UreI) (pH-sensitive). Allows the transmembrane flow of urea, hydroxyurea and (at a low rate) water. KB for urea is ~150mM (Sachs et al., 2006; Scott et al., 2010). Transport kinetics and selectivity have been defined (Gray et al., 2011). The 3-d structure reveals a hexameric protein with a channel included within the twisted 6 TMS bundle of each protomer. It displays a two helix hairpin structure repeated three times around the central axis of the channel (Strugatsky et al. 2012).
Ryanodine receptor Ca2+ release channel, RyR2. Causes Ca2+ release from the E.R. and consequent cardiac arrhythmia (Chelu and Wehrens, 2007). Associates with FKBP12.6, but phosphorylation by protein kinase A on serine-2030 causes dissociation (Jones et al., 2008). An interaction site for FKBP12.6 may be present at the RyR2 C terminus, proximal to the channel pore, a sterically appropriate location that would enable this protein to play a role in the modulation of this channel (Zissimopoulos and Lai 2005). Enhanced binding of calmodulin corrects arrhythmogenic channel disorder in myocytes (Fukuda et al. 2014). RyR2s can open spontaneously, giving rise to spatially-confined Ca2+ release events known as "sparks." They are organized in a lattice to form clusters in the junctional sarcoplasmic reticulum membrane. The spatial arrangement of RyR2s within clusters strongly influences the frequency of Ca2+ sparks (Walker et al. 2015). Structures of RyR2 from porcine heart in both the open and closed states at near atomic resolutions have been determined using single-particle electron cryomicroscopy (Peng et al. 2016). Structural comparisons revealed breathing motions of the overall cytoplasmic region resulting from the interdomain movements of amino-terminal domains (NTDs), Helical domains, and Handle domains, whereas little intradomain shifts are observed in these armadillo repeat-containing domains. Outward rotations of the central domains, which integrate the conformational changes of the cytoplasmic region, lead to the dilation of the cytoplasmic gate through coupled motions. These observations provide insight into the gating mechanism of RyRs (Peng et al. 2016). RyR2 is subject ot regulation by cytoplasmic Zn2+ (>1nM), and this regulation plays a key role in diastolic SR Ca2+ leakage in cardiac muscle (Reilly-O'Donnell et al. 2017). Ryanodine receptor-mediated SR Ca2+ efflux is apparently balanced by concomitant counterion currents across the SR membrane (Sanchez et al. 2018). Electrical polarity-dependent gating and a unique subconductance of RyR2 is induced by S-adenosyl methionine via the ATP binding site. Thus, SAM may alter the conformation of the RyR2 ion conduction pathway (Kampfer and Balog 2021).
The Ryanodine receptor Ca2+/K+ release tetrameric channel, RyR1, present in skeletal muscle, is 5038 aas long. Mutants are linked to core myopathies such as Central Core Disease, Malignant Hyperthermia and Multiple Minicore Disease) (Xu et al., 2008). RyR1 interacts with CLIC2 to modulate its channel activity (Meng et al., 2009). A model pf RyR1 has been constructed encompassing the six transmembrane helices to calculate the RyR1 pore region conductance, to analyze its structural stability, and to hypothesize the mechanism of the Ile4897 CCD-associated mutation. The calculated conductance of the wild-type RyR1 suggests that the pore structure can sustain ion currents measured in single-channel experiments. Shirvanyants et al. 2014 observed a stable pore structure with multiple cations occupying the selectivity filter and cytosolic vestibule, but not the inner chamber. Stability of the selectivity filter depends on interactions between the I4897 residue and several hydrophobic residues of the neighboring subunit. Loss of these interactions in the case of the polar substitution, I4897T, results in destabilization of the selectivity filter, a possible cause of the CCD-specific reduced Ca2+ conductance. A 4.8 Å structure of the rabbit orthologue in the closed state of this 2.3 MDa tetramer (3757 aas/protomer) reveals the pore, the VIC superfamily fold and a potential mechanism of Ca2+ gating (Zalk et al. 2015). A cryo-electron microscopy analysis revealed the structure at 6.1 Å resolution (Efremov et al. 2015). The transmembrane domain represents a chimaera of voltage-gated sodium and pH-activated ion channels. They identified the calcium-binding EF-hand domain and showed that it functions as a conformational switch, allosterically gating the channel. Malignant hyperthermia-associated RyR1 mutations in the S2-S3 loop confer RyR2-type Ca2+- and Mg2+-dependent channel regulation (Gomez et al. 2016). Structural analyses have elucidated a novel channel-gating mechanism and a novel ion selectivity mechanism for RyR1 (Wei et al. 2016). Samsó 2016 reviewed structural determinations of RyR by cryoEM and analyzed the first near-atomic structures, revealing a complex orchestration of domains controlling channel function. The structural basis for gating and activation have been determined (des Georges et al. 2016). Junctin and triadin bind to different sites on RyR1; triadin plays an important role in ensuring rapid Ca2+ release during excitation-contraction coupling in skeletal muscle. RyR1 structure/functioin has been reviewed (Zalk and Marks 2017). Possibly, luminal Ca2+ activates RyR1 by accessing a cytosolic Ca2+ binding site in the open channel as the Ca2+ ions pass through the pore (Xu et al. 2017). The 3-d structures of the native protein in membranes has been determined (Chen and Kudryashev 2020) (see family description). The most common cause of nondystrophic congenital myopathies is mutations in RYR1 (Sorrentino 2022).
Ryanodine-sensitive Ca2+ release channel RyR1 of 5117 aas and 6 TMSs. Diamide insecticides, such as flubendiamide and chlorantraniliprole, selectively activate insect ryanodine receptors of Lepidoptera and Coleoptera pests (Samurkas et al. 2020). They are particularly active against lepidopteran pests of cruciferous vegetable crops, including the diamondback moth, Plutella xylostella. Resistance results from mutation(s) in the ryanodine receptors' transmembrane domain at the C-termini of these proteins (Troczka et al. 2017). Other diamide insecticides, including phthalic and anthranilic diamides, target insect ryanodine receptors (RyRs) and cause misregulation of calcium signaling in insect muscles and neurons. Homology modeling and docking studies with the diamondback moth ryanodine receptor revealed the mechanisms for channel activation, insecticide binding, and resistance (Lin et al. 2019).
Inositol 1,4,5-trisphosphate receptor type 1 (IP3 receptor isoform 1) (IP3R 1; InsP3R1; Itpr1) (Type 1 inositol 1,4,5-trisphosphate receptor) (Type 1 InsP3 receptor) of 2758 aas and 6 TMSs near the C-terminus. An intronic variant in ITPR1 causes Gillespie syndrome, characterized by bilateral symmetric partial aplasia of the iris presenting as a fixed and large pupil, cerebellar hypoplasia with ataxia, congenital hypotonia, and varying levels of intellectual disability (Keehan et al. 2021). The cryoEM structure has been determined (Baker et al. 2021). Binding of the erlin1/2 complex (TC# 8.A.195) to the third intralumenal loop of IP3R1 triggers its ubiquitin-proteasomal degradation (Gao et al. 2022).
The flagellar motor (smf-dependent) (PomAB; MotXY) (Okabe et al., 2005). PomB interacts with the third TMS of PomA in the Na+-driven polar flagellum (Yakushi et al. 2004). Sodium-powered stators of the flagellar motor can generate torque in the presence of the sodium channel blocker, phenamil, with mutations near the peptidoglycan-binding region of PomB (Ishida et al. 2019). FliL associates with the flagellar stator in the sodium-driven Vibrio motor (Lin et al. 2018). When the ion channel is closed, PomA and PomB interact strongly. When the ion channel opens, PomA interacts less tightly with PomB. The plug and loop between TMSs 1 and 2 regulate activation of the stator, which depends on the binding of sodium ion to the D24 residue of PomB (Nishikino et al. 2019). The PomA helices parallel to the inner membrane play iroles in the hoop-like function in securing the stability of the stator complex and the ion conduction pathway (Nishikino et al. 2022).
The flagellar motor (pmf-dependent) (MotAB) (Ito et al., 2004)
The TonB energy-transducing system. ExbB/D (the putative H+ channel) are listed here; TonB is listed under TC# 2.C.1.1.1. Deletion of the cytoplasmic loop gives rise to immediate growth arrest (Bulathsinghala et al. 2013). The rotational surveillance and energy transfer (ROSET) model of TonB action postulates a mechanism for the transfer of energy from the IM to the OM, triggering iron uptake and concentration in the periplasm (Klebba 2016).
Annexin A1 (McNeil et al., 2006)
Annexin 2 or Annexin A2 (ANXA2) of 339 aas. Forms a tetrameric complex with the S100A10 protein and binds the C-terminus of the AHNAK protein via the N-terminus of annexin 2 (De Seranno et al., 2006). Direct translocation of Annexin 2 to the cell surface occurs by pore-formation. External annexin A2 acts as a plasminogen receptor, able to stimulate fibrinolysis and cell migration (Pompa et al. 2017).
Annexxin of 369 aas. Schistosomiasis, a major parasitic disease of humans, is second only to malaria in its global impact. The disease is caused by digenean trematodes that infest the vasculature of their human hosts. These flukes are limited externally by a body wall composed of a syncytial epithelium, the apical surface membrane, a parasitism-adapted dual membrane complex. Annexins are important for the stability of this apical membrane system. Leow et al. 2013 presented the first structural and immunobiochemical characterization of an annexin from Schistosoma mansoni. The crystal structures of annexin B22 (4MDV and 4MDU) in the apo and Ca2+ bound forms confirmed the presence of the previously predicted α-helical segment in the II/III linker and revealed a covalently linked head-to-head dimer. The dimeric arrangement revealed a non-canonical membrane binding site and a probable binding groove opposite the binding site. Annexin B22 expression correlated with life stages of the parasite that possess the syncytial tegument layer, and ultrastructural localization by immuno-electron microscopy confirmed the occurrence of annexins in the tegument of S. mansoni.
Annexin A5 of 320 aas. Annexin A5 (ANXA5), a Ca2+ and phospholipid binding protein, interacts with the N-terminal leucine-rich repeats of polycystin-1 (TC# 1.A.5.1.2). This interaction is direct and specific, and involves a conserved sequence of the ANXA5 N-terminal domain (Markoff et al. 2007).
Annexin D1 (Anx23; Ann1; AnnAT1; AtoxY; Oxy5) of 317 aas. It has a peroxidase activity and may act to
counteract oxidative stress (Gorecka et al. 2005). May also mediate regulated, targeted
secretion of Golgi-derived vesicles during seedling development (Clark et al. 2005). Can transport Ca2+ (Demidchik et al. 2018).
Annexin XII, Annexin 12, Annexin-12, AnnexinB12 of 316 aas. It is a calcium- and phospholipid-binding protein, phosphorylated by PKC. The x-ray structure of the heximer has been solved (Luecke et al. 1995). A reversible transition occurs between the surface trimer and membrane-inserted monomer (Ladokhin and Haigler 2005).
Heat shock protein-70 homologue, DnaK. Although DnaK homologues are ubiquitous, a transport function in eukaryotes, but not in prokaryotes has been demonstrated.
|1.A.33.1.3||Heat shock protein 70(1B)||
Glucose regulated protein, GRP78 of 654 aas. GRP78, a member of the ER stress protein family. It can relocate to the surface of cancer cells, playing a role in promoting cell proliferation and metastasis. GRP78 consists of two major functional domains: the ATPase and protein/peptide-binding domains. The protein/peptide-binding domain of cell-surface GRP78 has served as a novel functional receptor for delivering cytotoxic agents (e.g., a apoptosis-inducing peptide or taxol) across the cell membrane. The ATPase domain of GRP78 (GRP78ATPase) has potential as a transmembrane delivery system of cytotoxic agents including nucleotides (e.g., ATP-based nucleotide triphosphate analogs) (Hughes et al. 2016). May also play a role in facilitating the assembly of multimeric protein complexes inside the endoplasmic reticulum (Evensen et al. 2013). It is involved in the correct folding of proteins and degradation of misfolded proteins via its interaction with DNAJC10, probably to facilitate the release of DNAJC10 from its substrate (Evensen et al. 2013).
The Bacillus SpoIIQ/SpoIIIAH transcompartment channel interconnects the forespore and the mother cell. The activity of sigmaG requires this channel apparatus through which the adjacent mother cell provides substrates that generally support gene expression in the forespore. Flanagan et al. 2016 reported that SpoIIQ is bifunctional, specifically maximizing sigmaG activity as part of a regulatory circuit that prevents sigmaG from activating transcription of the gene encoding its own inhibitor, the anti-sigma factor CsfB.
Divalent cation (Mg2+, Co2+ and Ni2+) transport system, CorA. Helical tilting and rotation in TM1 generates an iris-like motion that increases the diameter of the permeation pathway, triggering ion conduction, thus defining the gating mechanism (Dalmas et al. 2014).
Divalent metal ion (Mg2+, Ca2+, Ni2+, etc.) transporter of 317 aas and 3 TMSs. The cryo-EM structure shows a pentameric channel with an asymmetric domain structure and featuring differential separations between the trans-segments, probably reflecting mechanical coupling of the cytoplasmic domain to the transmembrane domain and suggesting a gating mechanism (Cleverley et al. 2015).
Magnesium transport protein, CorA. The structure at 2.7 Å resolution is known. The CorA monomer has a C-terminal membrane domain containing two transmembrane segments and a large N-terminal cytoplasmic soluble domain. In the membrane, CorA forms a homopentamer shaped like a funnel which binds fully hydrated Mg2+ in the periplasm (Maguire 2006). A ring of positive charges are external to the ion-conduction pathway at the cytosolic membrane interface, and highly negatively charged helices in the cytosolic domain appear to interact with the ring of positive charge to facilitate Mg2+ entry. Mg2+ ions are present in the cytosolic domain that are well placed to control the interaction of the ring of positive charge and the negatively charged helices, and thus, control Mg2+ entry (Maguire 2006). Gating is achieved by helical rotation upon the binding of a metal ion substrate to the regulatory binding sites. The preference for Co2+ over Mg2+ has been reported to be determined by the presence of threonine side chains in the channel (Nordin et al. 2013), but more recently, Kowatz and Maguire 2018 showed that Co2+ is not a substrate, and that the intersubunit bound Mg2+ is not required for function and does not control the open versus closed states.
Zn2+/Cd2+ efflux system, ZntB. Mg2+ is not transported. Wan et al. 2011 reported crystal structures in dimeric and physiologically relevant homopentameric forms at 2.3 Å and 3.1 Å resolutions, respectively. The funnel-like structure is similar to that of the homologous Thermotoga maritima CorA Mg2+ channel and a Vibrio parahaemolyticus ZntB (VpZntB). However, the central α7 helix forming the inner wall of the StZntB funnel is oriented perpendicular to the membrane instead of the marked angle seen in CorA or VpZntB. Consequently, the StZntB funnel pore is cylindrical, not tapered, which may represent an "open" form of the ZntB soluble domain. There are three Zn2+ binding sites in the full-length ZntB, two of which could be involved in Zn2+ transport.
The ZntB Zn2+/Cd2+ transporter. The 1.9Å structure of the N-terminal cytoplasmic domain of ZntB has been solved (Tan et al., 2009).
Mitochondrial inner membrane Mg2+ channel protein, Mrs2 (Schindl et al., 2007). Mutational analyses have been carried out, suggesting that internal Mg2+ affects intron splicing (Weghuber et al. 2006). MRS2 is involved in mitochondrial Mg2+ homeostasis (Schäffers et al. 2018). The G-M-N motif determines the ion selectivity, likely together with the negatively charged loop at the entrance of the channel, thereby forming the Mrs2p selectivity filter (Sponder et al. 2013).
The CD20 (Cluster of differentiation-20) protein (297 aas and 4 TMSs) is a putative cation channel (B-lymphocyte CD20 antigen) or an indirect regulator of calcium release. The 3-d structure has been determined (Rougé et al. 2020). It is targeted by monoclonal antibodies for the treatment of malignancies and autoimmune disorders. Rituximab (RTX) activates complement to kill B cells. Rougé et al. 2020 obtained a structure of CD20 in complex with RTX, revealing a compact double-barrel dimer bound by two RTX antigen-binding fragments (Fabs), each of which engages a composite epitope. RTX cross-links CD20 into circular assemblies and lead to a structural model for complement recruitment.
Transient receptor potential (TRP) protein. Assembles in vivo as a homomultimeric channel, not as a heteromeric channel with TrpL as the subunit (Katz et al. 2013).
TRPC3 store-operated non-selective cation channel (activated by thapsigargin and 2 acyl glycerol; forms a heteromeric channel with TrpC1, TC #1.A.4.1.3) (Liu et al., 2005). A structural model of the TRPC3 permeation pathway based on a sodium channel (TC# 1.A.1.14.5) with a localized selectivity filter and an occluding gate with evidence for allosteric coupling between the gate and the selectivity filter has been proposed (Ko et al. 2009; Lichtenegger et al. 2013). The channel may have a large internal chamber surrounded by signal sensing antennas (Mio et al. 2007). TRPC channels are involved in store-operated calcium entry and calcium homeostasis, and they are implicated in human diseases such as neurodegenerative disease, cardiac hypertrophy, and spinocerebellar ataxia (Fan et al. 2018). The structure in a lipid-occupied, closed state has been solved at 3.3 Å resolution. TRPC3 has four elbow-like membrane reentrant helices prior to the first transmembrane helix. The TRP helix is perpendicular to, and thus disengaged from, the pore-lining S6, suggesting a different gating mechanism from other TRP subfamily channels. The third transmembrane helix S3 is remarkably long, shaping a unique transmembrane domain, and constituting an extracellular domain that may serve as a sensor of external stimuli. Fan et al. 2018 identified two lipid binding sites, one being sandwiched between the pre-S1 elbow and the S4-S5 linker, and the other being close to the ion-conducting pore, where the conserved LWF motif of the TRPC family is located. The cytoplasmic domain allosterically modulates channel gating (Sierra-Valdez et al. 2018). This channel may be present in mitochondria (Parrasia et al. 2019). TRPC3 and TRPC6 channels are calcium-permeable non-selective cation channels. The gain-of-function (GOF) mutations of TRPC6 lead to familial focal segmental glomerulosclerosis (FSGS) in humans. Guo et al. 2022 reported the cryo-EM structures of human TRPC3 in both high-calcium and low-calcium conditions. They identified both inhibitory and activating calcium-binding sites in TRPC3 that couple intracellular calcium concentrations to the basal channel activity. These calcium sensors are structurally and functionally conserved in TRPC6. The GOF mutations of TRPC6 activate the channel by allosterically abolishing the inhibitory effects of intracellular calcium. Structures of human TRPC6 in complex with two chemically distinct inhibitors bound at different ligand-binding pockets revealed different conformations of the transmembrane domain (Guo et al. 2022). TRPC3 is primarily gated by lipids, and its surface expression is dependent on cholesterol (Clarke et al. 2022).
Transient receptor potential canonical-6, TRPC6, a non-selective cation channel that is directly activated by diacylglycerol (DAG (Szabó et al. 2015). Mutation causes a particularly aggressive form of familial focal segmental glomerulosclerosis (Winn et al., 2005; Mukerji et al., 2007). Tang et al. 2018 presented the structure of the human TRPC6 homotetramer in complex with a high-affinity inhibitor, BTDM, solved by single-particle cryo-electron microscopy to 3.8 Å resolution. The structure shows a two-layer architecture in which the bell-shaped cytosolic layer holds the transmembrane layer. Extensive inter-subunit interactions of cytosolic domains, including the N-terminal ankyrin repeats and the C-terminal coiled-coil, contribute to the tetramer assembly. The high-affinity inhibitor BTDM wedges between the S5-S6 pore domain and voltage sensor-like domain to inhibit channel opening (Tang et al. 2018). TRPC6 may regulate the glomerular filtration rate by modulating mesangial cell contractile function through multiple Ca2+ signaling pathways (Li et al. 2017). Several proteins including podocin (8.A.21.1.2), nephrin (8.A.23.1.33), CD2AP (8.A.34.1.5) and TRPC6 form a macromolecular assembly that constitutes the slit-diaphragm in podocytes that resembles tight junctions (Mulukala et al. 2020). Two small molecules, GSK1702934A and M085, directly activate TRPC6 via a mechanism involving stimulation of the extracellular cavity formed by the pore helix and transmembrane helix S6 (Yang et al. 2021). Na+/Ca2+ exchanger, NCX1, and canonical transient receptor potential channel 6 (TRPC6) are recruited by STIM1 to mediate Store-Operated Calcium Entry in primary cortical neurons (Tedeschi et al. 2022). Guo et al. 2022 reported the cryo-EM structures of human TRPC3 in both high-calcium and low-calcium conditions. They identified both inhibitory and activating calcium-binding sites in TRPC3 that couple intracellular calcium concentrations to the basal channel activity. These calcium sensors are structurally and functionally conserved in TRPC6. The GOF mutations of TRPC6 activate the channel by allosterically abolishing the inhibitory effects of intracellular calcium. Structures of human TRPC6 in complex with two chemically distinct inhibitors bound at different ligand-binding pockets revealed different conformations of the transmembrane domain (Guo et al. 2022).
Vanilloid receptor subtype 1 (VR1 or TRPV1) (noxious, heat-sensitive [opens with increasing temperatures; e.g., >42°C]; also sensitive to acidic pH and voltage and inflamation; serves as the receptor for the alkaloid irritant, capsaicin, for resiniferatoxin and for endo-cannabinoids (Murillo-Rodriguez et al. 2017). Resiniferatoxin binds to the capsaicin receptor (TRPV1) near the extracellular side of the S4 transmembrane domain (Chou et al. 2004). It is regulated by bradykinin and prostaglandin E2) (contains a C-terminal region, adjacent to the channel gate, that determines the coupling of stimulus sensing and channel opening) (Garcia-Sanz et al., 2007; Matta and Ahern, 2007). It is activated and sensitized by local anesthetics in sensory neurons (Leffler et al., 2008). A bivalent tarantula toxin activates the capsaicin receptor (TRPV1) by targeting the outer pore domain (Bohlen et al., 2010). Single-channel properties of TRPV1 are modulated by phosphorylation (Studer and McNaughton, 2010). TRPV1 mediates an itch associated response (Kim et al., 2011). The thermosensitive TRP channel pore turret is part of the temperature activation apparatus (Yang et al., 2010). Modular thermal sensors in temperature-gated transient receptor potential (TRP) channels have been identified (Yao et al., 2011). TRPV1 opening is associated with major structural rearrangements in the outer pore, including the pore helix and selectivity filter, as well as pronounced dilation of a hydrophobic constriction at the lower gate, suggesting a dual gating mechanism (Cao et al. 2013). Allosteric coupling between upper and lower gates may account for modulation exhibited by TRPV1 and other TRP channels (Liao et al. 2013). TRPV1 regulates longevity and metabolism by neuropeptides in mice (Riera et al. 2014). The pore of TRPV1 contains the structural elements sufficient for activation by noxious heat (Zhang et al. 2017). In bull sperm, TRPV1 functions in the regulation of motility and the acrosome reaction (Kumar et al. 2019). The dynamics of water in the transmembrane pore of TRPV1 have been studied (Trofimov et al. 2019). TRPV1 - 6 channel subunits do not combine arbitrarily. With the exception of TRPV5 and TRPV6, TRPV channel subunits preferentially assemble into homomeric complexes (Hellwig et al. 2005). TrpV1-gated ion channels have been used as sensors for imaging applications (Zhu et al. 2021). Capsaicin and protons differently modulate the activation kinetics of the mouse TrpV1 channel induced by depolarization (Takahashi et al. 2021). The impact of TRPV1 on cancer pathogenesis and therapy has been reviewed (Li et al. 2021). TRPV1 may be an analgesic target for patients experiencing pain after oral irradiation (Lai et al. 2021).
TRPV5 epithelial Ca2+ channel (ECaC1) (forms homo- and heterotetrameric channels with TRPV6; requires the S100A10-annexin 2 complex for routing to the plasma membrane) (Hoenderop et al., 2003; van de Graaf et al., 2003). The kidney maintains whole body calcium homoeostasis due to the reabsorption of Ca2+ filtered by the kidney glomerulus. TRPV5 regulates urinary Ca2+ excretion by mediating active Ca2+ reabsorption in the distal convoluted tubule of the kidney. The histidine kinase, nucleoside diphosphate kinase B (NDPK-B), activates TRPV5 channel activity and Ca2+ flux, and this activation requires histidine 711 in the carboxy terminal tail of TRPV5. In addition, the histidine phosphatase, protein histidine phosphatase 1 (PHPT1), inhibits NDPK-B activated TRPV5 (Cai et al. 2014). TRPV5 also transports cadmium (Cd2+). The L530R mutation is associated with recurrent kidney stones (Wang et al. 2017). May be stabilized by Mucin-1 (Muc1; P15941) (Al-Bataineh et al. 2017). TRPV5 inhibitors have been identified (Hughes et al. 2019).
TRPV6 epithelial Ca2+ channel (ECaC2) (forms homo- and heterotetrameric channels with TRPV5; requires the S100A10-annexin 2 complex for routing to the plasma membrane) (Hoenderop et al., 2003; van de Graaf et al., 2003). Epithelial TrpV6, but not TrpV5, is inhibited by the regulator of G-protein signaling 2 (RGS2; Q9JHX0; 211 aas) by direct binding (Schoeber et al., 2006). Calmodulin (CaM) positively affects TRPV6 activity upon Ca2+ binding to EF-hands 3 and 4, located in the high Ca2+ affinity CaM C-terminus (Lambers et al. 2004). Cyclophilin B is an accessory activating protein (Stumpf et al., 2008). The crystal structure of rat TRPV6 at 3.25 A resolution revealed shared and unique features compared with other TRP channels (Saotome et al. 2016). Intracellular domains engage in extensive interactions to form an intracellular 'skirt' involved in allosteric modulation. In the K+ channel-like transmembrane domain, Ca2+ selectivity is determined by direct coordination of Ca2+ by a ring of aspartate side chains in the selectivity filter (Saotome et al. 2016). Replacing Gly-516 within the cytosolic S4-S5 linker (conserved in all TRP channel proteins) by ser forces the channels into an open conformation, thereby enhancing constitutive Ca2+ entry and preventing inactivation (Hofmann et al. 2016). Tetrameric ion channels have either swapped or non-swapped arrangements of the S1-S4 and pore domains. Singh et al. 2017 showed that mutations in the transmembrane domain can result in conversion from a domain-swapped to the non-swapped fold. These results raise the possibility that a single ion channel subtype can fold into either arrangement in vivo, affecting its function in normal or disease states. Cryo-EM structures of human TRPV6 in the open and closed states shows that the channel selectivity filter adopts similar conformations in both states, consistent with its explicit role in ion permeation. The iris-like channel opening is accompanied by an alpha-to-pi-helical transition in the pore-lining transmembrane helix S6 at an alanine hinge just below the selectivity filter. As a result of this transition, the S6 helices bend and rotate, exposing different residues to the ion channel pore in the open and closed states (McGoldrick et al. 2017). TRPV6 is an epithelial Ca2+-selective channel associated with transient neonatal hyperparathyroidism (TNHP), an autosomal-recessive disease caused by TRPV6 mutations that affect maternal-fetal calcium transport (Suzuki et al. 2018). TRPV6 mediates calcium uptake in epithelia, and its expression increases in numerous types of cancer while inhibitors suppress tumor growth. Singh et al. 2018 presented crystal and cryo-EM structures of human and rat TRPV6 bound to 2-aminoethoxydiphenyl borate (2-APB), a TRPV6 inhibitor and modulator of numerous TRP channels. 2-APB binds to TRPV6 in a pocket formed by the cytoplasmic half of the S1-S4 transmembrane helix bundle. 2-APB induces TRPV6 channel closure by modulating protein-lipid interactions. The 2-APB binding site may be present in other members of vanilloid subfamily TRP channels. The crystal structure has been determined (see 30299652 and Yelshanskaya et al. 2020). Novel mutations in TRPV6 give rise to the spectrum of transient neonatal hyperparathyroidism (Suzuki et al. 2020). TRPV6) plays roles in calcium absorption in epithelia and bone and is involved in human diseases including vitamin-D deficiency, osteoporosis, and cancer. Cai et al. 2020 showed that the TRPV6 intramolecular S4-S5 linker to the C-terminal TRP helix (L/C) and N-terminal pre-S1 helix to TRP helix (N/C) interactions, mediated by Arg470:Trp593 and Trp321:Ile597 bonding, respectively, are autoinhibitory and are required for maintaining TRPV6 at basal states. Disruption of either interaction by mutations or blocking peptides activates TRPV6. The N/C interaction depends on the L/C interaction but not inversely. Three cationic residues in S5 or the C terminus are involved in binding PIP2 to suppress both interactions, thereby activating TRPV6 (Cai et al. 2020).
TrpV1 of 839 aas and ~ 6 TMSs. Molecular determinants of vanilloid sensitivity have been examined (Gavva et al. 2004). Ligand-activated non-selective calcium permeant cation channel involved in detection of noxious chemical and thermal stimuli. TRPV1 channels are present in odontoblasts, suggesting that odontoblasts may directly respond to noxious stimuli such as a thermal-heat stimulus (Okumura et al. 2005). It may mediate proton influx and be involved in intracellular acidosis in nociceptive neurons. It is also involved in mediating inflammatory pain and hyperalgesia (Benemei et al. 2015). The 3.4 Å resolution structure shows that the overall fold is the same as for voltage-gated ion channels (TC# 1.A.1) (Liao et al. 2013). Capsaicin-induced apoptosis in glioma cells is mediated by TRPV1 (Amantini et al. 2007). Capsaicin binds to a pocket formed by the channel's TMSs, where it takes a ""tail-up, head-down"" configuration. Binding is mediated by both hydrogen bonds and van der Waals interactions. Upon binding, capsaicin stabilizes the open state of TRPV1 by ""pull-and-contact"" with the S4-S5 linker (Yang and Zheng 2017). Several protein kinases, including PKD1 (protein kinase D1), Cdk5 (cyclin-dependent kinase 5) and LIMK (LIM- motif containing kinase) regulate TRPV1 and inflammatory thermal hyperalgesia (Zhang and Wang 2017). TrpV1 and TrpA1 are inflammatory mediators causing cutaneous chronic itch in several diseases (Xie and Li 2018). The locations and characteristics of volatile general anesthetic binding sites in the transmembrane domain of TRPV1 have been examined (Jorgensen and Domene 2018). The TRPV1 ion channel is a neuronal sensor that plays an important role in nociception and neuropathic as well as inflammatory pain. In clinical trials, hyperthermia and thermo-hypoaesthesia are major side effects of TRPV1 antagonists (Damann et al. 2020). The TRPV1 ion channel is a polymodal sensor integrating stimuli from molecular modulators with temperature, pH and transmembrane potential. Temperature-dependent gating may constitute the molecular basis for its role in heat sensation and body temperature regulation. Damann et al. 2020 characterized the prototypic small molecule TRPV1 inhibitors GRT12360V and GRTE16523. The oxidizing reagent copper-o-phenanthroline is an open channel blocker of TRPV1 (Tousova et al. 2004). Lack of TRPV1 aggravates obesity-associated hypertension through the disturbance of mitochondrial Ca2+ homeostasis in brown adipose tissue (Li et al. 2022).
Vitamin D-responsive, apical, epithelial Ca2+ channel, ECaC
Intestinal endocyte Ca2+ (Sr2+; Ba2+) entry channel, CaT1. Excision of the Trpv6 gene leads to severe defects in epididymal Ca2+ absorption and male fertility as does the single D541A pore mutation (Weissgerber et al., 2012).
The noxious heat (>52°C)-sensitive vanilloid-like receptor cation selective channel, TRPV2. Ca2+-dependent desensitization of TRPV2 channels is mediated by hydrolysis of phosphatidylinositol 4,5-bisphosphate (Mercado et al., 2010). Deleting the first N-terminal 74 residues preceding the ankyrin repeat domain (ARD) shows a key role for this region in targeting the protein to the membrane. Co-translational insertion of the membrane-embedded region occurs with the TM1-TM4 and TM5-TM6 regions assembling as independent folding domains. ARD is not required for TM domain insertion into the membrane (Doñate-Macian et al. 2015). The TRPV2 structure has been solved at 4 Å resolution by cryoEM (Zubcevic et al. 2016). Formation of a physical complex between mouse TRPV2 (GRC) and the mouse RGA protein promotes cell surface expression of TRPV2 (Stokes et al. 2005). The role of Ca2+ infllux via TRPV1 in cell death and survival related to cancer has been evaluated (Zhai et al. 2020). A helix-turn-helix motif for high temperature dependence of TRPV2 has been identified (Liu and Qin 2021).
The temperature (heat; >39°C)-sensitive, capsaicin-insensitive receptor cation-selective channel, TRPV3 or TRL3 (may form heterooligomers with VR1 (TRPV1; TC #1.A.4.2.1)). Incensole acetate, an incense component, elicits psychoactivity by activating TRPV3 channels in the brain (Moussaieff et al., 2008). TRPV3 is activated by synthetic small-molecule chemicals and natural compounds from plants as well as warm temperatures. Its function is regulated by a variety of physiological factors including extracellular divalent cations and acidic pH, intracellular ATP, membrane voltage, and arachidonic acid. It shows a broad expression pattern in both neuronal and non-neuronal tissues including epidermal keratinocytes, epithelial cells in the gut, endothelial cells in blood vessels, and neurons in dorsal root ganglia and the CNS. TRPV3 null mice exhibit abnormal hair morphogenesis and compromised skin barrier function, and it may play critical roles in inflammatory skin disorders, itch, and pain sensation (Luo and Hu 2014). TRPV3 gating involves large rearrangements at the cytoplasmic inter-protomer interface, and this motion triggers coupling between cytoplasmic and transmembrane domains, priming the channel for opening (Zubcevic et al. 2019). Mutations in TRPV3 cause painful focal plantar keratoderma (Peters et al. 2020). TRPV3 is a temperature-sensitive, nonselective cation channel expressed prominently in skin keratinocytes that plays important roles in hair morphogenesis and maintenance of epidermal barrier function. Mechanisms of proton inhibition and sensitization have been discussed (Wang et al. 2021). Mechanisms of proton inhibition and sensitization of TRPV3 have been considered (Wang et al. 2021). TRPV3 is predominantly expressed in skin keratinocytes and has been implicated in cutaneous sensation and associated with numerous skin pathologies and cancers. TRPV3 is inhibited by the natural coumarin derivative osthole, an active ingredient of Cnidium monnieri, which has been used in traditional Chinese medicine for the treatment of various human diseases. Neuberger et al. 2021 presented cryo-EM structures of TRPV3 in complex with osthole, revealing two types of osthole binding sites in the transmembrane region of TRPV3 that coincide with the binding sites of agonist 2-APB. Osthole binding converts the channel pore into a previously unidentified conformation with a widely open selectivity filter and closed intracellular gate. The structures provide insight into competitive inhibition of TRPV3 by osthole (Neuberger et al. 2021). Scutellarein attenuates atopic dermatitis by selectively inhibiting TRP Vanilloid 3 (Wang et al. 2022).
TrpM4 of 1213 aas and 6 TMSs. Calcium-activated non selective cation channel that mediates membrane depolarization. While it is activated by increases in intracellular Ca2+, it is impermeable to it. It does mediate transport of monovalent cations (Na+ > K+ > Cs+ > Li+), leading to depolarize the membrane. It thereby plays a central role in the function of cardiomyocytes, neurons from entorhinal cortex, dorsal root and vomeronasal neurons, endocrine pancreas cells, kidney epithelial cells, cochlea hair cells etc. It also participates in T-cell activation by modulating Ca2+ oscillations after T lymphocyte activation (Demion et al. 2007). The structure has been determined by cryo EM both with and without ATP (Guo et al. 2017). It consists of multiple transmembrane and cytosolic domains, which assemble into a three-tiered architecture. The N-terminal nucleotide-binding domain and the C-terminal coiled-coil participate in the tetrameric assembly of the channel; ATP binds at the nucleotide-binding domain to inhibit channel activity. TRPM4 has an exceptionally wide filter although it is only permeable to monovalent cations; filter residue Gln973 is essential in defining monovalent selectivity. The S1-S4 domain and the post-S6 TRP domain form the central gating apparatus that probably houses the Ca2+- and PtdIns(4,5)P2-binding sites (Guo et al. 2017). TRPM4 currents are activated by micromolar concentrations of cytoplasmic Ca2+and progressively desensitized. Zhang et al. 2005 showed that desensitization can be explained by a loss of phosphatidylinositol 4,5-bisphosphate (PI(4,5)P(2)) from the channels. TrpM4 interacts directly with glutamate N-methyl-D-aspartate receptor channels (NMDARs) to promote excitotoxicity. Small-molecule interface inhibitors prevent NMDAR-TRPM4 physical coupling and eliminate excitotoxicity. They are therefore neuroprotectants (Yan et al. 2020).
TRPM8 of the collared flycatcher of 1103 aas. It is 83% identical to the human ortholog. Its structure has been determined to ~4.1 Å resolution by cryo EM (Yin et al. 2018). The structure reveals a three-layered architecture. The amino-terminal domain with a fold distinct among known TRP structures, together with the carboxyl-terminal region, forms a large two-layered cytosolic ring that extensively interacts with the transmembrane channel layer. The structure suggests that the menthol-binding site is located within the voltage-sensor-like domain and thus provides a structural glimpse of the design principle of the molecular transducer for cold and menthol sensation (Yin et al. 2018).
Intracellular Ca2+-activated nonselective monovalent cation (Na+ and K+) channel (non-permeable to Ca2+), TRPM4b, involved in inherited cardiac arrhythmia syndromes (Amarouch and El Hilaly 2020). It interacts with the TRPC3 channel and suppresses store-operated Ca+ entry (Park et al., 2008). Contributes to the mammalian atrial action potential (Simard et al. 2013). TRPM4 is widely expressed and is associated with a variety of cardiovascular disorders. Autzen et al. 2018 presented two structures of full-length human TRPM4 embedded in lipid nanodiscs at ~3-angstrom resolution, as determined by single-particle cryo-electron microscopy. These structures, with and without calcium bound, reveal the general architecture for this major subfamily of TRP channels and a well-defined calcium-binding site within the intracellular side of the S1-S4 domain. The structures correspond to two distinct closed states. Calcium binding induces conformational changes that likely prime the channel for voltage-dependent opening (Autzen et al. 2018). TRPM4 functions as a limiting factor for antigen evoked calcium rise in connective tissue type mast cells, and concurrent translocation of TRPM4 into the plasma membrane is part of this mechanism (Rixecker et al. 2016). Gain-of-function mutations in the TRPM4 activation gate cause progressive symmetric erythrokeratoderma (Wang et al. 2018).
ADP-ribose/NAD/pyrimidine nucleotide-gated Ca2+ permeable, cation nonselective, long transient receptor potential channel-2, LTRPC2; Melastatin 2; TRPM2 (ATP inhibitable). The 3-D structure resembles a swollen bell shaped structure (Maruyama et al., 2007). It can be converted to an anion-selective channel by introducing a lysyl residue in TMS 6 (Kuhn et al., 2007). It transports Ca2+ and Mg2+ with equal facility (Xia et al., 2008). Four Ca2+ ions activate TRPM2 channels by binding in deep crevices near the pore but intracellularly of the gate (Csanády and Törocsik, 2009). Protons also regulate activity (Starkus et al., 2010). It is present in the plasma membrane and lysosomes, and plays a role in ROS-induced inflammatory processes and cell death. Melastatin is required for innate immunity against Listeria monocytogenes (Knowles et al., 2011). It functions in pathogen-evoked phagocyte activation, postischemic neuronal apoptosis, and glucose-evoked insulin secretion, by linking these cellular responses to oxidative stress (Tóth and Csanády, 2012). Pore collapse upon prolonged stimulation underlies irreversible inactivation (Tóth and Csanády 2012). TRPM2 is preferentially expressed in cells of the myeloid lineage and modulates signaling pathways converging into NF-kB but does not seem to play a major role in myeloid leukemogenesis. Its loss does not augment the cytotoxicity of standard AML chemotherapeutic agents (Haladyna et al. 2016). TrpM2, expressed in hypothalamic neurons in the brain is a thermosensitive, redox-sensitive channel, required for thermoregulation. It regulates body temperature, limiting fever and driving hypothermia (Song et al. 2016). Tseng et al. 2016 suggested a mechanistic link between TRPM2-mediated Ca2+ influx and p47 phox signaling to induce excess ROS production and TXNIP-mediated NLRP3 inflammasome activation under high gllucose in Type 2 diabetes Mellitus. The cryoEM strcuture reveals a C-terminal NUDT9 homology (NUDT9H) domain responsible for binding ADP-ribose(ADPR) (Wang et al. 2018). Both ADPR and Ca2+ are required for TRPM2 activation, and structures with ADPR and Ca2+ show both intra- and inter-subunit interactions with the N-terminal TRPM homology region (MHR1/2/3) in the apo state, but undergoing conformational changes upon ADPR binding, resulting in rotation of MHR1/2 and disruption of the inter-subunit interaction. Ca2+ binding further engages transmembrane helices and the conserved TRP helix to cause conformational changes at the MHR arm and the lower gating pore to potentiate channel opening (Wang et al. 2018). Consecutive structural rearrangements and channel activation are induced by binding of ADPR in two indispensable locations, and the binding of Ca2+ in the transmembrane domain (Huang et al. 2019). An N-terminal TRPC2 splice variant of 213 aas inhibits calcium influx (Chu et al. 2005). An antogonists of channel function has been identified (Cruz-Torres et al. 2020). A point mutant of TrpM2 (rs93315) has been identified as a risk factor for bipolar disorder (Mahmuda et al. 2020). Two gates orchestrate the opening of human TRPM2 (Rish et al. 2022). Protein kinase C (PKC)-mediated phosphorylation of TRPM2 Thr738 counteracts the effect of cytosolic Ca2+ and elevates the temperature threshold (Kashio et al. 2022).
The nociceptive neuron TRPA1 (Trp-ankyrin 1) (also called the Wasabi Receptor) senses peripheral damage by transmitting pain signals (activated by cold temperatures, pungent compounds and environmental irritants). Noxious compounds also activate through covalent modification of cysteyl residues (Macpherson et al., 2007). TRPA1 is an excitatory, nonselective cation channel implicated in somatosensory function, pain, and neurogenic inflammation. Through covalent modification of cysteine and lysine residues, TRPA1 can be activated by electrophilic compounds, including active ingredients of pungent natural products (e.g., allyl isothiocyanate), environmental irritants (e.g., acrolein), and endogenous ligands (4-hydroxynonenal) (Chen et al., 2008). General anesthetics activate TRPA1 nociceptive ion channels to enhance pain and inflammation (Matta et al., 2008; Leffler et al., 2011). TMS5 is a critical molecular determinant of menthol sensitivity (Xiao et al., 2008) and a variety of inhibitors which are analgesics. Another class of inhibitors are in the thiadiazole structural class of compounds, and they bind to the TRPA1 ankyrin repeat 6 (Tseng et al. 2018). Inhibitors are potential analgesics. The majority of TRPA1 inhibitors interact with the S5 transmembrane helices, forming part of the pore region of the channel. TRPA1 is a component of the nociceptive response to CO2 (Wang et al., 2010). TRPA1 is a polyunsaturated fatty acid sensor in mammals but not in flies and fish (Motter and Ahern, 2012). It is regulated by its N-terminal ankyrin repeat domain (Zayats et al., 2012). Mutations in TrpA1 cause alterred pain perception (Kremeyer et al. 2010). The hop compound, eudesmol, an oxygenated sesquiterpene, activates the channel (Ohara et al. 2015). These channels regulate heat and cold perception, mechanosensitivity, hearing, inflammation, pain, circadian rhythms, chemoreception, and other processes (Laursen et al. 2014). TRPA1 is a polymodal ion channel sensitive to temperature and chemical stimuli, but its resposes are species specific (Laursen et al. 2015). A probable binding site for general anesthetics has been identified (Ton et al. 2017), and specific residues involved in binding of the anesthetic, propofol, are known (Woll et al. 2017). TrpV1 and TrpA1 are inflammatory mediators causing cutaneous chronic itch in several diseases (Xie and Li 2018). TRPA1 is specifically activated by natural products including allyl isothiocyanate (mustard oil), cinnamaldehyde (cinnamon), allicin (garlic) and trans-anethole in Fennel Oil (FO) (Memon et al. 2019). Mutations in TRPA1 result in insensitivity to pain promoting algogens such as capsaicin, acid, and allyl isothiocyanate (AITC), have been documented (Eigenbrod et al. 2019). TRPA1 transduces noxious chemical stimuli into nociceptor electrical excitation and neuropeptide release, leading to pain and neurogenic inflammation. It is regulated by the membrane environment. Startek et al. 2019 found that mouse TRPA1 localizes to cholesterol-rich domains, and that cholesterol depletion decreases channel sensitivity to chemical agonists. Two structural motifs in TMSs 2 and 4 are involved in cholesterol interactions that are necessary for normal agonist sensitivity and plasma membrane localization. TRPA1 is an irritant sensor and a therapeutic target for treating pain, itch, and respiratory diseases. It can be activated by electrophilic compounds such as allyl isothiocyanate (AITC). A class of piperidine carboxamides (PIPCs) are potent noncovalent agonists (Chernov-Rogan et al. 2019). Saikosaponins are channel antogonists (Lee et al. 2019). hTRPA1 is activated by electrophiles such as N-methyl maleimide (NMM). A conformational switch of the protein, possibly associated with activation or desensitization of the ion channel, involves covalent derivatization of several cysteyl and lysyl residues in the transmembrane domain and the proximal N-terminal region as targets for electrophilic activation (Moparthi et al. 2020). Altering expression of the genes encoding Kv1.1, Piezo2, and TRPA1 regulate the response of mechanosensitive muscle nociceptors (Nagaraja et al. 2021). As a polymodal nocisensor, TRPA1 can be activated by thermal and mechanical stimuli as well as a wide range of chemically damaging molecules including small volatile environmental toxicants and endogenous algogenic lipids (Zsidó et al. 2021). After activation by such compounds, the ion channel opens up, allowing calcium influx into the cytosol, inducing signal transduction pathways. Then, calcium influx desensitizes irritant evoked responses and results in an inactive state of the ion channel. It was shown how reversible interactions with binding sites contribute to structural changes of TRPA1, leading to covalent bonding of agonists (Zsidó et al. 2021). The binding site(s) for antagonists have been determined for the TRPA1 ion channel (Gawalska et al. 2022).
The ion channel viral protein U, Vpu of 81 aas and 1 TMS. Vpu(1-32), forms a helix bundle with characteristic open states. Different amilorides inhibit channel activity (Römer et al. 2004). The mutation A18H converts a non-specific channel to a selective proton channel that is sensitive to rimantadine (Sharma et al., 2011). Vpu forms stable pentamers (Padhi et al. 2013). The mechanism of Vpu, a weakly conducting cation-selective channel that assists in detachment of the virion from infected cells, has been proposed (Padhi et al. 2014). Interactions of Vpu with host cellular constituents have been reviewed (González 2015). Vpu forms large homo aggregates of 16 or 32 subunits (Lin et al. 2016). Vpu is involved in the enhancement of virion release via formation of an ion channel. Cyclohexamethylene amiloride (Hma) inhibits ion channel activity. A putative binding site for Hma blockers in a pentameric model bundle built of parallel aligned helices of the first 32 residues of Vpu was found near Ser-23. Hma orientates along the channel axis with its alkyl ring pointing inside the pore, which leads to a blockage of the pore (Lemaitre et al. 2004).
Vpr of HIV of 96 aas and one TM
Fluoride ion channel of 128 aas and 4 TMSs, Fluc or CrcB. The crystal structure is known (PDB5A40; 5A43).
Bestrophin-1 (Best1) of 689 aas and 4 TMSs in a 2 + 2 arrangement. The x-ray structure has been determined at 2.85 Å resolution with permeant anions and Ca2+ bound (Kane Dickson et al. 2014). The channel is formed from a pentameric assembly of subunits. Ca2+ binds to the channel's large cytosolic region. A single ion pore, approximately 95 Å in length, is located along the central axis and contains at least 15 binding sites for anions. A hydrophobic neck within the pore probably forms the gate. Phenylalanine residues within it may coordinate permeating anions via anion-π interactions. Conformational changes observed near the 'Ca2+ clasp' hint at the mechanism of Ca2+-dependent gating (Kane Dickson et al. 2014).
Polycystin 1 (PKD1 or PC1) assembles with TRPP2 (Q86VP3) in a stoichiometry of 3TRPP2: 1PKD1, forming the receptor/ion channel complex (Yu et al., 2009). The C-terminal coiled-coil complex is critical for proper assembly (Zhu et al., 2011). Missense mutations have been identified that affect membrane topogenesis (Nims et al. 2011). Biomarkers for polycystic kidney diseases have been identified (Hogan et al. 2015). Extracellular divalent ions, including Ca2+, inhibit permeation of monovalent ions by directly blocking the TRPP2 channel pore. D643, a negatively charged amino acid in the pore, is crucial for channel permeability (Arif Pavel et al. 2016). Polycystin (TRPP/PKD) complexes, made of transient receptor potential channel polycystin (TRPP)4 and polycystic kidney disease (PKD) proteins, play key roles in coupling extracellular stimuli with intracellular Ca2+ signals. PKD1 and PKD2 form a complex, the structure of which has been solved in 3-dimensions at high resolution. The complex consists of PKD1:PKD2 = 3:1. PKD1 consists of a voltage-gated ion channel fold that interacts with PKD2 to complete a domain-swapped TRP architecture with unique features (Su et al. 2018; Su et al. 2018). The C-terminal tail of PKD1 may play a role in the prognosis of renal disease (Higashihara et al. 2018). TRPP2 uses 2 gating charges found in its fourth TMS (S4) to control its conductive state (Ng et al. 2019). Rosetta structural predictions demonstrated that the S4 undergoes approximately 3- to 5-Å transitional and lateral movements during depolarization coupled to opening of the channel pore. Both gating charges form state-dependent cation-pi interactions within the voltage sensor domain (VSD) during membrane depolarization. The transfer of a single gating charge per channel subunit is required for voltage, temperature, and osmotic swell polymodal gating. Thus, TRPP2 channel opening is dependent on activation of its VSDs (Ng et al. 2019). Polycystin-1 assembles with Kv channels to govern cardiomyocyte repolarization and contractility (Altamirano et al. 2019). Three-dimensional in vitro models answer questions about ADPKD cystogenesis (Dixon and Woodward 2018). The polycystin-1 subunit directly contributes to the channel pore, and its eleven TMSs are sufficient for its channel function (Wang et al. 2019). Polycystin-1 inhibits cell proliferation through phosphatase PP2A/B56alpha (Tang et al. 2019). Polycystin-1 regulates cardiomyocyte mitophagy (Ramírez-Sagredo et al. 2021). Maser and Calvet 2020 reviewed structural and functional features shared by polycystin-1 and the adhesion GPCRs (TC# 9.A.14.6.2) and discussed the implications of such similarities for our understanding of the functions of these proteins. Mutations in PKD1 and PKD2 cause autosomal dominant polycystic kidney disease (ADPKD). Polycystins are expressed in the primary cilium, and disrupting cilia structure slows ADPKD progression following inactivation of polycystins. Dysregulation of cyclin-dependent kinase 1 (Cdk1) is an early driver of cyst cell proliferation in ADPKD due to Pkd1 inactivation (Zhang et al. 2021). Genetic removal of c-Jun N-terminal kinases, Jnk1 and Jnk2, suppresses the nuclear accumulation of phospho c-Jun, reduces proliferation and reduces the severity of cystic disease. While Jnk1 and Jnk2 are thought to have largely overlapping functions, Jnk1 loss is nearly as effective as the double loss of Jnk1 and Jnk2 (Smith et al. 2021). Polycystic kidney disease (PKD), comprising autosomal dominant polycystic kidney disease (ADPKD) and autosomal recessive polycystic kidney disease (ARPKD), is characterized by incessant cyst formation in the kidney and liver. ADPKD and ARPKD represent the leading genetic causes of renal disease in adults and children, respectively. ADPKD is caused by mutations in PKD1 encoding polycystin1 (PC1) and PKD2 encoding polycystin 2 (PC2). PC1/2 are multi-pass transmembrane proteins that form a complex localized in the primary cilium. Predominant ARPKD cases are caused by mutations in polycystic kidney (Ma 2021). The mechanism of tethered agonist-mediated signaling by polycystin-1 has been investigated (Pawnikar et al. 2022).
Heteromeric polycystic kidney disease proteins 1 and 2-like 1 (PKD1L1/PKD2L1) cation (calcium) channel of kidney primary cilia (DeCaen et al. 2013). PKD2L1 is probably orthologous to mouse TC# 1.A.5.2.2. The voltage dependence of PKD2L1 may reflect the charge state of the S4 domain (Numata et al. 2017). PKD2L1, (TRPP3) is involved in the sour sensation and other pH-dependent processes and is a nonselective cation channel that can be regulated by voltage, protons, and calcium. The 3-d structure has been determined by cryoEM at 3.4 Å resolution (Su et al. 2018). Unlike its ortholog PKD2, the pore helix and TMS6, which are involved in upper and lower-gate opening, adopt an open conformation. The pore domain dilation is coupled to conformational changes of voltage-sensing domains via a series of pi-pi interactions, suggesting a potential PKD2L1 gating mechanism (Su et al. 2018).
Polycystin 2 (PKD2, PC2 or TRPP2) of 968 aas and 8 or 9 TMSs (Anyatonwu and Ehrlich, 2005). It is regulated by α-actinin (AAC17470) by direct binding, influencing its channel activity (Li et al., 2007), and is also regulated also by diaphanous-related formin 1 (mDia1) (Bai et al., 2008). It has 8 TMSs with 6 TMSs in the channel domain with N- and C- termini inside (Hoffmeister et al., 2010). PC2 interacts with the inositol 1,4,5-trisphosphate receptor (IP(3)R) to modulate Ca2+ signaling (Li et al. 2009). The PKD2 voltage-sensor domain retains two of four gating charges commonly found in voltage-gated ion channels. The PKD2 ion permeation pathway is constricted at the selectivity filter near the cytoplasmic end of S6, suggesting that two gates regulate ion conduction (Shen et al. 2016). 15% of cases of polycystic kidney disease result from mutations in the gene encoding this protein, while 85% are in PKD1 (Ghata and Cowley 2017). Topological changes between the closed and open sub-conductance states of the functional channel are observed with an inverse correlation between conductance and height of the channel. Intrinsic PC2 mechanosensitivity in response to external forces was also observed (Lal et al. 2018). PC2 is present in ciliary membranes of the kidney and shares a transmembrane fold with other TRP channels as well as an extracellular domain found in TRPP and TRPML channels. Wang et al. 2019 characterized the phosphatidylinositol biphosphate (PIP2) and cholesterol interactions with PC2. PC2 has a PIP binding site close to the equivalent vanilloid/lipid binding site in the TRPV1 channel and a binding site for cholesterol. The two classes of lipid binding sites were compared with sites observed in other TRPs and in Kv channels, suggesting that PC2, in common with other ion channels, may be modulated by both PIPs and cholesterol (Wang et al. 2019). Genetic removal of c-Jun N-terminal kinases, Jnk1 and Jnk2, suppresses the nuclear accumulation of phospho c-Jun, reduces proliferation and reduces the severity of cystic disease. While Jnk1 and Jnk2 are thought to have largely overlapping functions, Jnk1 loss is nearly as effective as the double loss of Jnk1 and Jnk2 (Smith et al. 2021). Polycystin-2 (TRPP2): ion channel properties and regulation have been described (Del Rocío Cantero and Cantiello 2022).
Polycystin-2, PKD2 or PKD-REJ2 of 907 aas and 8 TMSs (Gunaratne et al. 2007). Polycystin-2 associates with the polycystin-1 homolog, suREJ3 (TC# 1.A.5.1.6), and localizes to the acrosomal region of sea urchin spermatozoa (Neill et al. 2004).
The lysosomal monovalent cation/Ca2+ channel, TRP-ML1 (Mucolipin-1) (associated with the human lipid storage disorder, mucolipidosis type IV (MLIV)) (Kiselyov et al., 2005; Luzio et al., 2007). TRPML1 is an endolysosomal iron release channel (Dong et al., 2008). It interacts with TMEM163, a CDF heavy metal transporter (TC# 2.A.4.8.3). Together these proteins function in Zn2+ homeostasis, possibly by exporting Zn2+ (Cuajungco et al. 2014). The MLIV disease could result from Zn2+ overload. TrpML1 is probably involved in Zn2+ uptake into lysosomes (Cuajungco and Kiselyov 2017). Asp residues within the luminal pore may control calcium/pH regulation. A synthetic agonist, ML-SA1, can bind to the pore region to force a direct dilation of the lower gate (Schmiege et al. 2018). This channel plays a role in vesicle contraction following phagocytosis or pinocytosis, allowing maintenance of cell volume (Freeman et al. 2020). A mutation gave rise to progressive psychomotor delay, and atrophy of the corpus callosum and cerebellum was observed on brain magnetic resonance images (Hayashi et al. 2020).
Mucolipin-2 (TRPML2) non-selective plasma membrane cation channel (Ca2+ permeable). Shows inward rectification like TRPML1 and TRPML3 (Lev et al., 2010). Induces cell degeneration. Causes embryonic lethality, pigmentation defects and deafness, and regulates the acidification of early endosomes (Noben-Trauth, 2011). Found in the plasma membrane and early- and late-endosomes as well as lysosomes. Activated by a transient reduction of extracellular sodium followed by sodium replenishment, by small chemicals related to sulfonamides, and by PI(3,5)P2, a rare phosphoinositide that naturally accumulates in the membranes of endosomes and lysosomes, and thus could act as a physiologically relevant agonist (García-Añoveros and Wiwatpanit 2014). TRPML2 can form heteromultimers with TRPML1 and TRPML3; in B-lymphocytes, TRPML2 and TRPML1 may play redundant roles. TRPML2 may play a role in immune cell development and inflammatory responses (Cuajungco et al. 2015). The TRPML family hallmark is a large extracytosolic/lumenal domain (ELD) between TMSs S1 and S2. Viet et al. 2019 presented crystal structures of the tetrameric human TRPML2 ELD. The structures reveal structural responses to the conditions the TRPML2 ELD encounters as the channel traffics through the endolysosomal system.
Mucolipin-3 (Mcoln3, TRPML3). Orthologue of 1.A.5.3.2. Asp residues within the luminal pores of all mucolipins may function to control calcium/pH regulation. A synthetic agonist, ML-SA1, can bind to the pore region of TRPMLs to force a direct dilation of the lower gate. These proteins have multiple ligand binding sites (Schmiege et al. 2018).
Phospholamban (PLB or PLN) pentameric Ca2+/K+ channel (Kovacs et al., 1988; Smeazzetto et al. 2013; Smeazzetto et al. 2014). In spite of extensive experimental evidence, suggesting a pore size of 2.2 Å, the conclusion of ion channel activity for phospholamban has been questioned (Maffeo and Aksimentiev 2009). Phosphorylation by protein kinase A and dephosphorylation by protein phosphatase 1 modulate the inhibitory activity of phospholamban (PLN), the endogenous regulator of the sarco(endo)plasmic reticulum calcium Ca2+ ATPase (SERCA). This cyclic mechanism constitutes the driving force for calcium reuptake from the cytoplasm into the myocyte lumen, regulating cardiac contractility. PLN undergoes a conformational transition between a relaxed (R) and tense (T) state, an equilibrium perturbed by the addition of SERCA. Phosphoryl transfer to Ser16 induces a conformational switch to the R state. The binding affinity of PLN to SERCA is not affected ((Kd ~ 60 μM). However, the binding surface and dynamics in domain Ib (residues 22-31) change substantially upon phosphorylation. Since PLN can be singly or doubly phosphorylated at Ser16 and Thr17, these sites may remotely control the conformation of domain Ib (Traaseth et al. 2006). Phospholamban interests with SERCA with conformational memory (Smeazzetto et al. 2017). Under physiological conditions, PLB phosphorylation induces little or no change in the interaction of the TMS with SERCA, so relief of inhibition is predominantly due to the structural shift in the cytoplasmic domain (Martin et al. 2018). The phospholamban pentamer alters the function of the sarcoplasmic reticulum calcium pump, SERCA (Glaves et al. 2019). PLB phosphorylation serves as an allosteric molecular switch that releases inhibitory contacts and strings together the catalytic elements required for SERCA activation (Aguayo-Ortiz and Espinoza-Fonseca 2020).
Sarcolipin (SLN) anion pore-forming protein of 31 aas and 1 TMS, with selectivity for Cl- and H2PO4-. Oligomeric interactions of sarcolipin and the Ca-ATPase have been documented (Autry et al., 2011). Sarcolipin, but not phospholamban, promotes uncoupling of the SERCA pump (3.A.3.2.7; Sahoo et al. 2013). SNL forms pentameric pores that can transport water, H+, Na+, Ca2+ and Cl-. Leu21 serves as the gate (Cao et al. 2015). In the channel, water molecules near the Leu21 pore demonstrated a clear hydrated-dehydrated transition (Cao et al. 2016). Small ankyrin 1 (sAnk1; TC#8.A.28.1.2) and SLN interact with each other in their transmembrane domains to regulate SERCA (TC# 3.A.3.2.7) (Desmond et al. 2017). The TM voltage has a positive effect on the permeability of water molecules and ions (Cao et al. 2020). The conserved C-terminus is an essential element required for the dynamic control of SLN regulatory function (Aguayo-Ortiz et al. 2020).
The voltage-gated proton channel, mVSOP (269 aas and 2 TMSs) (Sasaki et al., 2006). A hydrophobic plug functions as the gate (Chamberlin et al. 2013). Gating current measurements revealed that voltage-sensor (VS) activation and proton-selective aqueous conductance opening are thermodynamically distinct steps in the Hv1 activation pathway and showed that pH changes directly alter VS activation. Gating cooperativity, pH-dependent modulation, and a high degree of H+ selectivity have been demonstrated (De La Rosa and Ramsey 2018).
The voltage-gated proton channel, Hv1, Hv1, HV1 or HVCN1 (273 aas) (Ramsey et al., 2006). Thr29 is a phosphorylation site that activates the HVCN1 channel in leukocytes (Musset et al., 2010). The condctivity pore has been delineated and depends of a carboxyl group (Asp or Glu) in the channel (Morgan et al. 2013). The four transmembrane helices sense voltage and the pH gradient, and conduct protons exclusively. Selectivity is achieved by the unique ability of H3O+ to protonate an Asp-Arg salt bridge. Pathognomonic sensitivity of gating to the pH gradient ensures HV1 channel opening only when acid extrusion will result, which is crucial to its biological functions (DeCoursey 2015). An exception occurs in dinoflagellates (see 1.A.51.1.4) in which H+ influx through HV1 triggers a bioluminescent flash. The gating mechanism of Hv1, cooperativity within dimers and the sensitivity to metal ions have been reviewed (Okamura et al. 2015). How this channel is activated by cytoplasmic [H+] and depolarization of the membrane potential has been proposed by Castillo et al. 2015. The extracellular ends of the first transmembrane segments form the intersubunit interface that mediates coupling between binding sites, while the coiled-coil domain does not directly participate in the process (Hong et al. 2015). Deep water penetration through hHv1 has been observed, suggesting a highly focused electric field, comprising two helical turns along the fourth TMS. This region likely contains the H+ selectivity filter and the conduction pore. A 3D model offers an explicit mechanism for voltage activation based on a one-click sliding helix conformational rearrangement (Li et al. 2015). Trp-207 enables four characteristic properties: slow channel opening, highly temperature-dependent gating kinetics, proton selectivity, and ΔpH-dependent gating (Cherny et al. 2015). The native Hv structure is a homodimer, with the two channel subunits functioning cooperatively (Okuda et al. 2016). Segment S3 plays a role in activating gating (Sakata et al. 2016). Two sites have been identified: one is the binding pocket of 2GBI (accessible to ligands from the intracellular side); the other is located at the exit site of the proton permeation pathway (Gianti et al. 2016). Crystal structures of Hv1 dimeric channels revealed that the primary contacts between the two monomers are in the C-terminal domain (CTD), which forms a coiled-coil structure. Molecular dynamics (MD) simulations of full-length and truncated CTD models revealed a strong contribution of the CTD to the packing of the TMSs (Boonamnaj and Sompornpisut 2018). Histidine-168 is essential for the ΔpH-dependent gating (Cherny et al. 2018). Proton transfer in Hv1 utilizes a water wire, and does not require transient protonation of a conserved aspartate in the S1 transmembrane helix (Bennett and Ramsey 2017). Hv1 channels are present in bull spermatozoa, and these regulate sperm functions like hypermotility, capacitation and acrosome reaction through a complex interplay between different pathways involving cAMP, PKC, and Catsper (Mishra et al. 2019). A zinc binding site influences gating configurations of HV1 (Cherny et al. 2020).
The voltage-sensor containing phosphatase, VSP, of 576 aas and 4 TMSs N-terminal to the phosphatase domain. The enzyme region of VSP contains the phosphatase and C2 domains, is structurally similar to the tumor suppressor phosphatase PTEN, and catalyzes the dephosphorylation of phosphoinositides. The transmembrane voltage sensor is connected to the phosphatase through a short linker region, and phosphatase activity is induced upon membrane depolarization (Zhang et al. 2018). The coupling between the two domains has been studied (Sakata et al. 2017). Membrane depolarization activates the phosphatase activity of the enzyme, presumably via electroconformational coupling between the sensor domain and the enzyme (Sanders and Hutchison 2018). Both the phosphatase domain and the C2 domain move with similar timing upon membrane depolarization (Sakata and Okamura 2018).
The CRAC channel protein, Orai1 (CRACM1) (Prakriya et al. 2006), complexed with the STIM1 or STIM2 protein (Feske et al., 2006). Replacement of the conserved glutamate in the first TMS with glutamine (E106Q) acts as a dominant-negative protein, and substitution with aspartate (E106D) enhances Na+, Ba2+, and Sr2+ permeation relative to Ca2+. Mutating E190Q in TMS3 also affects channel selectivity, suggesting that glutamate residues in both TMS1 and TMS3 face the lumen of the pore (Vig et al. 2006). The Orai1:Stim stoichiometry = 4:2 (Ji et al., 2008). Human Orai1 and Orai3 channels are dimeric in the closed resting state and open states. They are tetrameric when complexed with STIM1 (Demuro et al., 2011). A dimeric form catalyzes nonselective cation conductance in the STIM1-independent mode. STIM1 domains have been characterized (How et al. 2013). Alternative translation initiation of the Orai1 message produces long and short types of Ca2+ channels with distinct signaling and regulatory properties (Desai et al. 2015). STIM2 plays roles similar to STIM1 in regulating basal cytosolic and endoplasmic reticulum Ca2+ concentrations by controling Orai1, 2 and 3. STIM2 may inhibit STIM1-mediated Ca2+ influx. It also regulates protein kinase A-dependent phosphorylation and trafficking of AMPA receptors (TC# 1.A.10) (Garcia-Alvarez et al. 2015). A mechanistic model for ROS (H2O2)-mediated inhibition of Orai1 has been determined (Alansary et al. 2016). Regions that are important for the optimal assembly of hetero-oligomers composed of full-length STIM1 with its minimal STIM1-ORAI activating region, SOAR, have been identified (Ma et al. 2017). Orai1 may be multifunctional (Carrell et al. 2016). Activatioin of Orai1 requires communication between the N-terminus and loop 2 (Fahrner et al. 2017). STIM1 dimers unfold to expose a discrete STIM-Orai activating region (SOAR1) that tethers and activates Orai1 channels within discrete ER-PM junctions (Zhou et al. 2018). SOAR dimer cross-linking leads to substantial Orai1 channel clustering, resulting in increased efficacy and cooperativity of Orai1 channel function. In addition to being an ER Ca2+ sensor, STIM1 functions within the PM to exert control over the operation of SOCs. As a cell surface signaling protein, STIM1 represents a key pharmacological target to control fundamental Ca2+-regulated processes including secretion, contraction, metabolism, cell division, and apoptosis (Spassova et al. 2006). STIM1 also contributes to smooth muscle contractility (Feldman et al. 2017). STIM1-mediated Orai1 channel gating, involves bridges between TMS 1 and the surrounding TMSs 2/3 ring, and these are critical for conveying the gating signal to the pore (Yeung et al. 2018). A review article summarizes the current high resolution structural data on specific EF-hand, sterile alpha motif and coiled-coil interactions which drive STIM function in the activation of Orai1 channels (Novello et al. 2018). Orai1 and STIM1 are involved in tubular aggregate myopathy (Wu et al. 2018). Knowledge of the structure-function relationships of CRAC channels, with a focus on key structural elements that mediate the STIM1 conformational switch and the dynamic coupling between STIM1 and ORAI1 has been discussed (Nguyen et al. 2018). While STIM1 is the native channel opener, a chemical modulator is 2-aminoethoxydiphenyl borate (2-APB) (Ali et al. 2017). ORAI1 channel gating and selectivity iare differentially altered by natural mutations in the first and third transmembrane domains (Bulla et al. 2018). Stim1 responds to both ER Ca2+ depletion and heat, mediates temperature-induced Ca2+ influx in skin keratinocytes via coupling to Orai Ca2+ channels in the plasma membrane, and thereby brings about thermosensing (Liu et al. 2019). Possibly, the interplay between STIM1 alpha3 and Orai1 TM3 allows STIM1 coupling to be transmitted into physiological CRAC channel activation (Butorac et al. 2019). Blockage of store-operated Ca2+ influx by synta66 is mediated by direct inhibition of the Ca2+ selective orai1 pore (Waldherr et al. 2020). The carboxy terminal coiled-coil region modulates Orai1 internalization during meiosis (Hodeify et al. 2021). ORAI1 mutations disrupt channel trafficking, resulting in combined immunodeficiency (Yu et al. 2021). Orai channel C-terminal peptides are key modulators of STIM-Orai coupling and calcium signal generation (Baraniak et al. 2021). Conformational surveillance of Orai1 by a rhomboid intramembrane protease prevents inappropriate CRAC channel activation (Grieve et al. 2021). STIM1-dependent peripheral coupling governs the contractility of vascular smooth muscle cells (Krishnan et al. 2022). Gating checkpoints in the Orai1 calcium channel have been identified (Augustynek et al. 2022).
Ca2+ release-activated Ca2+ (CRAC) channel subunit, Orai, which mediates Ca2+ influx following depletion of intracellular Ca2+ stores. In Greek mythology, the 'Orai' are the keepers of the gates of heaven. The crystal structure (3.35 Å), revealed a hexameric assembly of Orai subunits arranged around a central ion pore which traverses the membrane and extends into the cytosol. A ring of glutamate residues on its extracellular side forms the selectivity filter. A basic region near the intracellular side can bind anions that may stabilize the closed state. The architecture of the channel differs from those of other solved ion channels (Hou et al. 2012). Residues in the third TMS of orai affect the conduction properties of the channel (Alavizargar et al. 2018); a conserved glutamate residue (E262) contributes to selectivity. Mutation of this residue affected the hydration pattern of the pore domain, and impaired selectivity of Ca2+ over Na+. The crevices of water molecules are located to contribute to the dynamics of the hydrophobic gate and the basic gate, suggesting a possible role in channel opening and in selectivity function (Alavizargar et al. 2018).
The Orai channel is characterized by voltage independence, low conductance, and high Ca2+ selectivity and plays a role in Ca2+ influx through the plasma membrane (PM). Liu et al. 2019 reported the crystal structure and cryo-EM reconstruction of a mutant (P288L) channel that is constitutively active. The open state showed a hexameric assembly in which 6 TMS 1 helices in the center form the ion-conducting pore, and 6 TMS 4 helices in the periphery form extended long helices. Orai channel activation requires conformational transduction from TM4 to TM1 and causes the basic section of TM1 to twist outward. The wider pore on the cytosolic side aggregates anions to increase the potential gradient across the membrane and thus facilitate Ca2+ permeation (Liu et al. 2019).
Hepatitis GB virus B (GBV-B) polyprotein of 2864 aas, containing the p13 viroporin. It is found between residues 614 and 733 in the polyprotein and has 4 predicted TMSs. It is homologous to but larger than the p7 protein of hepatitis C virus (Ghibaudo et al. 2004).
The borine viral diarrhea virus (BVDV) p7 peptide, viral budding process initiator. It probably transports H+ and other cations (Scott and Griffin 2015).
Presenilin-1 (PS-1; STM-1; E5-1; AD) Ca2+ leak channel (part of the γ-secretase complex; expression alters the lipid raft composition in neuronal membranes (Eckert and Müller, 2009)). The first 5 TMSs of presenilin-1 are homologous to the 5 TMS CD47 antigenic protein, a constituent of the osteoclast fusion complex (1.N.1.1.1), and CD47 is therefore a presenilin homologue (unpublished observations). The active site of gamma-secretase resides in an aqueous catalytic pore within the lipid bilayer and is tapered around the catalytic aspartates (Sato et al. 2006). TMS 6 and TMS 7 contribute to the hydrophilic pore. Residues at the luminal portion of TMS 6 are predicted to form a subsite for substrate or inhibitor binding on the α-helix facing the hydrophilic milieu, whereas those around the GxGD catalytic motif within TMS 7 are water accessible (Sato et al. 2006).
Presenilin homologue (DUF1119) of 301 aas and 9 TMSs with known 3-d structure. The amino-terminal domain, consisting of TM1-6, forms a horseshoe-shaped structure, surrounding TM7-9 of the carboxy-terminal domain. The two catalytic aspartate residues are located on the cytoplasmic side of TMS 6 and TMS 7, spatially close to each other and approximately 8 Å into the lipid membrane surface. Water molecules gain constant access to the catalytic aspartates through a large cavity between the amino- and carboxy-terminal domains. (Li et al. 2013). Both protease and ion channel activities have been demostrated, and these two activities share the same active site (Kuo et al. 2015). Cleavage is controlled by both positional and chemical factors (Naing et al. 2018).
High affinity copper (Cu+) and silver (Ag+) uptake transporter, Ctr1 of 190 aas and 3 TMSs. The trimeric channel (Eisses and Kaplan, 2005) forms an oligomeric pore with each subunit displaying 3 TMSs and 2 metal binding motifs (Lee et al., 2007). TMS2 is sufficient to form the trimer, and the MXXM motif bind Ag+ (Dong et al. 2015). Ctr1 mediates basolateral uptakes of Cu+ in enterocytes (Zimnicka et al., 2007) and shows copper-dependent internalization and recycling which provides a reversible mechanism for the regulation of cellular copper entry (Molloy and Kaplan, 2009). It acts as a receptor for the two extinct viruses, CERV1 and CERV2 (Soll et al., 2010). Ctr1 takes up platinum anticancer drugs, cisplatin and carboplatin (Du et al., 2012). The 3-d structure is known (Yang et al., 2012). Ctr1 has a low turn over number of about 10 ions/second/trimer (Maryon et al. 2013). Methionine and histidine residues in the transmembrane domain are essential for transport of copper, but when mutated, they stimulated uptake of cisplatin (Larson et al. 2010). Plays important roles in the developing embryo as well as in adult ionic homeostasis (Wee et al. 2013). (-)-Epigallocatechin-3-gallate (EGCG), a major polyphenol from green tea, can enhance CTR1 mRNA and protein expression in ovarian cancer cells. EGCG inhibits the rapid degradation of CTR1 induced by cisplatin (cDDP). The combination of EGCG and cDDP increases the accumulation of cDDP and DNA-Pt adducts, and subsequently enhances the sensitivity of ovarian cancer (Wang et al. 2015). Steroid inhibitors may be able to overcome cycplatin resistance (Kadioglu et al. 2015). ctr1 is upregulated in colorectal cancer cells (Barresi et al. 2016). The N-terminus of CTR1 binds Cu2+ following transfer from blood copper carriers such as human serum albumin to the transporter (Bossak et al. 2018). Once in the cytosol, enzyme-specific chaperones receive copper from the CTR1 C-terminal domain and deliver it to their apoenzymes (Ilyechova et al. 2019). Ctr1 is part of the Sp1-Slc31a1/Ctr1 copper-sensing system, and carnosine, a brain dipeptide, influences copper homeostasis in murine CNS-derived cells (Barca et al. 2019). A proteomic view of cellular responses of macrophages to copper has appeared (Dalzon et al. 2021). Tetrahedral framework nucleic acid delivered RNA therapeutics significantly attenuate pancreatic cancer progression via inhibition of CTR1-dependent copper absorption (Song et al. 2021).
The pore-forming peptide, Pep46 (derived from the structural polyprotein (PP) precursor (1012 aas) (Galloux et al. 2007). The 3-D NMR structure of Pep46 is known: Acc# 2IMUA (Galloux et al. 2010).
Epithelial Na+ channel, ENaC (regulates salt and fluid homeostasis and blood pressure; regulated by Nedd4 isoforms and SGK1, 2 and 3 kinases) (Henry et al., 2003; Pao 2012). Cd2+ inhibits α-ENaC by binding to the internal pore where it interacts with residues in TMS2 (Takeda et al., 2007). The channel is regulated by palmitoylation of the beta subunit which modulates gating (Mueller et al. 2010). ENaCs are more selective for Naa+ over other cations than ASICs (Yang and Palmer 2018). ENaC plays a role in chronic obstructive pulmonary diseases (COPD) (Zhao et al. 2014). The hetrodimeric complex can consist of αβγ or δβγ subunits, depending on the tissue (Giraldez et al. 2012). The α- and γ-subunits of the epithelial Na+ channel interact directly with the Na+:Cl- cotransporter, NCC, in the renal distal tubule with functional cosequences, and together they determine bodily salt balance and blood pressure (Mistry et al. 2016). ENaC is regulated by syntaxins (Saxena et al. 2006). The cryoEM structure has been solved (Noreng et al. 2018). Interactions between the epithelial sodium channel gamma-subunit and claudin-8 modulates paracellular sodium permeability in the renal collecting duct (Sassi et al. 2020). Tumer necrosis factor, TNF, of 233 aas, is the source of a modified cyclic peptide of 17 aas, solnatide or the TIP peptide, (CGQRETPEGAEAKPWYC), residues 177 - 195), that activates ENaC (Madaio et al. 2019; Martin-Malpartida et al. 2022).
Neuronal acid-sensing cation channel-1, ASIC1 (>90% identical to ASIC1 of Rat (TC#1.A.6.1.2)). 3D structure (1.9Å resolution) has been solved (Jasti et al., 2007). Regulated by the glucocorticoid-induced kinase-1 isoform 1 (SGK1.1) (Arteaga et al., 2008). Residues in the second transmembrane domain of the ASIC1a that contribute to ion selectivity have been defined (Carattino and Della Vecchia, 2012). Outlines of the pore in open and closed conformations describe the gating mechanism (Li et al., 2011). Interactions between two extracellular linker regions control sustained channel opening (Springauf et al., 2011). Can form monomers, trimers and tetramers, but the tetramer may be the predominant species in the plasma membrane (van Bemmelen et al. 2015). The C-terminal tail projects into the cytosol by approximately 35 Å, and the N and C tails from the same subunits are closer than those of adjacent subunits (Couch et al. 2021).
Touch-responsive mechanosensitive degenerin channel complex (Mec-4/Mec-10 form the cation/Ca2+-permeable channel; Mec-2 and Mec-6 regulate) (Bianchi, 2007; Chelur et al., 2002; ). Mec-6 is a chaparone protein required for functional insertion (Matthewman et al. 2018). Mec-10 plays a role in the response to mechanical forces such as laminar shear stress (Shi et al. 2016). MEC-4 or MEC-10 mutants that alter the channel's LSS response are primarily clustered between the degenerin site and the selectivity filter, a region that likely forms the narrowest portion of the channel pore (Shi et al. 2018). TMS2 forms the Ca2+ channel of Mec-4. A C-terminal domain affects trafficking of a neuronally expressed DEG/ENaC. Neuronal swelling occurs prior to commitment to necrotic death (Royal et al. 2005).
Serum paraoxonase/arylesterase 1, PON 1 (Aromatic esterase 1) (A-esterase 1) (Serum aryldialkylphosphatase 1)
|1.A.61.1.1||Chain F or gamma-peptide (44aas; 1TMS), membrane active domain (Bong et al., 1999)||
Flock House virus (FHV) capsid protein-α of 407 aas; Its C-terminal 44 aas comprise a lytic peptide, one of the γ-peptides that inserts into endomembranes forming pores. Capsid protein alpha self-assembles to form an icosahedral procapsid with a T=3 symmetry, about 30 nm in diameter, and consisting of 60 capsid proteins trimers. 240 calcium ions are incorporated per capsid during assembly. The capsid encapsulates the two genomic RNAs. Capsid maturation occurs via autoproteolytic cleavage of capsid protein alpha, generating capsid protein beta and the membrane-active peptide gamma. Peptide γ is a membrane-permeabilizing peptide produced during virus maturation, thereby creating the infectious virion. After endocytosis into the host cell, peptide gamma is exposed in endosomes, where it permeabilizes the endosomal membrane, facilitating translocation of viral capsid or RNA into the cytoplasm. Nangia et al. 2019 shed light on the actions of varied forms of the FHV lytic peptide including membrane insertion, trans-membrane stability, peptide oligomerization, water permeation activity and dynamic pore formation.
TRICB1 and TRICB2 of 313 aas and 295 aas, respectively. Yang et al. 2016 presented the structures of TRIC-B1 and TRIC-B2 channels from Caenorhabditis elegans in complex with endogenous phosphatidylinositol-4,5-biphosphate (PtdIns(4,5)P2, also known as PIP2) lipid molecules. The TRIC-B1/B2 proteins and PIP2 assemble into a symmetrical homotrimeric complex. Each monomer contains an hourglass-shaped hydrophilic por within a seven-transmembrane-helix domain. Structural and functional analyses revealed the central role of PIP2 in stabilizing the cytoplasmic gate of the ion permeation pathway and showed a marked Ca2+-induced conformational change in a cytoplasmic loop above the gate. A mechanistic model was proposed to account for the complex gating mechanism of TRIC channels (Yang et al. 2016).
Archaeal TRIC family homologue of 205 aas and 7 TMSs. In animals, Ca2+ release from the sarcoplasmic reticulum (SR) or endoplasmic reticulum (ER) is crucial for muscle contraction, cell growth, apoptosis, learning and memory. The eukaryotic TRIC channels are cation channels balancing the SR and ER membrane potentials, and are implicated in Ca2+ signaling and homeostasis. Kasuya et al. 2016 presented crystal structures of two prokaryotic TRIC channels in the closed state and conducted structure-based functional analyses of these channels. Each trimer subunit consists of seven TMSs with two inverted 3 TMS repeats (Silverio and Saier 2011). The electrophysiological, biochemical and biophysical analyses revealed that TRIC channels possess an ion-conducting pore within each subunit, and that trimer formation contributes to the stability of the protein. The symmetrically related TMS2 and TMS5 helices are kinked at conserved glycine clusters, and these kinks are important for channel activity. The kinks in TMS2 and TMS5 generate lateral fenestrations at each subunit interface that are occupied by lipid molecules (Kasuya et al. 2016). TRIC channels are involved in K+ uptake in prokaryotes, and have ion-conducting pores contained within each monomer. In a 2.2-Å resolution K+-bound structure, ion/water densities have been resolved inside the pore (PDB# 5H35) (Su et al. 2017). At the central region, a filter-like structure is shaped by the kinks on the second and fifth transmembrane helices and two nearby phenylalanine residues. Below the filter, the cytoplasmic vestibule is occluded by a plug-like motif attached to an array of pore-lining charged residues (Kasuya et al. 2016). The asymmetric filter-like structure at the pore center of SsTRIC may serve as a basis for the channel to bind and select monovalent cations, K+ and Na+ (Ou et al. 2017).
Bactericidal pore-forming pardaxin (Pa4) permeabilized both lipid and lipopolysaccharide membranes. Five paralogues are known: Pa1, 2, 3, 4, and 5, all nearly identical to each other. The 3-d structure of Pa4 is known. It forms a helix-turn-helix conformation resembling a horseshoe (Bhunia et al., 2010).
ER membrane protein complex subunit 5, Emc5 of 141 aas and 2 TMSs. The EMC seems to be required for efficient folding of proteins in the endoplasmic reticulum (ER) and also for insertion of integral membrane proteins into the ER membrane (Guna et al. 2018).
ATP-gated P2X3 receptor. Tyr-37 stabilizes desensitized states and restricts calcium permeability (Jindrichova et al., 2011). Exhibits "high affinity desensitization" but slow reactivation from the desensitized state (Giniatullin and Nistri 2013). An endogenous regulator of P2X3 in bladder is the Pirt protein (TC#8.A.64.1.1) Gao et al. 2015). X-ray crystal structures of the human P2X3 receptor in apo/resting, agonist-bound/open-pore, agonist-bound/closed-pore/desensitized and antagonist-bound/closed states have been determined (Mansoor et al. 2016). The open state structure harbours an intracellular motif termed the 'cytoplasmic cap', which stabilizes the open state of the ion channel pore and creates lateral, phospholipid-lined cytoplasmic fenestrations for water and ion egress.
The p2X purinoreceptor 4a of 389 aas and 2 TMSs, P2X4a of 388 aas and 2 TMSs. A splice variant of 361 aas also exists and may form heterotrimers with P2RX4a (Townsend-Nicholson et al. 1999). Plays a role in alcoholism (Franklin et al. 2014). P2RX4 deficiency alleviates allergen-induced airway inflamation (Zech et al. 2016).
Purinorepector, P2X7 (P2RX7) of 595 aas and 2 TMSs. The crystal structure in complex with a series of allosteric antagonists were published, giving insight into the mechanism of channel antagonism (Pasqualetto et al. 2018). A P2RX7 single nucleotide polymorphism haplotype promotes exon 7 and 8 skipping and disrupts receptor function (Skarratt et al. 2020).
The MerF mercuric ion uptake transporter of 81 aas and 2 TMSs. The NMR structure of the helix-loop-helix core domain of MerF has been determined with a backbone RMSD of 0.58 Å (Howell et al. 2005). Moreover, the fold of this polypeptide demonstrates that the two vicinal pairs of cysteine residues, shown to be involved in the transport of Hg++ across the membrane, are exposed to the cytoplasm. This finding differs from earlier structural and mechanistic models that were based primarily on the somewhat atypical hydropathy plot for MerF and related transport proteins (Howell et al. 2005). The apo state positions one of the cysteine pairs closer to the periplasmic side of the membrane, while in the bound state, the same pair approaches the cytoplasmic side (Hwang et al. 2019). This is consistent with the functional requirement of accepting Hg2+ from the periplasmic space, sequestering it on acceptance, and transferring it to the cytoplasm. Conformational changes in the TMSs facilitate the functional interaction of the two cysteine pairs. Free-energy calculations provide a barrier of 16 kcal/mol for the association of the periplasmic Hg2+-bound protein, MerP, with MerF, and 7 kcal/mol for the subsequent association of MerF's two cysteine pairs (Hwang et al. 2019).
Piezo1 (Fam38a) of 2547 aas and ~ 38 TMSs. The three-bladed propeller-like cryoEM structure and its mechanotransduction components are known (Zhao et al. 2018). There are nine repeat units consisting of four transmembrane helices, each of which is termed a transmembrane helical unit (THU). These assemble into a highly curved blade-like structure. The last transmembrane helix encloses a hydrophobic pore, followed by three intracellular fenestration sites and side portals that contain pore-property-determining residues. The central region forms a 90 Å-long intracellular beam-like structure, which undergoes a lever-like motion to connect the THUs to the pore via the interfaces of the C-terminal domain, the anchor-resembling domain and the outer helix. Deleting extracellular loops in the distal THUs or mutating single residues in the beam impairs the mechanical activation of Piezo1. Thus, Piezo1 possesses a 38-transmembrane-helix topology with mechanotransduction components that enable a lever-like mechanogating mechanism (Zhao et al. 2018). The Piezo1 pore remains fully open if only one of the three subunits is activate, for example by binding the agonist, Yoda1 (Lacroix et al. 2018). Piezo1 mediates endothelial atherogenic inflammatory responses via regulation of YAP/TAZ activation (Yang et al. 2021).
Magnesium transporter, MagT1; Ost3_Ost6; SLC58A1 (Goytain and Quamme, 2005; Schmitz et al., 2007; Zhou and Clapham, 2009; Gyimesi and Hediger 2022). As of 2018, the function of this protein as a Mg2+ transporter was under debate (Schäffers et al. 2018). This protein is of 335 aas with 5 TMSs in a 1 (N-terminal) + 2 + 2 (C-terninal) TMS arrangement.
Mg2+ transporter; also called Tumor suppressor candidate 3 isoform a, Tusc3a (69% identity with MagT1) (Zhou and Clapham, 2009). It can transport Mg2+, Fe2+, Cu2+ and MnFe (Gyimesi and Hediger 2022).
Glycosyl transferase, Ost3 of 350 aas and 4 TMSs. This protein is a subunit of the yeast oligosaccharyltransferase complex involved in N-glycosylation (Wild et al. 2018). It is not the catalytic subunit (see TC# 9.B.142.3.14).
Oligosaccharidyl transferase, OstC of 149 aas and 3 TMSs in a 1 + 2 TMS arrangement. It may be involved in sperm membrane integrity (Illa et al. 2021). OSTA and OSTC are useful self-assessment tools for osteoporosis detection (Bui et al. 2022).
MCU of 488 aas and 2 TMSs. The 3.8 Å cryoEM structure has been solved (Nguyen et al. 2018). The channel is a homotetramer with two-fold symmetry in its amino-terminal domain (NTD) that adopts a structure similar to that of human MCU. The NTD assembles as a dimer of dimers to form a tetrameric ring that connects to the transmembrane domain through an elongated coiled-coil domain. The ion-conducting pore domain maintains four-fold symmetry, with the selectivity filter positioned at the start of the pore-forming TM2 helix. The aspartate and glutamate sidechains of the conserved DIME motif are oriented towards the central axis and separated by one helical turn (Nguyen et al. 2018).
Slime mold MCU homologue of 275 aas and 2 TMSs. The structure of the N-terminal domain (NTD) has been solved at 1.7 A resolution (Yuan et al. 2020). The oligomeric DdMCU-NTD contains four helices and two strands arranged in a fold that is completely different from the known structures of other MCU-NTD homologues. This domain may regulate channel activity (Yuan et al. 2020).
Fungal MCU homologue of 493 aas and 2 TMS. The cryo-electron microscopy structure of the full-length MCU to an overall resolution of ~3.7 Å has been determined (Yoo et al. 2018). The structure reveals a tetrameric architecture, with the soluble and transmembrane domains adopting different symmetric arrangements within the channel. The conserved W-D-Phi-Phi-E-P-V-T-Y sequence motif of the MCU pore forms a selectivity filter comprising two acidic rings separated by one helical turn along the central axis of the channel pore (Yoo et al. 2018).
Endosomal/Lysosomal K+ channel of 504 aas and 12 TMSs with two 6 TMS repeat units, KEL or TMEM175 (Cang et al. 2015). A mutation in the encoding gene is associated with Parkinson's disease (Jing et al. 2015). It forms a potassium-permeable leak-like channel, which regulates lumenal pH stability and is required for autophagosome-lysosome fusion (Lee et al. 2017). TMEM175 plays a direct and critical role in lysosomal and mitochondrial functions as well as Parkinson's Disease (PD) pathogenesis (Jinn et al. 2017). The 3-D structures of the open and closed channels are known (Oh et al. 2020). Coding variants in TMEM175 which increase the propensity for Parkinson's disease, are likely to be responsible for the association in the TMEM175/GAK/DGKQ locus, which could be mediated by affecting glucocerebrosidase activity (Krohn et al. 2020). It constitutes the major lysosomal potassium channel (Lee et al. 2017) and is the pore-forming subunit of the LysoK(GF) complex, a complex activated by extracellular growth factors (Wie et al. 2021). The LysoK(GF) complex is composed of TMEM175 and AKT (AKT1, AKT2 or AKT3). In the complex, the TMEM175 channel is opened by conformational changes in AKT, leading to its activation (Wie et al. 2021). The lysoK(GF) complex is required to protect neurons against stress-induced damage. Hydrophobic gating, exhibited by TMEM175, is the process by which a nanopore may spontaneously dewet to form a "vapor lock" if the pore is sufficiently hydrophobic and/or narrow. This occurs without steric occlusion of the pore (Lynch et al. 2021). In addition to lysosomes, protein kinase B (PKB)-dependent regulation also influences TMEM175 currents in the plasma membrane (Pergel et al. 2021). Large-conductance Ca2+-activated K+ channel (BK) and transmembrane protein 175 (TMEM175) are the only two K+ channels known in lysosomes (Wu et al. 2022). Differential ion dehydration energetics explains selectivity in the non-canonical lysosomal K+channel, TMEM175 (Oh et al. 2022).
TMEM175 lysosomal K+ channel of 203 aas and 6 TMSs. It's 3-d structure reveals a novel tetrameric arrangement (Lee et al. 2017). All six transmembrane helices of CmTMEM175 are tightly packed within each subunit without undergoing domain swapping. The highly conserved TM1 helix acts as the pore-lining inner helix, creating an hourglass-shaped ion permeation pathway in the channel tetramer. Three layers of hydrophobic residues on the carboxy-terminal half of the TM1 helices form a bottleneck along the ion conduction pathway and serve as the selectivity filter of the channel. Mutagenesis analysis suggests that the first layer of the highly conserved isoleucine residues in the filter is primarily responsible for channel selectivity (Lee et al. 2017).
Glycerol facilitator, GlpF. Transports various polyols with decreasing rates as size increases (Heller et al. 1980); also transports arsenite (As(III) and antimonite (Sb(III)) (Meng et al., 2004). Oligomerization may play a role in determining the rate of transport (Klein et al. 2019).
Aquaporin TIP2-1 (Delta-tonoplast intrinsic protein) (Delta-TIP) (Tonoplast intrinsic protein 2-1) (AtTIP2;1) (Daniels et al. 1996). Transports water and ammonia, and can be activated by mercury (Kirscht et al. 2016). The 3-d structure is known to 1.2Å resolution (Kirscht et al. 2016). It may participate in vacuolar compartmentation and detoxification of ammonium.
Nodulin-26 aquaporin and glycerol facilitator, NIP (de Paula Santos Martins et al. 2015). Transports NH3 5-fold better than water in Hg2+-sensitive fashion (Hwang et al., 2010).
|1.A.8.13.1||MIP family homologue||
Hg2+-inhibitable aquaporin, AqpM (transports both water and glycerol as well as CO2) (Kozono et al., 2003; Araya-Secchi et al., 2011). Its 3-d structure has been determined to 1.7 Å. In AqpM, isoleucine replaces a key histidine residue found in the lumen of water channels, which becomes a glycine residue in aquaglyceroporins. As a result of this and other side-chain substituents in the walls of the channel, the channel is intermediate in size and exhibits differentially tuned electrostatics when compared with the other subfamilies (Lee et al. 2005).
Aquaporin Z water channel (aqpZ gene expression is under sigma S control; induced at the onset of stationary phase) (Mallo and Ashby, 2006). The high resolution 3-d structure is available (PDB 1RC2) revealing two re-entrant coil-helix domains from the selectivity filter (Savage et al. 2003). Coupled mutations enabled glycerol transport (Ping et al. 2018).
Aquaporin, Aqy1 (PIP2-7 7). The subangstron (0.88Å) structure is available (Kosinska Eriksson et al. 2013). the H-bond donor interactions of the NPA motif''s asparagine residues to passing water molecules are revealed. A polarized water-water H-bond configuration is observed within the channel. Four selectivity filter water positions are too closely spaced to be simultaneously occupied. Strongly correlated movements break the connectivity of selectivity filter water molecules to other water molecules within the channel, thereby preventing proton transport via a Grotthuss mechanism.
Aquaporin 1 (CO2-, O2-, H202- and nitrous oxide-permeable and water-selective) (Zwiazek et al. 2017; Varadaraj and Kumari 2020). Aquaporin-1 tunes pain perception by interacting with Na(v)1.8 Na+ channels in dorsal root ganglion neurons (Zhang and Verkman, 2010). It is upregulated in skeletal muscle in muscular dystrophy (Au et al. 2008). AQP1 has been reported to first insert as a four-helical intermediate, where helices 2 and 4 are not inserted into the membrane. In a second step this intermediate is folded into a six-helical topology. During this process, the orientation of the third helix is inverted, and it can shift out the membrane core (Virkki et al. 2014). Its synthesis is regluated by Kruppel-like factor 2 (KLF2; Q9Y5W3) which also interacts directly with Aqp1 (Fontijn et al. 2015). A nanoscale ion pump has been derived artificially from Aqp1 (Decker et al. 2017). Mammalian AQP1 channels, activated by cyclic GMP, can carry non-selective monovalent cation currents, selectively blocked by arylsulfonamide compounds AqB007 (IC50 170 muM) and AqB011 (IC50 14 muM). Loop D-domain amino acids activate the channel for ion coductance (Kourghi et al. 2018). Water flux through AQP1s is inhibited by 1 - 10 mμM acetozolaminde (Gao et al. 2006). Aqp1 transports reactive oxygen and nitrogen species (RONS) which may induce oxidative stress in the cell interior. These RONS include both hydrophilic (H2O2 and OH) and hydrophobic (NO2 and NO) RONS (Yusupov et al. 2019). The position of the Arg-195 side chain shows a number of interactions for loop C (Dingwell et al. 2019). AQP1 play vital roles in cellular homeostasis at rest and during endurance running exercises (Rivera and Fahey 2019). AQP1 and AQP4 activities correlate with the severity of hydrocephalus induced by subarachnoid haemorrhage (Long et al. 2019). AQPs are related to osmoregulation and play a critical role in maturation, cryo-stability and motility activation in boar spermatozoa (Delgado-Bermúdez et al. 2019). In foetal kidney, AQP1 expression appeared in the apical and basolateral parts of cells, lining the proximal convoluted tubules and the descending limb of Henle's loop, then in the tubule pole of Bowman's capsule (Ráduly et al. 2019). Inhibition of aquaporin-1 prevents myocardial remodeling by blocking the transmembrane transport of hydrogen peroxide (Montiel et al. 2020). AQP1 Is up-regulated by hypoxia and leads to increased cell water permeability, motility, and migration in neuroblastoma (Huo et al. 2021). Aqp1 allows the transport of CO2 across membranes (Michenkova et al. 2021). Down-regulation of aquaporin-1 mediates a microglial phenotype switch affecting glioma growth (Hu et al. 2020). AQP1 expression is down-regulated following repeated exposure of UVB via MEK/ERK activation pathways, and this AQP1 reduction leads to changes of physiological functions in dermal fibroblasts (Kim et al. 2020). AQP1 and AQP7 are differentially regulated under hyperosmotic stress conditions, and AQP1 acts as an osmotic stress sensor and response factor (Aggeli et al. 2021).
The lens fiber MIP aquaporin (Aqp0) of B. taurus (forms membrane junctions in vivo and double layered crystals in vitro that resemble the in vivo junctions). The water pore is closed in the in vitro structure (Gonen et al., 2004b). It interacts directly with the intracellular loop of connexin 45.6 via its C-terminal extension (Yu et al., 2005). Forms human cataract lens membranes (Buzhynskyy et al., 2007; Yang et al., 2011). A mutation that causes congenital dominant lens cataracts has been identified (Varadaraj et al. 2008). AqpO catalyzes Zn2+-modulated water permeability as a cooperative tetramer (Nemeth-Cahalan et al., 2007). It transports ascorbic acid (Nakazawa et al., 2011). The Detergent organization around solubilized aquaporin-0 using Small Angle X-ray Scattering has been reported (Berthaud et al., 2012). Aquaporin 0 (AQP0) in the eye lens is truncated by proteolytic cleavage during lens maturation. This truncated AQP0 is no longer a water channel (Berthaud et al. 2015). A mutation that causes congenital dominant lens cataracts has been identified (Varadaraj et al. 2008). Cataractogenesis in MIP mutants are probably caused by defects in MIP gene expression in mice (Takahashi et al. 2017). This may be caused by the ability of Aqp0 (as well as Aqp1 and Aqp5) to transport hydrogen peroxide (H2O2) which can cause cataracts (Varadaraj and Kumari 2020). An automated data processing and analysis pipeline for transmembrane proteins including Aqp0 in detergent solutions has been presented (Molodenskiy et al. 2020). EphA2 is required for normal Cx50 localization to the cell membrane, and conductance of lens fiber cells requires normal Eph-ephrin signaling and water channel (Aqp0) localization (Cheng et al. 2021). The local curvature of cellular membranes acts as a driving force for the targeting of membrane-associated proteins to specific membrane domains, as well as a sorting mechanism for transmembrane proteins, as demonstrated for Aqp0; AQP0 causes small negative curvature (Kluge et al. 2022).
Aqp6 aquaporin (also transports NO3- and other anions at acidic pH or in the presence of Hg2+) (Ikeda et al., 2002). AQP6 flicker rapidly between closed and open states. Two well conserved glycine residues: Gly-57 in TMS 2 and Gly-173 in TMS 5 reside at the contact point where the two helices cross. Mammalian orthologs of AQP6 have an asparagine residue (Asn-60) at the position corresponding to Gly-57 in Aqp6. Liu et al. 2005 showed that a single residue substitution (N60G in rat AQP6) eliminates anion permeability but increases water permeability.
Aquaporin-4 (AQP4) is the major water channel in the central nervous system and plays an important role in the brain's water balance, including edema formation and clearance. There are 6 splice variants; the shorter ones assemble into functional, tetrameric square arrays; the longer is palmitoylated on N-terminal cysteyl residues) (Suzuki et al., 2008). The longest, Aqp4e, has a novel N-terminal domain and forms a water channel in the plasma membrane although various shorter variants don't (Moe et al., 2008). AQP4, like AQP0 (1.A.8.8.2), forms water channels but also forms adhesive junctions (Engel et al., 2008) (causes cytotoxic brain swelling in mice (Yang et al., 2008)) Mice lacking Aqp4 have impaired olfactions (Lu et al., 2008). Aqp4 is down regulated in skeletal muscle in muscular dystrophy (Au et al. 2008). The crystal structure is known to 2.8 Å resolution (Tani et al., 2009). The structure reveals 8 water molecules in each of the four channels, supporting a hydrogen-bond isolation mechanism and explains its fast and selective water conduction and proton exclusion (Tani et al., 2009; Cui and Bastien, 2011). It is an important antigen in Neuromyelitis optica (NMO) patients (Kalluri et al., 2011). A connection has been made between AQP4-mediated fluid accumulation and post traumatic syringomyelia (Hemley et al. 2013). AQP4 has increased water permeability at low pH, and His95 is the pH-dependent gate (Kaptan et al. 2015). Also transports NH3 but not NH4+ (Assentoft et al. 2016). Cerebellar damage following status epilepticus involves down regulation of AQP4 expression (Tang et al. 2017). SUR1-TRPM4 and AQP4 form a complex to increase bulk water influx during astrocyte swelling (Stokum et al. 2017). A mutation, S111T, causes intellectual disability, hearing loss, and progressive gait dysfunction (Berland et al. 2018). As in humans, the chicken ortholog, Aqp4, is found in brain > kidney > stomach (Ramírez-Lorca et al. 2006). A Molecular Dynamics Investigation on Human AQP4 has been published (Marracino et al. 2018). AQP1 and AQP4 activities correlate with the severity of hydrocephalus induced by subarachnoid haemorrhage (Long et al. 2019). Di-lysine motif-like sequences formed by deleting the C-terminal domain of aquaporin-4 prevent its trafficking to the plasma membrane (Chau et al. 2021). Kidins220 deficiency causes ventriculomegaly via SNX27-retromer-dependent AQP4 degradation (Del Puerto et al. 2021). AQP4 expression is upregulated in cells exposed to dexamethasone, and SUMOylation [Small ubiquitin-like modifiers (SUMOs)] may participate in this regulation (Zhang et al. 2020). Simultaneous calmodulin binding to the N- and C-terminal cytoplasmic domains of aquaporin 4 has been demonstrated (Ishida et al. 2021). Aqp-4 plays a role in secondary pathological processes (spinal cord edema, glial scar formation, and inflammatory response) after spinal cord injury, SCI. Loss of AQP-4 is associated with reduced spinal edema and improved prognosis after SCI in mice, and downregulation of AQP-4 reduces glial scar formation and the inflammatory response after SCI (Pan et al. 2022).
Vasopressin-sensitive aquaporin-2 (Aqp2) in the apical membrane of the renal collecting duct (Fenton et al., 2008). Controls cell volume and thereby influences cell proliferation (Di Giusto et al. 2012). It plays a key role in concentrating urine. Water reabsorption is regulated by AQP2 trafficking between intracellular storage vesicles and the apical membrane. This process is tightly controlled by the pituitary hormone arginine vasopressin, and defective trafficking results in nephrogenic diabetes insipidus (NDI). The crystal structure of Aqp2 has been solved to 2.75Å (Frick et al. 2014). In terrestrial vertebrates, AQP2 function is generally regulated by arginine-vasopressin to accomplish key functions in osmoregulation such as the maintenance of body water homeostasis by a cyclic AMP-independent mechanism (Olesen and Fenton 2017; Martos-Sitcha et al. 2015). AQP2 is expressed in the anterior vaginal wall and fibroblasts, and regulates the expression level of collagen I/III i, suggesting that AQP2 is associated with the pathogenesis of stress urinary incontinence through collagen metabolism during ECM remodeling (Zhang et al. 2017). As in humans, the chicken ortholog, Aqp2, is found only in the kidney (Ramírez-Lorca et al. 2006). AQP2 is critical in regulating urine concentrating ability. The expression and function of AQP2 are regulated by a series of transcriptional factors and post-transcriptional phosphorylation, ubiquitination, and glycosylation (He and Yang 2019). Mutation or functional deficiency of AQP2 leads to severe nephrogenic diabetes insipidus, and inhibition of various aquaporins leads to many water-related diseases such as, edema, cardiac arrest, and stroke. Maroli et al. 2019 reported on the molecular mechanisms of mycotoxin (citrinin, ochratoxin-A, and T-2 mycotoxin) inhibition of AQP2 and arginine vasopressin receptor 2 (AVPR2). Aquaporin-2 mutations cause Nephrogenic diabetes insipidus (Li et al. 2021). Meniere's disease is affected by dexamethasone which is a direct modulator of AQP2. The molecular mechanisms involved in dexamethasone binding to and its regulatory action upon AQP2 function have been described (Mom et al. 2022).
Aquaporin 5 (x-ray structure at 2.0 Å resolution (PDB# 3D9S) is available) (Horsefield et al., 2008). Aqp5 is a marker for proliferation and migration of human breast cancer cells (Jung et al., 2011). Plays a role in chronic obstructive pulmonary diseases (COPD) (Zhao et al. 2014). Its expression is regulated by androgens (Pust et al. 2015). As in humans, the chicken ortholog, Aqp5, is found in the intestine, the jejunum, ileum and colon (Ramírez-Lorca et al. 2006). Proteomic analyses of the ocular lens revealed palmitoylation (Wang and Schey 2018). Aquaporin 5 expression correlates with tumor multiplicity and vascular invasion in hepatocellular carcinoma (Vireak et al. 2019). The ability of Aqp5 (as well as Aqp0 and Aqp1) to transport hydrogen peroxide (H2O2) may cause cataracts in the eye (Varadaraj and Kumari 2020). AQP3 and AQP5 play important but different roles in spermatogenesis and sperm maturation in dogs (Mirabella et al. 2021). The up-regulation of AQP1, AQP3 and AQP5 in skin during summer season indicates roles in thermoregulation (Debbarma et al. 2020).
Aquaglycerolporin, Aqp (high permeability to ammonium, methylamine, glycerol and water) (Beitz et al., 2004) NH4+/NH3+CH3/glycerol/water transporter (Zeuthen et al., 2006).
Aquaporin 10 of 301 aas and 6 TMSs. Cell- and tissue-specific expression of AQP-0, AQP-3, and AQP-10 in the testis, efferent ducts, and epididymis has been demonstrated (Hermo et al. 2019). It is also present in keratinocytes and the stratum corneum (Jungersted et al. 2013).
Glycerol/water/urea/arsenic trioxide-transporting channel protein, aqaporin 7 or Aqp7, but water is a poor substrate (Palmgren et al. 2017). Present in adipose tissue where it allows glycerol efflux. Defects result in increased accumulation of triglycerides, obesity and adult onset (type 2) diabetes (Lebeck 2014). It may be a drug target for anti-type 2 diabetes (Méndez-Giménez et al. 2018). AQP-7- and AQP-9-mediated glycerol transport in tanycyte cells may be under hormonal control to use glycerol as an energy source during the mouse estrus cycle (Yaba et al. 2017). It may also influence whole body energy metabolism (Iena and Lebeck 2018).
The human calcium homeostasis modulator protein 2, CALHM2 or FAM16B, of 323 aas and 4 or 5 TMSs. The structures and gating mechanism of CALHM2 have been reported (Choi et al. 2019). Cryo-EM structures in the Ca2+-free active or open state and in the ruthenium red (RUR)-bound inhibited state, have been solved at 2.7 Å resolution (see also Syrjanen et al. 2020 and Demura et al. 2020. Purified CALHM2 channels form both gap junctions and undecameric hemichannels. The protomer shows a mirrored arrangement of the TMSs (helices S1-S4) relative to other channels with a similar topology, such as connexins, innexins and volume-regulated anion channels. Upon binding to RUR, a contracted pore with notable conformational changes of the pore-lining helix S1 was observed, which swings nearly 60 degrees towards the pore axis from a vertical to a lifted position. Possibly a two-section gating mechanism is operative in which the S1 helix coarsely adjusts, and the N-terminal helix fine-tunes, the pore size (Choi et al. 2019). The Kilifish CALHM1 octameric structure reveals that the N-terminal helix forms the constriction site at the channel pore in the open state and modulates the ATP conductance. The CALHM2 undecamer and CLHM-1 nonamer structures show different oligomeric stoichiometries among CALHM homologs. The cryo-EM structures of a chimeric construct revealed that the intersubunit interactions in the transmembrane region and the TMS-intracellular domain linker define the oligomeric stoichiometry (Demura et al. 2020).
Calcium homeostasis modulator 1 (CALHM1 or FAM26C) is the pore-forming subunit of an ion channel that mediates extracellular Ca2+ regulation of neuronal excitability (Ma et al. 2015). CALHM1 (CALHM-1 or CLHM-1) is of 329 aas and exhibits 4 or 5 TMSs. This protein forms a protein complex, assembling into voltage-gated, Ca2+-sensitive, nonselective channels. These complexes contain an ion-conduction pore sufficiently wide to permit the passing of ATP molecules serving as neurotransmitters. Calcium homeostasis modulators (CALHMs/CLHMs) comprise a family of pore-forming protein complexes assembling into voltage-gated, Ca2+-sensitive, nonselective channels. These complexes contain an ion-conduction pore sufficiently wide to permit the passing of ATP molecules serving as neurotransmitters. Yang et al. 2020 and Demura et al. 2020 presented the structure of the Caenorhabditis elegans CLHM1 channel (1.A.84.1.4) in its open state, solved through single-particle cryo-EM at 3.7Å resolution. The transmembrane region of the channel structure of the dominant class shows an assembly of tenfold rotational symmetry in one layer, and its cytoplasmic region is involved in additional twofold symmetrical packing in a tail-to-tail manner. A series of amino acyl residues are critical for the regulation of the channel. presented the structure of the channel in its open state, solved through single-particle cryo-EM at 3.7Å resolution. The transmembrane region of the channel shows an assembly of tenfold rotational symmetry in one layer, and its cytoplasmic region is involved in additional twofold symmetrical packing in a tail-to-tail manner. A series of amino acyl residues are critical for regulation of the channel (Calcium homeostasis modulators (CALHMs/CLHMs) comprise a family of pore-forming protein complexes assembling into voltage-gated, Ca2+-sensitive, nonselective channels. These complexes contain an ion-conduction pore sufficiently wide to permit the passing of ATP molecules serving as neurotransmitters. Yang et al. 2020 presented the structure of the Caenorhabditis elegans CLHM1 channel (1.A.84.1.4) in its open state, solved through single-particle cryo-EM at 3.7Å resolution. The transmembrane region of the channel structure of the dominant class shows an assembly of tenfold rotational symmetry in one layer, and its cytoplasmic region is involved in additional twofold symmetrical packing in a tail-to-tail manner. A series of amino acyl residues are critical for regulation of the channel (Yang et al. 2020).
CALHM4 or FAM26D of 314 aas and 4 TMSs
The CALHM6 or FAM26F channel protein of 315 aas and probably 5 TMSs. FAM26F (family with sequence similarity 26, member F) plays an important role in diverse immune responses (Malik et al. 2016).
Polyprotein of 2333 aas (includes the viroporin peptide, NS2B). Viroporin activity for the NS2B protein has been demonstrated (Ao et al. 2015).
Human rhinovirus 1A 2B protein of 2157 aas
The Viroporin, protein 2B, of 154 aas and 3 TMSs where TMS 2 provides the channel activity. Transports cations, Ca2+ and small molecules (Gladue et al. 2018). Present within the Polyprotein of 2332 aas.
Protein BRASSINOSTEROID INSENSITIVE 1, BRI1, of 1196 aas and 2 or 3 TMSs. Receptor with kinase activity
acting on both serine/threonine- and tyrosine-containing substrates. In response to brassinosteroid binding, it regulates a signaling cascade
involved in plant development, including expression of light- and
stress-regulated genes, promotion of cell elongation, normal leaf and
chloroplast senescence, and flowering. It binds brassinolide, and less
effectively, castasterone (Oh et al. 2009).
The phytosulfokine receptor, PSKR1, of 1008 aas with both a serine/threonine-protein kinase activity and a guanylate cyclase activity (Kwezi et al. 2011). In response to phytosulfokine binding, it activates a signaling cascade involved in plant cell differentiation, organogenesis, somatic embryogenesis, cellular proliferation and plant growth. It is also involved in plant immunity, with antagonistic effects on bacterial and fungal resistances (Mosher et al. 2013). CNGC17 and AHAs form a functional cation-translocating unit that is activated by PSKR1/BAK1 and possibly other BAK1/RLK complexes (Ladwig et al. 2015). PSKR is a transmembrane LRR-RLK family protein with a binding site for the small signalling peptide, phytosulfokine (PSK). There are 15 members in rice (Orysa sativa), induced under different conditions in different plant tissues (Nagar et al. 2020). PSKR1 and PSYR1 mediate a signaling pathway in response to two distinct ligands, which redundantly contribute to cellular proliferation and plant growth (Amano et al. 2007).
Nicotinic acetylcholine-activated cation-selective channel, pentameric α2βγδ (immature muscle) nα2βγδ (mature muscle). A combination of symmetric and asymmetric motions opens the gate, and the asymmetric motion involves tilting of the TM2 helices (Szarecka et al. 2007). Acetylcholine receptor δ subunit mutations underlie a fast-channel myasthenic syndrome and arthrogryposis multiplex congenita (Brownlow et al., 2001; Webster et al., 2012). Residues in TMS2 and the cytoplasmic loop linking TMSs 3 and 4 influence conductance, selectivity, gating and desensitization (Peters et al., 2010). nAChR and TRPC channel proteins (1.A.4) mediate nicotine addiction in many animals from humans to worms (Feng et al., 2006). Cholesterol recognition motifs in transmembrane domains of the human nicotinic acetylcholine receptor have been identified (Baier et al., 2011). Allosteric modulators of the α4β2 subtype of neuronal nicotinic acetylcholine receptors, the dominant type in the brain, are numerous (Pandya and Yakel, 2011). α2β2 and α4β2 nicotinic acetylcholine receptors are inhibited by the β-amyloid(1-42) peptide (Pandya and Yakel, 2011b). The A272E mutation in the alpha7 subunit gives rise to spinosad insensitivity without affecting activation by acetylcholine (Puinean et al. 2012). Inhibited by general anaesthetics (Nury et al., 2011). The X-ray crystal structures of the extracellular domain of the monomeric state of human neuronal alpha9 nicotinic acetylcholine receptor (nAChR) and of its complexes with the antagonists methyllycaconitine and alpha-bungarotoxin have been determined at resolutions of 1.8 A, 1.7 A and 2.7 A, respectively (Zouridakis et al. 2014). Structurally similar allosteric modulators of α7 nAChR exhibit five different pharmacological effects (Gill-Thind et al. 2015). Mutations causing slow-channel myasthenia show that a valine ring in the channel is optimized for stabilizing gating (Shen et al. 2016). Quinoline derivatives act as agonists or antagonists depending on the type and subunit (Manetti et al. 2016). Conformational changes stabilize a twisted extracellular domain to promote transmembrane helix tilting, gate dilation, and the formation of a ""bubble"" that collapses to initiate ion conduction (Gupta et al. 2016). A high-affinity cholesterol-binding domain has been proposed for this and other ligand-gated ion channels (Di Scala et al. 2017). Positive allosteric modulators have been identified (Deba et al. 2018). Menthol stereoisomers exhibit fifferent effects on alpha4beta2 nAChR upregulation and dopamine neuron spontaneous firing (Henderson et al. 2019). Corticosteroids exert direct inhibitory action on the muscle-type AChR (Dworakowska et al. 2018). Both deltaL273F and epsilonL269F mutations impair channel gating by disrupting hydrophobic interactions with neighboring alpha-subunits. Differences in the extent of impairment of channel gating in delta and epsilon mutant receptors suggest unequal contributions of epsilon/alpha and delta/alpha subunit pairs to gating efficiency (Shen et al. 2019). Diffusion dynamics of the gangliosides, GM1s and AChRs is uniformly affected by the intracellular ATP level of a living muscle cell (He et al. 2020). M4, the outermost helix, is involved in opening of the alpha4beta2 nACh receptor (Mesoy and Lummis 2020). Cholesterol modulates the organization of the gammaM4 transmembrane domain of the muscle nicotinic acetylcholine receptor (de Almeida et al. 2004). Cryo-EM images showed that cholesterol segregates preferentially around the constituent ion channel of the receptor, interacting with specific sites in both leaflets of the bilayer. Cholesterol forms microdomains - bridges of rigid sterol groups that link one channel to the next (Unwin 2021). Desnitro-imidacloprid (DN-IMI) functionally affects human neurons similarly to the well-established neurotoxicant nicotine by triggering activation of alpha7 and several non-alpha7 nAChRs (Loser et al. 2021).
Acetyl choline binding protein, AchBP, of 229 aas, corresponding to the N-terminal extracellular domain of AcChRs. The crystal structure is known (Lin et al. 2016). It modulates synaptic transmission (Smit et al. 2001). This soluble protein has enhanced our understanding of the requirements for agonistic and antagonistic interactions at the ligand recognition site of the nAChRs. Camacho-Hernandez and Taylor 2020 have reviewed the potential and limitations of soluble surrogates, termed the AChBP family, in drug development.
The α4β2 nicotinic acetylcholine receptor. The NMR structure of the transmembrane domain and the multiple anaesthetic binding sites are known (Bondarenko et al., 2012). Mutations cause autosomal dominant nocturnal frontal lobe epilepsy (ADNFLE; Díaz-Otero et al. 2000).
The alpha7 (α-7) nicotinic acetylcholine receptor (alpha-7 nAcChR) of 502 aas is encoded by the CHRNA7 gene. Acetylcholine binding induces conformational changes that result in open channel formation; opening is blocked by α-bungarotoxin. The protein is a homopentamer. It interacts with RIC3 for proper folding and assembly. The nAChR, but not the glycine receptor, GlyR, exhibits hydrophobic gating (Ivanov et al. 2007). Low resolution NMR structures with associated anesthetics have been reported (Bondarenko et al. 2013). Allosteric modulators exhibit up to 5 distinct pharmacological effects (Gill-Thind et al. 2015). Based on pore hydration and size, a high resolution structure for the channel in the open conformation has been proposed (Chiodo et al. 2015). Agonists reduce dyskinesias in both early- and later-stage Parkinson's disease (Zhang et al. 2015). Monoterpenes inhibit the alpha7 receptor in the order: carveol > thymoquinone > carvacrol > menthone > thymol > limonene > eugenole > pulegone = carvone = vanilin. Among the monoterpenes, carveol showed the highest potency (Lozon et al. 2016). A revised structural model has been proposed (Newcombe et al. 2017). In humans, exons 5-10 in CHRNA7 are duplicated and fused to the FAM7A genetic element, giving rise to the hybrid gene CHRFAM7A. Its product, dupalpha7, is a truncated subunit lacking part of the N-terminal extracellular ligand-binding domain and is associated with neurological disorders, including schizophrenia, and immunomodulation (Lasala et al. 2018). alpha7 and dupalpha7 subunits co-assemble into functional heteromeric receptors, in which at least two alpha7 subunits are required for channel opening. Dupalpha7's presence in the pentameric arrangement does not affect the duration of the potentiated events. Using an alpha7 subunit mutant, activation of (alpha7)2(dupalpha7)3 receptors occurs through ACh binding at the alpha7/alpha7 interfacial binding site (Lasala et al. 2018). B-973 is an efficacious type II positive allosteric modulator (PAM) of alpha7 nicotinic acetylcholine receptors that, like 4BP-TQS and its active isomer GAT107, is able to produce direct allosteric activation in addition to potentiation of orthosteric agonist activity, which identifies it as an ago-PAM (Quadri et al. 2018). DB04763, DB08122 and pefloxacin are antagonists (they are NAMs) while furosemide potentiated ACh responses (it is a Pam) (Smelt et al. 2018). At nM concentration, APPsα (amyloid precursor protein) is an allosteric activator of α7-nAChR, mediated by the C-terminal 16 amino acids (CTα16) (Korte 2019). At µM concentrations, Rice et al. 2019 identified the GABABR1a as a target of APPsα, binding the sushi 1 domain via a 17–amino acid sequence (17-mer). These receptors activate opposing downstream cascades. The intrasubunit cavity of the α7 AcChR is important for the activity of type II positive allosteric modulators while the ECD-TMD junction and intersubunit sites are probably important for the activity of type I positive allosteric modulators (Targowska-Duda et al. 2019). Flavonoids are positive allosteric modulators of alpha7 nicotinic receptors (Nielsen et al. 2019). Active and desensitized state conformations have been examined (Chiodo et al. 2018). Modulators are able to activate or deactivate a7 receptors via allosteric binding; they are called positive allosteric modulators (PAMs) or negative allosteric modulators (NAMs) (Al Rawashdah et al. 2019). Functional divergence related sites cluster in the ligand binding domain, the beta2-beta3 linker close to the N-terminal alpha-helix, the intracellular linkers between transmembrane domains, and the "transition zone" (Pan et al. 2019). A series of phosphonate-functionalized 1,2,3-triazoles are positive allosteric modulators of alpha7 nicotinic acetylcholine receptors (Nielsen et al. 2020). The E-1' --> A-1' substitution at the cytoplasmatic selectivity filter strongly affects sodium and chloride permeation in opposite directions, leading to a complete inversion of selectivity. Thus, structural determinants for the observed cationic-to-anionic inversion reveal a key role of the protonation state of residue rings far from the mutation, in the proximity of the hydrophobic channel gate (Cottone et al. 2020). Outer membrane mitochondrial nAChRs (e.g., α7 NAChR) regulate apoptosis-induced mitochondrial channel formation by modulating the interplay of apoptosis-related proteins (VDAC1 and Bax) in the mitochondrial outer membrane (Kalashnyk et al. 2020). PNU-120596, a positive allosteric modulator of mammalian alpha7 nicotinic acetylcholine receptor, increases the neuron response to alpha7 agonists while retarding desensitization (Vulfius et al. 2020).
The cation-selective pentameric nicotinic acetylcholine receptor, nAChR, with α (461 aas; P02710), β (493 aas; P02712), γ (506 aas; P02714) and δ (522 aas; P02718) subunits. The transmembrane domain of the uncoupled nAChR adopts a conformation distinct from that of the resting or desensitized state (Sun et al. 2016). Studies with this receptor have been reviewed (Unwin 2013). Many small molecules interact with nAChRs including d-tubocurarine, snake venom protein α-bungarotoxin (α-Bgt), and α-conotoxins, neurotoxic peptides from Conus snails. Various more recently discovered compounds of different structural classes also interact with nAChRs including the low-molecular weight alkaloids, pibocin, varacin and makaluvamines C and G. 6-Bromohypaphorine from the mollusk Hermissenda crassicornis does not bind to Torpedo nAChR but behaves as an agonist on human α7 nAChR (Kudryavtsev et al. 2015). Dimethylaniline mimics the low potency and non-competitive actions of lidocaine on nAChRs, as opposed to the high potency and voltage-dependent block by lidocaine (Alberola-Die et al. 2016). Cholesterol is a potent modulator of the Torpedo nAChR (Baenziger et al. 2017). Cholesterol may play a mechanical role by conferring local rigidity to the membrane so that there is productive coupling between the extracellular and membrane domains, leading to opening of the channel (Unwin 2017). 11beta-(p-azidotetrafluorobenzoyloxy)allopregnanolone (F4N3Bzoxy-AP), a general anesthetic, a photoreactive allopregnanolone analog and a potent GABAAR PAM,was used to characterize steroid binding sites in the Torpedo nAChR in its native membrane environment (Yu et al. 2019). The steroid-binding site in the nAChR ion channel was identified, and additional steroid-binding sites could also be occupied by other lipophilic nAChR antagonists. Structural features of the αM4 TMS determine how lipid dependent changes in alphaM4 structure may ultimately modify nAChR function (Thompson et al. 2020).
Adult strychnine-sensitive glycine-inhibited chloride (anion selective) heteropentameric channel (GlyR; GLRA1) consisting of α1- and β-subunits (Cascio, 2004; Sivilotti, 2010). Ivermectin potentiates glycine-induced channel activation (Wang and Lynch, 2012). Molecular sites for the positive allosteric modulation of glycine receptors by endocannabinoids have been identified (Yévenes and Zeilhofer, 2011). Different subunits contribute asymmetrically to channel conductances via residues in the extracellular domain (Moroni et al., 2011; Xiong et al., 2012). Dominant and recessive mutations in GLRA1 are the major causes of hyperekplexia or startle disease (Gimenez et al., 2012). Open channel 3-d structures are known (Mowrey et al. 2013). Desensitization is regulated by interactions between the second and third transmembrane segments which affect the ion channel lumen near its intracellular end. The GABAAR and GlyR pore blocker, picrotoxin (TC# 8.C.1), prevents desensitization (Gielen et al. 2015). The x-ray structure of the α1 GlyR transmembrane domain has been reported (Moraga-Cid et al. 2015), and residue S296 in hGlyR-alpha1 is involved in potentiation by Delta(9)-tetrahydrocannabinol (THC) (Wells et al. 2015). The structure has also been elucidated by cryo EM (Du et al. 2015) and by x-ray crystalography (Huang et al. 2015). The latter presented a 3.0 A X-ray structure of the human glycine receptor-alpha3 homopentamer in complex with the high affinity, high-specificity antagonist, strychnine. The structure allowed exploration of the molecular recognition of antagonists. Comparisons with previous structures revealed a mechanism for antagonist-induced inactivation of Cys-loop receptors, involving an expansion of the orthosteric binding site in the extracellular domain that is coupled to closure of the ion pore in the transmembrane domain. The GlyR beta8-beta9 loop is an essential regulator of conformational rearrangements during ion channel opening and closing (Schaefer et al. 2017). Association of GlyR with the anchoring protein, gephyrin (Q9NQX3), is due to a hydrophobic interaction formed by Phe 330 of gephyrin and Phe 398 and Ile 400 of the GlyR beta-loop (Kim et al. 2006). Alcohols and volatile anesthetics enhance the function of inhibitory glycine receptors (GlyRs) by binding to a single anaesthetic binding site (Roberts et al. 2006). Aromatic residues in the GlyR M1, M3 and M4 α-helices are essential for receptor function (Tang and Lummis 2018). The neurological disorder, startle disease, is caused by glycinergic dysfunction, mainly due to missense mutations in genes encoding GlyR subunits (GLRA1 and GLRB). Another neurological disease with a phenotype similar to startle disease is a special form of stiff-person syndrome (SPS), which is most probably due to the development of GlyR autoantibodies (Schaefer et al. 2018). GlyRs can be modulated by positive allosteric modulators (PAMs) that target the extracellular, transmembrane and intracellular domains (Lara et al. 2019). Mutations in GLRA1 give rise to hyperekplexia (Milenkovic et al. 2018). Neurosteroid binding sites of GABAARs are conserved in the GlyRs (Alvarez and Pecci 2019). The intracellular domain of homomeric glycine receptors modulates agonist efficacy (Ivica et al. 2020). Inhibitory glycinergic transmission in the adult spinal cord is primarily mediated by glycine receptors (GlyRs) containing the alpha1 subunit. Alpha1ins, a longer alpha1 variant with 8 amino acids inserted into the intracellular large loop between TMSs 3 and 4, is expressed in the dorsal horn of the spinal cord, distributed at inhibitory synapses, and it is engaged in negative control over nociceptive signal transduction. Activation of metabotropic glutamate receptor 5 (mGluR5; TC# 9.A.14.7.1) specifically suppressed alpha1ins-mediated glycinergic transmission and evoked pain sensitization. Extracellular signal-regulated kinase (ERK) was critical for mGluR5 to inhibit alpha1ins. By binding to a D-docking site created by the 8-amino-acid insert ERK catalyzed alpha1ins phosphorylation at Ser380, which favored alpha1ins ubiquitination at Lys379 and led to alpha1ins endocytosis. Disruption of the ERK interaction with alpha1ins blocked Ser380 phosphorylation, potentiated glycinergic synaptic currents, and alleviated inflammatory and neuropathic pain (Zhang et al. 2019). The startle disease mutation (αS270T) affects the opening state for activation of presynaptic homomeric GlyRs, as well as postsynaptic heteromeric GlyRs, but the former are affected more. Both respond to glycine less efficiently (Wu et al. 2020). Cannabinoids exert therapeutic effects on several diseases such as chronic pain and startle disease by targeting glycine receptors (GlyRs). They target a serine residue at position 296 in the third TMS of the alpha1/alpha3 GlyR on the outside of the channel at the lipid interface where cholesterol concentrates. GlyRs are associated with cholesterol/caveolin-rich domains. and cholesterol reduction significantly inhibits cannabinoid potentiation of glycine-activated currents (Yao et al. 2020). Residues involved in glucose sensitivity of recombinant human glycine receptors have been identified (Hussein et al. 2020). Lipid-protein interactions are dependent on the receptor state, suggesting that lipids may regulate the receptor's conformational dynamics ((Dämgen and Biggin 2021)). Some protein-lipid interactions occur at a site at the communication interface between the extracellular and transmembrane domain, and in the active state, cholesterol can bind to the binding site of the positive allosteric modulator, ivermectin (Dämgen and Biggin 2021). An intracellular domain determines the agonist specificity (Ivica et al. 2021). The general anesthetic etomidate and fenamate mefenamic acid oppositely affect GABAAR and GlyR. These drugs potentiated GABAARs but blocked GlyRs (Rossokhin 2020). Alpha 1 glycine receptors are strongly inhibited by two flavanoids, quercetin and naringenin (Breitinger et al. 2021). The glycine receptor beta-subunit A455P variant occurs in a family affected by hyperekplexia syndrome (Aboheimed et al. 2022).
γ-Aminobutyric acid (GABA)-inhibited chloride channel, GABARA1 or GABAAR. The major central endocannabinoid, 2-arachidonoyl glycerol (2-AG), directly acts at GABA(A) receptors. It potentiates the receptor at low GABA concentrations (Sigel et al., 2011). Hydrophobic anions potently and uncompetitively antagonize GABA (A) receptor function (Chisari et al., 2011). Regulated by neurosteroids; activated by pregnenolone and allopregnenalone (Costa et al., 2012). Different subunits contribute asymmetrically to channel conductances via residues in the extracellular domain (Moroni et al., 2011). Potentiated by general anaesthetics (Nury et al., 2011). Direct physical coupling between the GABA-A receptor and the KCC2 chloride transporter underlies ionic plasticity in cerebellar purkinje neurons in response to brain-derived neurotrophic factor (BDNF) (Huang et al. 2013). GABA type A receptors, the brain's major inhibitory neurotransmitter receptors, are the targets for many general anesthetics, including volatile anesthetics, etomidate, propofol, and barbiturates. Anesthetics usually bind at intersubunit sites (Chiara et al. 2013). Etomidate and propofol are potent general anesthetics that act via GABAA receptor allosteric co-agonist sites located at transmembrane beta+/alpha- inter-subunit interfaces. In heteromeric receptors, betaN265 (M2-15') on beta2 and beta3 subunits are important determinants of sensitivity to these drugs (Stewart et al. 2014). A P302L mutation in the gamma2 (γ2) subunit (Dravet syndrome in humans) of the mouse when expressed with the α1 and β3 subunits, produced a 90% decrease in conductance due to slow activation and enhance desensitization. It shifted the channel to a low-conductance state by reshaping the hour-glass-like pore cavity during transitions between closed, open, and desensitized states (Hernandez et al. 2017). Numerous postive and negative allosteric modulators have been identified (Maldifassi et al. 2016). Crystal structures of neurosteroids bound to alpha homopentameric GABAARs have revealed binding to five equivalent sites (Alvarez and Pecci 2018). Masiulis et al. 2019 reported high-resolution cryo-EM structures in which the full-length human alpha1beta3gamma2L GABAA receptor in lipid nanodiscs is bound to (1) the channel-blocker picrotoxin, (2) the competitive antagonist bicuculline, (3) the agonist GABA, and (4 AND 5) the classical benzodiazepines alprazolam and diazepam. They described the binding modes and mechanistic effects of these ligands, the closed and desensitized states of the GABAA receptor gating cycle, and the basis for allosteric coupling between the extracellular, agonist-binding region and the transmembrane, pore-forming region (Masiulis et al. 2019). Rare variants in the ε-subunit have been identified in patients with a wide spectrum of epileptic phenotypes (Markus et al. 2020). Many (but not all) sedative-hypnotics are capable of positively modulating the GABAA receptor by binding within a common set of hydrophobic cavities (McGrath et al. 2020). Isoflurane binds to a site within the transmembrane domains of the receptor and suggest functional similarity between the GABA(A) alpha-1, -2, and -3 subunits (Schofield and Harrison 2005). Mutations ain the M2 and M3 TMSs of the GABAARs alpha1 and beta2 subunits affect late gating transitions including opening/closing and desensitization (Terejko et al. 2021). The distance between an alpha1beta3gamma2L GABA type A receptor residue and the drug, etomidate, when bound in the transmembrane beta+/alpha- interface, has been determined (Fantasia et al. 2021). There is a binding site in the beta(+)alpha(-) interface for the anesthetic, propofol (Borghese et al. 2021). Delta selective compound 2 (DS2; 4-chloro-N-[2-(2-thienyl)imidazo[1,2-a]pyridin-3-yl]benzamide) is widely used to study selective actions mediated by delta-subunit-containing GABAA receptors. The molecular determinants responsible for positive modulation by DS2 have been identified (Falk-Petersen et al. 2021). Two high-resolution structures of GABAA receptors in complex with zolpidem, a positive allosteric modulator and heavily prescribed hypnotic, and DMCM, a negative allosteric modulator with convulsant and anxiogenic properties. These two drugs share the extracellular benzodiazepine site at the alpha/gamma subunit interface and two transmembrane sites at beta/alpha interfaces. Structural analyses reveal a basis for the subtype selectivity of zolpidem that underlies its clinical success (Zhu et al. 2022). Molecular dynamics simulations provided insight into how DMCM switches from a negative to a positive modulator as a function of binding site occupancy (Zhu et al. 2022). Avermectin-imidazo[1,2-a]pyridine hybrids are potent GABAA receptor modulators (Volkova et al. 2022).
γ-aminobutyric acid (GABA)-inhibited Cl- channel, type A (α-, β- γ-subunit precursors), GABRA2 or GABAAR2, regulated by GABA receptor accessory protein, GABARAP (Luu et al., 2006) and FRMD7 (TC# 8.A.25.1.5) (Jiang et al. 2020). A mutation in the GABAA receptor alpha 1 subunit, linked to human epilepsy, affects channel gating properties (Fisher 2004). The anti-convulsant stiripentol acts directly on the GABA(A) receptor as a positive allosteric modulator (Fisher 2009). The major central endocannabinoid, 2-arachidonoyl glycerol (2-AG), also directly acts at GABA(A) receptors to potentiate the receptor at low GABA concentrations (Sigel et al., 2011). The recpetor is also allosterically regulated by neurosteroids via TMS1 of the beta subunit (Baker et al. 2010). General anesthetic binding site(s) have been identified (Chiara et al., 2012; Woll et al. 2018). Hydrophobic anions potently and uncompetitively antagonize GABA (A) receptor function (Chisari et al., 2011). Regulated by neurosteroids; activated by pregnenolone and allopregnenalone (Costa et al., 2012). Allopregnanolone and its synthetic analog alphaxalone are GABAAR positive allosteric modulators (Yu et al. 2019). Different subunits contribute asymmetrically to channel conductances via residues in the extracellular domain (Moroni et al., 2011). Potentiated by general anaesthetics (Nury et al., 2011). Both the alpha and beta subunits are important for activation by alcohols and anaesthetics (McCracken et al. 2010). Direct physical coupling between the GABA-A receptor (of 4 TMSs) and the KCC2 chloride transporter underlies ionic plasticity in cerebellar purkinje neurons in response to brain-derived neurotrophic factor (BDNF) (Huang et al. 2013). An anesthetic binding site has been identified (Franks 2015). Desensitization is regulated by interactions between the second and third transmembrane segments which affect the ion channel lumen near its intracellular end. The GABAAR and GlyR pore blocker, picrotoxin (TC# 8.C.1), prevents desensitization (Gielen et al. 2015). The mechanism of action of methaqualone (2-methyl-3-O-tolyl-4(3H)-quinazolinone, Quaalude(R)), a sedative-hypnotic and recreational drug. Methaqualone is a positive allosteric modulator (PAM) at human alpha1,2,3,5beta2,3gamma2S GABAA receptors (GABAARs) expressed, whereas it displays diverse functionalities at the alpha4,6beta1,2,3delta GABAAR subtypes, ranging from inactivity (alpha4beta1delta), through negative (alpha6beta1delta) or positive allosteric modulation (alpha4beta2delta, alpha6beta2,3delta), to superagonism (alpha4beta3delta) (Hammer et al. 2015). The thyroid hormone L-3,5,3'-triiodothyronine (T3) inhibits GABAA receptors at micromolar concentrations and has common features with neurosteroids such as allopregnanolone (ALLOP). Westergard et al. 2015 used functional experiments on alpha2beta1gamma2 GABAA receptors to detect competitive interactions between T3 and an agonist (ivermectin, IVM) with a crystallographically determined binding site at subunit interfaces in the transmembrane domain of a homologous receptor (glutamate-gated chloride channel, GluCl). T3 and ALLOP showed competitive effects, supporting the presence of a T3 and ALLOP binding site at one or more subunit interfaces. Residues in the beta3 subunit, at or near the etomidate/propofol binding site(s), form part of the valerenic acid modulator binding pocket (Luger et al. 2015). IV general anesthetics, including propofol, etomidate, alphaxalone, and barbiturates, enhance GABAA receptor activation. These anesthetics bind in transmembrane pockets between subunits of typical synaptic GABAA receptors (Forman and Miller 2016). Carisoprodol can directly gate and allosterically modulate type A GABA (GABAA) receptors (Kumar et al. 2017). The former sedative-hypnotic and recreational drug methaqualone (Quaalude) is a moderately potent, non-selective positive allosteric modulator of GABAA receptors (GABAARs) (Hammer et al. 2015). A methaqualone analog, 2-phenyl-3-(p-tolyl)quinazolin-4(3H)-one (PPTQ) exhibits intrinsic activity at micromolar concentrations and potentiates the GABA-evoked signaling at concentrations down to the low-nanomolar range (Madjroh et al. 2018). The PPTQ binding site is allosterically linked with sites targeted by neurosteroids and barbiturates. Anesthetic pharmacophore binding has been studied (Fahrenbach and Bertaccini 2018). GABAA receptors are modulated via several sites by GABA, benzodiazepines, ethanol, neurosteroids and anaesthetics among others. Amundarain et al. 2018 presented a model of the alpha1beta2gamma2 subtype GABAA receptor in the APO state and in complex with selected ligands, including agonists, antagonists and allosteric modulators. Sites in TMSs 2 and 3 are important for alcohol-induced conformational changes (Jung and Harris 2006). Many anesthetics and neurosteroids act through binding to the GABAAR transmembrane domainnad x-ray structures have revealed how α-xalone, a neurosteroid anaesthetic, binds and influences potentiation, activation and desensitization (Chen et al. 2018). AA29504 is an allosteric agonist and positive allosteric modulator of GABAA receptors (Olander et al. 2018). Allosteric shift analysis in mutant α1β3γ2L GABAA receptors indicates selectivity and cross-talk among intersubunit transmembrane anesthetic sites (Szabo et al. 2019). Several epilepsy-causing mutations have been identified in the genes of the α1, β3, and γ2 subunits comprising the GABAA receptor (Absalom et al. 2019). Constituents of the GABAA receptor include a transmembrane GARLH/LHFPL protein (TC# 1.A.82.1.7) and the inhibitory synaptic protein, neuroligin 2 (TC# 8.A.117.1.1) (Tomita 2019). GABAA receptors containing mutant alpha5 and alpha1 subunits all had reduced cell surface and total cell expression with altered endoplasmic reticulum processing, impaired synaptic clustering, reduced GABAA receptor function and decreased GABA binding potency. Thus, GABRA5 is a causative gene for early onset epileptic encephalopathy (Hernandez et al. 2019). Mutations at Gln242 or Trp246 that eliminate neurosteroid effects do not eliminate neurosteroid binding within the intersubunit site, but significantly alter the preferred orientation of the neurosteroid (Sugasawa et al. 2019). Binding sites and interactions of propanidid and AZD3043 within GABAAR have been identified (Wang et al. 2018). Clptm1 limits GABAAR forward trafficking from the ER to the plasma membrane, and it regulates inhibitory homeostatic plasticity (Ge et al. 2018). The mechanisms of potentiation and inhibition of GABAA receptors by non-steroidal anti-inflammatory drugs, niflumic and mefenamic acids, have been described (Rossokhin et al. 2019). GABAARs are targets for important classes of clinical agents (e.g., anxiolytics, anticonvulsants, and general anesthetics) that act as positive allosteric modulators (PAMs). PAMs bind selectively to a single intersubunit site in the GABAAR transmembrane domain (Jayakar et al. 2019). The gamma2 subunit is required for clustering of these receptors, for recruitment of the submembrane scaffold protein gephyrin to postsynaptic sites, and for postsynaptic function of GABAergic inhibitory synapses (Alldred et al. 2005). The fourth TMS of the gamma2 subunit is required for postsynaptic clustering, but both the major cytoplasmic loop and the fourth transmembrane domain contribute to efficient recruitment of gephyrin to postsynaptic receptor clusters and are essential for restoration of miniature IPSCs (Alldred et al. 2005). Oligomerization and cell surface expression of recombinant GABAA receptors tagged in the delta subunit have been examined (Oflaz et al. 2019). The isoxazoline ectoparasiticide, fluralaner, exerts antiparasitic effects by inhibiting the function of GABARs, but substitutions of Gly333 in TMS3 led to substantial reductions in the sensitivity to fluralaner (Yamato et al. 2020). A potent photoreactive general anesthetic with novel binding site selectivity for GABAA receptors has been identified (Shalabi et al. 2020). GABAA receptor neurosteroid binding sites have been reviewed (Alvarez et al. 2019). Missense variants in GABRA2 are associated with early infantile epileptic encephalopathy (EIEE) as well as other disorders (Sanchis-Juan et al. 2020). Elevin novel molecules, identified using reinforcement learning, showed positive allosteric modulation, with two showing 50% activation in the low micromolar range (Michaeli et al. 2020). GABAA Receptor ligands interact with binding sites in the transmembrane domain and in the extracellular domain (Iorio et al. 2020). Many (but not all) sedative-hypnotics are capable of positively modulating the GABAA receptor by binding within a common set of hydrophobic cavities (McGrath et al. 2020). Allopregnanolone (3alpha5alpha-P), pregnanolone), and their synthetic derivatives are potent positive allosteric modulators (PAMs) of GABAA receptors with in vivo anesthetic, anxiolytic, and anti-convulsant effects. Photoaffinity labeling procedures have been used to identify an intersubunit steroid-binding site in heteromeric GABA type A (GABAA) receptors (Jayakar et al. 2020). Diazepam binds to etomidate binding sites in the transmembrane receptor domain giving rise to antagonism (McGrath et al. 2020). The alpha1 subunit histidine 55 at the interface between the extracellular and transmembrane domains affects preactivation and desensitization of the GABAA receptor (Kaczor et al. 2021). Coordinated downregulation of KCC2 and the GABAA receptor contributes to inhibitory dysfunction during seizure induction (Wan et al. 2020). Loss of GABAergic inhibition provides a mechanism underlying GABRB2-associated neurodevelopmental disorders (El Achkar et al. 2021). GABAAR binds the anaesthetic, Propofol, to induced conformational changes (Yuan et al. 2021). Methaqualone (2-methyl-3-(o-tolyl)-quinazolin-4(3H)-one, MTQ) is a moderately potent positive allosteric modulator (PAM) of GABAA receptors (GABAARs). Several additional potent GABAAR PAMs include 2,3-diphenylquinazolin-4(3H)-one (PPQ), 3-(2-chlorophenyl)-2-phenylquinazolin-4(3H)-one (Cl-PPQ), and others (Wang et al. 2020). Interfacial binding sites for cholesterol on GABAA receptors compete with neurosteroids (Lee 2021). GABAAR is inhibited by L-type calcium channel blockers (Das et al. 2004). In in vivo studies, Stigmasterol (0.5-3.0 mg/kg, i.p.) exerted significant anxiolytic and anticonvulsant effects in an identical manner to allopregnanolone, indicating the involvement of a GABAergic mechanism. Thus, GABAA receptors are subject to anxiolytic and anticonvulsant activities of stigmasterol. Thus, stigmasterol is a candidate steroidal drug for the treatment of neurological disorders due to its positive modulation of GABA receptors (Karim et al. 2021). Sesquiterpenes and sesquiterpenoids harbor modulatory allosteric properties that affect inhibitoryGABAA receptors (Janzen et al. 2021). High-dose benzodiazepines positively modulate GABAA receptors via a flumazenil-insensitive mechanism (Wang et al. 2021). Benzodiazepine binding to transmembrane anaesthetic binding sites of the GABAA receptor can produce positive or negative modulation manifesting as decreases or increases in locomotion, respectively. Selectivity for these sites may contribute to the distinct GABAA receptor and behavioural actions of different benzodiazepines, particularly at high anaesthetic concentrations (McGrath et al. 2021). (+)-Catharanthine potentiates the GABAA receptor by binding to a transmembrane site at the beta(+)/alpha(-) interface near the TMS2-TMS3 loop (Arias et al. 2022). Diazepam derivatives are allosteric modulators of GABAA receptor alpha1beta2gamma2 subtypes (Djebaili et al. 2022).
The GABA receptor consisting of α1, β3, and γ2 subunits. Heteropentameric receptor for GABA, the major inhibitory neurotransmitter in the vertebrate brain. Functions also as the histamine receptor and mediates cellular responses to histamine. Functions as a receptor for diazepines and various anesthetics, such as pentobarbital which bind to separate allosteric effector binding sites. Functions as ligand-gated chloride channel (Jayakar et al. 2015). GABRA1 mutations are associated with familial juvenile myoclonic epilepsy, sporadic childhood absence epilepsy, idiopathic familial generalized epilepsy, infantile spasms and Dravet syndrome. Thus, GABRA1 mutations are associated with infantile epilepsy including early onset epileptic encephalopathies including Ohtahara syndrome and West syndrome (Kodera et al. 2016). A variant of GABRA1 (A332V) causes increased sensitivity for GABA and alterred desensitization (Steudle et al. 2020). Pathogenic variants in GABRB3 have been associated with a spectrum of phenotypes from severe developmental disorders and epileptic encephalopathies to milder epilepsy syndromes and mild intellectual disability (Johannesen et al. 2021).
The prokaryotic H+-gated ion channel, GlvI or GLIC (Bocquet et al., 2007), solved at 2.9 Å resolution in the open pentameric state (3EHZ_E) (Bocquet et al., 2009; Corringer et al. 2010). The basis for ion selectivity has been reported (Fritsch et al., 2011). Two stage tilting of the pore lining helices results in channel opening and closing (Zhu and Hummer, 2010). The mechanical work of opening the pore is performed primarily on the M2-M3 loop. Strong interactions of this short and conserved loop with the extracellular domain are therefore crucial to couple ligand binding to channel opening. The H+-activated GLIC has an extracellular domain between TMSs M3 and M4 but lacks the intracellular domain (ICD) which is a distinct folding domain (Goyal et al., 2011). The structural basis for alcohol modulation of GLIC has been reported (Howard et al., 2011). The structure of the M2 TMS indicates that the charge selectivity filter is in the cytoplasmic half of the channel (Parikh et al. 2011). Below pH 5.0, GLIC desensitizes on a time scale of minutes. During activation, the extracellular hydrophobic region undergoes changes involving outward translational movement, away from the pore axis, leading to an increase in pore diameter. The lower end of M2 remains relatively immobile (Velisetty et al., 2012). During desensitization, the intervening polar residues in the middle of M2 move closer to form a solvent-occluded barrier and thereby reveal the location of a distinct desensitization gate. In comparison to the crystal structure of GLIC, the structural dynamics of the channel in a membrane environment suggest a more loosely packed conformation with water-accessible intrasubunit vestibules penetrating from the extracellular end all the way to the middle of M2 in the closed-state (Velisetty et al. 2012). Pore opening and closing is well understood (Zhu and Hummer 2010). X-ray structures of general anaesthetics bound to GLIC revealed a common general-anaesthetic binding site, which pre-exists in the apo-structure in the upper part of the transmembrane domain of each protomer (Nury et al., 2011). Large blockers bind in the center of the membrane, but divalent transition metal ions bind to the narrow intracellular pore entry (Hilf et al., 2010). Alcohols and anaesthetics induce structural changes and activate ligand-gated ion channels of the LIC family by binding in intersubunit cavities (Sauguet et al. 2013; Ghosh et al. 2013). Gating at pH 4 has been visualized by x-ray crystallography (Gonzalez-Gutierrez et al. 2013) Site-directed spin labeling and x-ray analyses have revealed gating transition motions and mechanisms that distinguish active from desensitized states (Dellisanti et al. 2013; Sauguet et al. 2013). Gating involves major rearrangements of the interfacial loops (Velisetty et al. 2014). A single point mutation can change the effect of an anesthetic (desfurane; chloroform) from an inhibitor to a potentiator (Brömstrup et al. 2013). An interhelix hydrogen bond involving His234 is important for stabilization of the open state (Rienzo et al. 2014). The outermost M4 TMS makes distinct contributions to the maturation and gating of the related GLIC and ELIC homologs, suggesting that they exhibit divergent mechanisms of channel function (Hénault et al. 2015). The same allosteric network may underlie the actions of various anesthetics, regardless of binding site (Joseph and Mincer 2016). GLIC and ELIC (TC# 1.A.9.9.1) may represent distinct transmembrane domain archetypes (Therien and Baenziger 2017). Arcario et al. 2017 have demonstrated an anesthetic binding site in GLIC which is accessed through a membrane-embedded tunnel. The anesthetic interacts with a previously known site, resulting in conformational changes that produce a non-conductive state of the channel (Arcario et al. 2017). The gating mechanism has been studied (Lev et al. 2017). R-Ketamine inhibits members of the LIC family, and the structural and dynamics basis for the assymetric inhibitory modulation of ketamine has been revealed (Ion et al. 2017). Residue E35 has been identified as a key proton-sensing residue, as neutralization of its side chain carboxylate stabilizes the active state. Thus, proton activation occurs allosterically at the level of multiple loci with a key contribution of the coupling interface between the extracellular and transmembrane domains (Nemecz et al. 2017). General anesthetics can allosterically favor closed channels by binding in the pore or favor open channels via various subsites in the transmembrane domain (Fourati et al. 2018). GLIC's gating by protonation proceeds by making use of loop F, already known as an allosteric site in other pLGICs, instead of the classic orthosteric site (Hu et al. 2018). Binding of fentanyl to its binding site within GLIC results in conformational changes that inhibit conduction through the channel (Faulkner et al. 2019). This channel and others have been studied by high-speed atomic force microscopy (HS-AFM) which has made it possible to characterized the conformational dynamics of single unlabeled transmembrane channels and transporters (Heath and Scheuring 2019). Pentameric ligand-gated ion channels undergo subtle conformational cycling to control electrochemical signal transduction. Lycksell et al. 2021 used small-angle neutron scattering (SANS) to probe ambient solution-phase properties of GLIC under resting and activating conditions. Resting-state GLIC was the best-fit crystal structure to SANS curves, with no evidence for divergent mechanisms. Thus, the findings demonstrate state-dependent changes in a pentameric ion channel by SANS. A 3-state model has been proposed; mutations at the subunit interface in the extracellular domain (ECD) principally alter pre-activation, while mutations in the lower ECD and the transmembrane domain principally alter activation. Propofol alters both transitions (Lefebvre et al. 2021). Cryo-EM structures of GLIC under three pH conditions showed that decreased pH is associated with improved resolution and side chain rearrangements at the subunit/domain interface, particularly involving functionally important residues in the beta1-beta2 and M2-M3 loops. Molecular dynamics simulations substantiated flexibility in the closed-channel extracellular domains relative to the transmembrane ones and supported electrostatic remodeling around E35 and E243 in proton-induced gating. Exploration of secondary cryo-EM classes further indicated a low-pH population with an expanded pore (Rovšnik et al. 2021). Polyunsaturated fatty acids (PUFAs) inhibit pentameric ligand-gated ion channels (pLGICs) by selectively binding to a single site in the outer transmembrane domain of ELIC (Dietzen et al. 2022).
The bacterial pentameric Cys-loop ligand-gated ion channel (Erwinia chrysanthemi ligand-gated ion channel), ELIC. A 3.3 Å resolution structure is available (Hilf and Dutzler, 2008; Corringer et al., 2010). X-ray analyses have identified three distinct binding sites for anaesthetics, one in the channel, one at the end of a TMS, and one in a hydrophobic pocket of the extracellular domain (Spurny et al. 2013). Motions involving desensitization have been defined (Dellisanti et al. 2013). Simulations indicate the similarities with and differences between the Acetylcholine receptor (Cheng et al. 2009). This family includes members with very divergent properties (Gonzalez-Gutierrez and Grosman 2015). Cysteamine is an agonist for ELIC (Hénault and Baenziger 2016). X-ray structures and functional measurements support a pore-blocking mechanism for the inhibitory action of short-chain alcohols which bind to the TMSs (Chen et al. 2016). GLIC (TC# 1.A.9.8.1) and ELIC may represent distinct transmembrane domain archetypes (Therien and Baenziger 2017), and both bind hopenoids at the mamalian cholesterol binding site (Barrantes and Fantini 2016). A high-resolution structure of ELIC in a lipid-bound state has revealed a phospholipid binding site at the lower half of pore-forming transmembrane helices M1 and M4 and at a nearby site for neurosteroids, cholesterol or general anesthetics (Hénault et al. 2019). This site is shaped by an M4-helix kink and a Trp-Arg-Pro triad that is highly conserved in eukaryote GABAA/C and glycine receptors. M4 is intrinsically flexible, and M4 deletions or disruptions of the lipid-binding site accelerate desensitization, suggesting that lipid interactions shape the agonist response (Hénault et al. 2019). 1-Palmitoyl-2-oleoyl phosphatidylglycerol (POPG) stabilizes the open state of ELIC relative to the desensitized state by direct binding to specific sites (Tong et al. 2019). The nicotinic acetylcholine receptor from the Torpedo electric organ, when reconstituted in membranes formed by zwitterionic phospholipids alone, exposure to agonist fails to elicit ion-flux activity, and ELIC has a similar lipid sensitivity. Structures of ELIC in palmitoyl-oleoyl-phosphatidylcholine- (POPC-) only nanodiscs in both the unliganded (4.1-Å resolution) and agonist-bound (3.3 Å) states using single-particle cryoEM have been solved (Kumar et al. 2020). The largest differences occur at the level of loop C - at the agonist-binding sites - and the loops at the interface between the extracellular and transmembrane domains (ECD and TMD, respectively). The transmembrane pore is occluded similarly in both structures. POPC-only membranes prevent ECD-TMD coupling so that the "conformational wave" of liganded-receptor gating takes place in the ECD and the interfacial M2-M3 linker, but fails to penetrate the membrane and propagate into the TMD. The higher affinity for agonists, characteristic of the open- and desensitized-channel conformations, results from the tighter confinement of the ligand to its binding site; this limits the ligand's fluctuations, and thus delays its escape into bulk solvent (Kumar et al. 2020).
Non-structural glycoprotein 4, NSP4 or enterotoxin, of 175 aas and 2 TMSs (Hyser et al. 2012). A pentatmeric structure of a 53 aas NSP4 fragment has been solved (3MIW). NSP4 viroporin is involved in activation. It increases the endoplasmic reticulum (ER) permeability, resulting in decreased ER calcium stores and activation of plasma membrane (PM) calcium influx channels, ultimately causing the elevation in cytoplasmic calcium (Hyser et al. 2013). It activates ER calcium store-operated calcium entry (Hyser et al. 2013). NSP4 VPD is a Ca2+/Ba2+-conducting cation-selective viroporin that transports monovalent and divalent cations equally well (Pham et al. 2017). It may be involved in particle production (Scott and Griffin 2015).
Agnoprotein viroporin of 71 aas and 1 TMS (Suzuki et al. 2010). It is cation-selective, capable of Ca2+ accomodation, and is involved in particle production (Scott and Griffin 2015).
OmpF general porin. OmpF can deliver peptides of >6 KDa (epitopes) including protamine, through the pore lumen from the periplasm to the outside (Housden et al., 2010; Ghale et al. 2014). For cephalosporin antibiotics, the interaction strength series is ceftriaxone > cefpirome > ceftazidime (Lovelle et al. 2011). An unfolded protein such as colicin E9 can thread through OmpF from the outside to reach the periplasm (Housden et al. 2013). Polynucleotides can pass through OmpF (Hadi-Alijanvand and Rouhani 2015). LPS influences the movement of bulk ions (K+ and Cl-), but the ion selectivity of OmpF is mainly affected by bulk ion concentrations (Patel et al. 2016). OMPs such as OmpF cluster into islands that restrict their lateral mobility, while IMPs generally diffuse throughout the cell. Rassam et al. 2018 demonstrated that when transient, energy-dependent transmembrane connections are formed, IMPs become subjugated by the inherent organisation of OMPs, and that such connections impact IMP function. They showed that while establishing a translocon for import, colicin ColE9 sequesters the IMPs of the proton motive force (PMF)-linked Tol-Pal complex into islands mirroring those of colicin-bound OMPs. Through this imposed organisation, the bacteriocin subverts the outer-membrane stabilizing role of Tol-Pal, blocking its recruitment to cell division sites and slowing membrane constriction. The ordering of IMPs by OMPs via an energised inter-membrane bridge represents an emerging functional paradigm in cell envelope biology (Rassam et al. 2018). Colicin E9 (ColE9) disordered regions exploit OmpF for direction-specific binding, which ensures the constrained presentation of an activating signal within the bacterial periplasm (Housden et al. 2018). Anionic lipid binding can prevent closure of OmpF channels, thereby increasing access of antibiotics that use porin-mediated pathways (Liko et al. 2018). OmpF may be the major route of D-lactate/D-3-hydroxybutyrate oligo-ester secretion (Utsunomia et al. 2017). Lipid Headgroup Charge and Acyl Chain Composition Modulate Closure of the channel (Perini et al. 2019). Piperacillin, tazobactam, ampicillin and sulbactam interact strongly with OmpF, and may be transported (Wang et al. 2019). Gating kinetics are governed by lipid characteristics so that each stage of a sequential closure is different from the previous one, probably because of intra- or intermonomeric rearrangements (Perini et al. 2019). OmpF transports fosfomycin (Golla et al. 2019) and bacteriocins into cells. Polypeptide transport/binding processes generate an essentially irreversible, hook-like assembly that constrains an import activating peptide epitope between two subunits of the OmpF trimer (Lee et al. 2020).
OmpU porin (cation-selective; PK/PCl = 14; bile salt inducible) (low permeability to bile) (Simonet et al., 2003). OmpU influences sensitivities to β-lactam antibiotics and sodium deoxycholate induction of biofilm formation and growth on large sugars (Pagel et al., 2007). The effective pore radus is 0.55 nm which increases with acidic pH but decreases with increasing ionic strength (Duret and Delcour 2010). OmpU induces target animal cell death after it inserts into host mitochondrial membranes (Gupta et al. 2015). The high resolution structures of OmpT and OmpU, the two major porins in V. cholerae, have been determined, and both have unusual constrictions that create narrower barriers for small-molecule permeation and change the internal electric fields of the channels (Pathania et al. 2018).
PhoE phosphoporin. The 3-d structure is available (PDB#1PHO)
Porin 2 (Omp-Pst2 or OmpPst2) of 365 aas. Voltage gating is observed for Omp-Pst2, where the binding of cations in-between L3 and the barrel wall results in exposing a conserved aromatic residue in the channel lumen, thereby halting ion permeation. Comparison of Omp-Pst1 (TC# 1.B.1.1.20) with Omp-Pst2 suggested that their differing sensitivities to voltage is encoded in the hydrogen-bonding network anchoring L3 onto the barrel wall. The strength of this network governs the probability of cations binding behind L3. That Omp-Pst2 gating is observed only when ions flow against the electrostatic potential gradient of the channel suggests a possible role for this porin in the regulation of charge distribution across the outer membrane and bacterial homeostasis (Song et al. 2015).
OmpC general porin. Expression of OmpC and OmpF is reciprocally regulated by the EnvZ/OmpR sensor kinase/response regulator system (Egger et al. 1997). Mutants isolated from patients with MDR E. coli, resistant to several antibiotics, showed decreased permeability to these antibiotics (Lou et al. 2011). The diffusion route of the fluoroquinolone, enrofloxacin, through the OmpC porin has been reported (Prajapati et al. 2018).
PorB (Class 2). The 2.3 Å structure has been determined by x-ray crystallography. There are three putative solute translocation pathways through the channel pore: One pathway transports anions nonselectively, one tranports cations nonselectively, and one facilitates the specific uptake of sugars. Regulated by ATP binding (Tanabe et al., 2010). Exhibits voltage-dependent closure (Jadhav et al. 2013).
Anion-selective porin protein 32, Omp32. The structure is known to 1.5 Å resolution (Zachariae et al. 2006).
Sugar-specific chitoporin of 375 aas, ChiP. The best substrate is chitohexose, but ChiP transports a variety of chitooligosaccharides. Trp136 is important for the binding affinity for chitohexaose (Chumjan et al. 2015). X-ray crystal structures of ChiP from V. harveyi in the presence and absence of chito-oligosaccharides have been solved (Aunkham et al. 2018). Structures without bound sugar reveal a trimeric assembly with an unprecedented closing of the transport pore by the N-terminus of a neighboring subunit. Substrate binding ejects the pore plug to open the transport channel.The structures explain the exceptional affinity of ChiP for chito-oligosaccharides and point to an important role of the N-terminal gate in substrate transport (Aunkham et al. 2018). Hydrogen-bonds contribute to sugar permeation (Chumjan et al. 2019). This protein is 90% identical to the chitoporin of the Vibrio campbellii chitoporin (Aunkham et al. 2020). The C2 entity of chitosugars is crucial for the molecular selectivity of the Vibrio campbellii chitoporin (Suginta et al. 2021).
Low ion selective porin (PK/PCl = 4), OmpT (high permeability to bile) (Simonet et al., 2003). OmpT has an effective radius of 0.43nm, and acidic pH, high ionic strength, or exposure to polyethyleneglycol stabilizes a less conductive state (Duret & Delcour, 2010). It binds the biofilm matrix protein, Bap1, which influences antimicrobial peptide (polymyxin B and LL-37) resistance (Duperthuy et al. 2013). The high resolution structures of OmpT and OmpU, the two major porins in V. cholerae, have been determined, and both have unusual constrictions that create narrower barriers for small-molecule permeation and change the internal electric fields of the channels (Pathania et al. 2018).
Nucleoside-specific channel forming protein, Tsx (Benz et al. 1988).
Type π fimbrial usher, PapC. The crystal structure of the PapC usher translocation domain has been solved (Daniels and Normark, 2008; Remaut et al., 2008). The crystal structure of the full-length PapC usher in complex with its cognate PapDG chaperone-subunit complex in a pre-activation state has been solved. This elucidated the molecular details of how the usher is specifically engaged by allosteric interactions with its substrate, preceding activation, and how the usher facilitates the transfer of subunits from the amino-terminal periplasmic domain to the CTDs during pilus assembly (Omattage et al. 2018).
Usher, Caf1A, important for F1 antigen assembly
Fimbial usher protein, FimD
|1.B.12.1.1||Autotransporter of adhesin involved in diffuse adherence, AidA (Charbonneau and Mourez, 2007). Heptosylated on 16 ser and thr residues which is required for adhesion (Charbonneau et al., 2007).||
|1.B.12.1.2||Autoexporter of virulence factor G, VirG or IcsA||
Autoexporter of pertactin, Ptt of 910 aas with a C-terminal β-barrel domain which has been crystalized (Zhu et al. 2007). It is a bacterial adhesin and vaccine target which influences the duration of B. pertussis infections but does not otherwise affect the disease (Vodzak et al. 2016).
|1.B.12.2.3||Autoexporter of Bordetella resistance to killing proteins||
Autoexporter of adhesion and penetration protein
Autoexporter of temperature-sensitive hemagglutinin, a hemoglobin binding protease, Tsh/Hbp (1377 aas) (Jong and Luirink, 2008; Peterson et al., 2006). The pore of the Hbp TD is largely obstructed, but a variant that lacked one amino acid residue from the N-terminus showed the opening and closing of a channel comparable to what was reported for the TD of NalP. Hbp is processed by an autocatalytic intramolecular mechanism resulting in the stable docking of the α-helical plug in the barrel.
Autotransporter of serine protease, EspP (with long N-terminal leader that prevents improper folding in the periplasm) (Szabady et al., 2005; Ieva et al., 2008). Energy for export is provided by the folding of the C-terminal domain (Peterson et al., 2010).
Autotransporter-1, Pet (serine protease; 1295 aas)) (Eslava et al., 1998; Leyton et al., 2010). The first stage of autotransporter folding determines whether subsequent translocation can deliver the N-terminal domain to its functional form on the bacterial cell surface. Paired conserved glycine-aromatic 'mortise and tenon' motifs join neighbouring beta-strands in the C-terminal barrel domain, and mutations within these motifs slow the rate and extent of passenger domain translocation to the surface of bacterial cell (Leyton et al. 2014).
|1.B.12.5.9||Autoexporter of lipase/esterase, EstA||
Autotransporter-1, TibA (989 aas; an Adhesin/Invasin associated with some enterotoxigenic E. coli) (Lindenthal and Elsinghorst et al., 1999; Klemm et al. 2006).
Autotransporter of N-terminal protease passenger domain that cleaves surface-localized virulence factors. The 3-d structure is known (Oomen et al., 2004). The crystal structure of the NalP translocator domain revealed a 12 β-stranded transmembrane beta-barrel containing a central alpha-helix. The transmembrane beta-barrel is stable even in the absence of the alpha-helix. Removal of the helix results in an influx of water into the pore region, suggesting the helix acts as a 'plug' (Khalid and Sansom 2006). The dimensions of the pore fluctuate, but the NalP monomer is sufficient for the transport of the passenger domain in an unfolded or extended conformation (Khalid and Sansom 2006). NalP is subject to phase variation (Oldfield et al. 2013).
Alginate export porin, AEP or AlgE (Rehm et al. 1994). A monomeric 18 stranded beta-barrel that is part of a multicomponent, two membrane, envelope-spanning complex that includes AlgK, AlgX and Alg44 (Rehman and Rehm 2013).
FhuE ferric-coprogen receptor of 729 aas and 1 N-terminal TMS. It is required for the uptake of Fe3+ via coprogen, ferrioxamine B, and rhodotorulic acid (Hantke 1983). The crystal structure of FhuE in complex with coprogen was determined, providing a structural basis to explain its selective promiscuity (Grinter and Lithgow 2019). The structural data, in combination with functional analysis, showed that FhuE has evolved to specifically engage with planar siderophores. A potential evolutionary driver, and a critical consequence of this selectivity, is that it allows FhuE to exclude antibiotics that mimic nonplanar hydroxamate siderophores. These toxic molecules could otherwise cross the outer membrane barrier through a Trojan horse mechanism (Grinter and Lithgow 2019).
|1.B.14.1.14||Ferric-pseudobactin 358 receptor||
FhuA ferrichrome (also albomycin and rifamycin; Colicin M; Microcin J25; Phage T5) receptor (transports phage T1, T5 and φ80 DNA across the outer membrane, dependent on DcrA (SdaC; TC #2.A.42.2.1) and DcrB) (Forms a complex with and acts with TonB and FhuD (the periplasmic binding receptor (3.A.1.14.3) to deliver siderophore to FhuD (Carter et al., 2006; Braun et al., 2009)). Deletion of the 160-residue cork domain and five large extracellular loops converted this non-conductive, monomeric, 22-stranded beta-barrel protein into a large-conductance protein pore (Wolfe et al. 2015).
The iron-citrate receptor/transporter, FecA. TonB mediates both signaling and transport by unfolding portions of the transporter (Mokdad et al. 2012). The ferric citrate regulator, FecR, is translocated across the bacterial inner membrane via a unique Twin-arginine transport dependent mechanism (Passmore et al. 2020).
FepA ferri-enterobactin (also Colicins B and D) receptor for the 37 aas disulfide-containing K+ channel toxin, BgK (Braud et al., 2004). Functions by a "ball and chain" mechanism; The transport process involves expulsion of the N-terminal globular domain from the C-terminal beta-barrel (Ma et al. 2007). Conformational rearrangements occur in the N-terminus of FepA during FeEnt transport, but disengagement of the N-domain, out of the rigid channel suggests that it remains within the transmembrane pore as FeEnt enters the periplasm (Majumdar et al. 2020).
CirA Fe3+-catecholate receptor. Serves as the receptor for the TonB- and proton-dependent uptake of the E. coli bacteriocin, Microcin L (MccL) (Morin et al., 2011). CirA is also the translocator for colicin Ia (Jakes and Finkelstein, 2010). Plays roles in cefiderocol and ceftazidime resistance (Ito et al. 2018).
|1.B.14.1.5||PfeA ferric enterobactin receptor||
Ferripyoverdine/pyocin S3 receptor, FpvA (Adams et al., 2006; Nader et al., 2007; Schalk et al., 2009; Nader et al., 2011)
The Ferripyochelin receptor, FptA (Michel et al., 2007). In addition to Fe3+, FptA takes up Co2+, Ga3+, and Ni2+ at low rates (Braud et al., 2009). The high resolution 3-d structure of FptA (2.0 Å) bound to iron-pyochelin has been solved (Cobessi et al. 2005). The pyochelin molecule provides atetra-dentate coordination of iron. The structure is typical of the TonB-dependent receptor/transporter superfamily.
Ferric-catecholate siderophore (dihydroxybenzoylserine, dihydroxybenzoate) uptake receptor, Fiu or YbiL (Hantke, 1990; Curtis et al., 1988). Plays roles in cefiderocol and ceftazidime resistance (Ito et al. 2018). It can also transport catechol-substituted cephalosporins and is a receptor for microcins M, H47 and E492 (Patzer et al. 2003; Destoumieux-Garzón et al. 2006).
Putative TonB-dpenedent receptor of 790 aas, YddB. It is encoded by a gene adjacent to the YddA-encoding gene (TC# 3.A.1.203.11). YddA is a probable fatty acid exporter. the yddB gene is adjacent to a gene encoding a putative Zn2+ protease, PqqL.
Heme/hemoglobin receptor of 660 aas and 22 C-terminal β-strands with an N-terminal "plug" domain, ShuA. The 3-d structure is known to 2.6 Å resolution, revealing the histidyl residues in the barrel and plug that can interact with heme (Cobessi et al. 2010).
|1.B.14.2.9||Probable TonB-dependent receptor NMB0964||
BtuB cobalamin receptor (also transports phage C1 DNA across the outer membrane). Two Ca2+ binding sites in BtuB mediate cobalamine binding (Cadieux et al., 2007). Cobalamine uptake into the periplasm is reversible, but efflux is pmf-independent (Cadieux et al., 2007). The 3-d structure is available (PDB#1NQE). The Ton box and the extracellular substrate binding site are allosterically coupled (bidirectional), and TonB binding may initiate a partial round of transport (Sikora et al. 2016). Substrate binding to the extracellular surface of the protein triggers the unfolding of an energy coupling motif at the periplasmic surface. Thus, substrate binding reduces the interaction free energy between certain residues, thereby triggering the unfolding of the energy coupling motif (Lukasik et al. 2007). Multiple extracellular loops contribute to substrate binding and transport by BtuB (Fuller-Schaefer and Kadner 2005).
HasR receptor-HasA haemophore heme receptor complex (HasA, an extracellular heme binding protein, binds one heme and transfers it directly to HasR, which uses HasB (2.C.1.1.2) (a TonB homologue) instead of TonB (2.C.1.1.1) for energization) (Benevides-Matos et al., 2008; Izadi-Pruneyre et al., 2006; Lefèvre et al., 2008; Benevides-Matos and Biville, 2010). A signaling domain in HasR interacts with a partially unfolded periplasmic domain of an antisigma factor, HasS, to control transcription by an ECF sigma factor (Malki et al. 2014). The HasR domain responsible for signal transfer is highly flexible in two stages of signaling, extends into the periplasm at about 70 to 90 A from the HasR beta-barrel and exhibits local conformational changes in response to the arrival of signaling activators (Wojtowicz et al. 2016).
SusC of 1041 aas and 1 N-terminal TMS (Joglekar et al. 2018).
FyuA Fe3+-yersiniabactin and pesticin (Psn; a bacteriocin) receptor and uptake protein of 673 aas. It contributes to biofilm formation and infection (Hancock et al., 2008). It is similar to FrpA, an outer membrane protein involved in piscibactin secretion in Vibrio anguillarum (Lages et al. 2022).
TonB-dependent receptor of 700 aas, YncD, a probable iron transporter/receptor in the outer membrane. Deletion of the orthologous yncD genes in Salmonella strains leads to attenuated strains, potentially useful for vaccine development (Xiong et al. 2012; Xiong et al. 2015). Its synthesis is depressed by inclusion of high glucose concentrations in the medium (Yang et al. 2011). YncD is a receptor for a T1-like Escherichia coli phage named vB_EcoS_IME347 (IME347) (Li et al. 2018).
TolC outer membrane exporter of hemolysin, drugs, siderophores such as enterobactin, etc. (Bleuel et al., 2005). The 3-d structure is available (PDB#1EK9). The three monomers form a continuous channel, and each monomer contributes 4 β-strands to the 12 stranded β-barrel (Koronakis et al. 2000). The Salmonella enterica subspecies Typhi homologue is the ST50 antigen (G4C2H4) used in tests for typhoid fever, and a 2.98 Å resolution structure revealed a trimer that forms an alpha-helical tunnel and a beta-barrel transmembrane channel traversing the periplasmic space and outer membrane, respectively (Guan et al. 2015). K. pneumoniae TolC plays a role in resistance towards most antibiotics, suggesting that it can interact with the AcrB efflux pump (Iyer et al. 2019).
CusC outer membrane exporter of copper ion, Cu+, and silver ion Ag+. The crystal structure of CusC is known (Lei et al. 2013) providing evidnce concerning the folding mechanism giving rise to the channel.
Outer membrane hemagglutinin secretion protein, FhaC. Functionally important conserved motifs have been identified (Delattre et al., 2010). The x-ray structure reveals a beta-barrel pore obstructed by two structural elements conserved in all two partner secretion systems, an N-terminal α-helix and an extracellular loop. FhaC goes from the closed to the open state in the presence of the filamentous haemagglutinin adhesin, FHA. The N-terminal α-helix is displaced into the periplasm during FHA secretion (Guérin et al. 2014). With two POTRA domains in the periplasm, a transmembrane beta barrel and a large loop harboring a functionally important motif, FhaC epitomizes the conserved features of the superfamily (Jacob-Dubuisson et al. 2009). The conserved secretion domain of FHA interacts with the POTRA domains, specific extracellular loops and strands of FhaC and the inner beta-barrel surface. The interaction map indicates a funnel-like pathway, with conformationally flexible FHA entering the channel in a non-exclusive manner and exiting along a four-stranded beta-sheet at the surface of the FhaC barrel. This sheet of FhaC guides the secretion domain of FHA along discrete steps of translocation and folding (Baud et al. 2014). The membrane-proximal POTRA domain exists in several conformations, and the binding of FHA displaces this equilibrium (Guérin et al. 2015). TpsB (Two Partner Secretion) transporters belong to the Omp85 or OMPPI superfamily, whose members catalyze protein insertion into, or translocation across membranes. They are composed of a transmembrane β barrel preceded by two periplasmic POTRA domains that bind the incoming protein substrate. Sicoli et al. 2022 detected minor states in heterogeneous populations, identifying transient conformers of FhaC. This revealed substantial, spontaneous conformational changes on a slow time scale, with parts of the POTRA2 domain approaching the lipid bilayer and the protein's surface loops. An amphipathic POTRA2 β hairpin inserts into the β barrel, and these motions enlarge the channel to initiate substrate secretion. This shows how TpsB transporters mediate protein secretion without the need for cofactors, by utilizing intrinsic protein dynamics (Sicoli et al. 2022).
Non-specific, 14 β-stranded monomeric OmpG porin (Conlan et al. 2000). pH-induced conformational changes of OmpG have been studied after reconstitution in native E. coli lipids (Mari et al., 2010). Encoded by a gene in a gene cluster also encoding an ABC sugar uptake system (TC# 3.A.1.1.46), a glucosyl hydrolase and two oxidoreductases. Therefore it's phsiological function may be glucoside uptake. At neutral/high pH, the channel is open and permeable to substrates of size up to 900Da. At acidic pH, loop L6 folds across the channel and blocks the pore. The channel blockage at acidic pH appears to be triggered by the protonation of a histidine pair on neighboring β-strands, which repel one another, resulting in the rearrangement of loop L6 and channel closure (Köster et al. 2015). Crystallization and analysis by electron microscopy and X-ray crystallography revealed the fundamental mechanisms essential for channel activity. A 28 aa extension has been added to the 14 β-TMS barrel to make a 16 β-TMS barrel with normal activity and stability but differing pH sensitivity (Korkmaz et al. 2015). A minimized OmpG porin of only 220 aas still exhibits gating, but it was 5-fold less frequent than in native OmpG. The residual gating of the minimal pore is independent of L6 rearrangements and involves narrowing of the ion conductance pathway, most probably driven by global stretching-flexing deformations of the membrane-embedded β-barrel (Grosse et al. 2014). pH-dependent gating is controlled by an electrostatic interaction network formed between the gating loop and charged residues in the lumen (Perez-Rathke et al. 2018). 3-d structures of the protein in lipid bilayers have been solved (Retel et al. 2017). OmpG may provide a route for D-lactate/D-3-hydroxybutyrate oligo-ester secretion as well as sugar uptake (Utsunomia et al. 2017). OmpG lacks a central constriction and has an exceptionally wide pore diameter of about 13 Å. The equatorial plane of OmpG harbors an annulus of four alternating basic and acidic patches, and manipulation of charge distribution in the arginine and glutamate clusters alters sugar specificity and ion selectivity (Schmitt et al. 2019).
|1.B.22.1.2||XcpQ secretin protein||
The dodecameric secretin, GspD of 650 aas. The 3-d structure is known (PDB 5WQ8) (Korotkov et al. 2013). It reveals a double β-barrel channel with about 60 β-strands in each barrel (Yan et al. 2017).
The secretin, PilQ (SglA) of 901 aas, required for pilus biogenesis, social motility and development of fruiting bodies (Wall et al. 1999).
|1.B.22.3.2||InvG invasion protein secretin||
M. smegmatis porin, MspA (cation selective due to a high density of negative charges in the constriction zone, but it transports glucose, serine, hydrophilic β-lactams and (slowly) phosphate (Wolschendorf et al., 2007)) The MspC paralogue appears to have the same specificity as MspA. Both can also transport fluoroquinolones and chloramphenicol but not the larger erythromycin, kanamycin, and vancomycin (Danilchanka et al., 2008). Also allows uptake of ferric iron (Jones and Niederweis, 2010). The 3-d structure is known (PDB#1UUN). It is a β-barrel with N- and C-termini of their single hairpins on the outside, and their chains run in an anti-clockwise direction around the central pore. Both of these characteristics are opposite in most gram-negative bacterial β-barrels (Remmert et al., 2010). Forms octameric voltage-gated nanopores where each subunit contributes 2 TMSs to the 16 stranded β-barrel (Faller et al. 2004; Rodrigues et al. 2011; Pavlenok et al. 2012) that can be used for nanopore sequencing (Laszlo et al. 2016). MspA is a biosensor for DNA sequencing and many other applications by enabling the production of pores with distinct subunit mutations and pore diameters (Pavlenok et al. 2022).
OprD2; OccD1; porin D transports cationic amino acids, peptides and other compounds: lysine, arginine, histidine, ornithine, basic di- and tri-peptides, and cationic antibiotics such as imipenem (n-formimidoylthienamycin) and other penems and carbapenems (Tamber et al., 2006). The 3-d structure and drugs transported are known (4FOZ; Parkin and Khalid 2014). OprD is the vitronectin receptor. Vitronectin enhances P. aeruginosa adhesion to host epithelial cells and thereby enhances virulence (Paulsson et al. 2015). Loss promotes carbapenem resistance (Shen and Fang 2015; Cavalcanti et al. 2015). Loss results in resistance to meropenem (Fluit et al. 2019).
A tricarboxylate transporting porin, OdpH (Occk5) induced by and transports cis-aconitate, isocitrate and citrate; exhibits a large single channel conductance (Tamber et al., 2006; 2007). This porin exhibits a high degree of anion selectivity, and the outer core and O-antigens of LPS sterically occlude the channel entrance to decrease the diffusion constants of approaching ions (Lee et al. 2018).
OpdC or OccD2 histidine-selective porin (Tamber et al., 2006). The 3-D structure and substrate spcificities are known (PDB 3SY9; Eren et al. 2012).
OdpF (OccK2) glucuronate-selective porin; may also transport benzoate and vanillate (Eren et al., 2012). 3-d structure is known (3SZD).
|1.B.25.1.7||OpdO pyroglutamate-specific porin (Tamber et al., 2006)||
Anion-selective OpdK (OccK1 or OpdK) benzoate/vanillate-selective porin (Tamber et al., 2006; Eren et al., 2012; Liu et al. 2012). The structure of the OpdK porin, specific for vanillate and related small aromatic acids, has been solved by x-ray crystallography (3SYS_A). It is a labile trimer with monomers of an 18 β-stranded barrel and with an inner diameter of 8Å (Biswas et al., 2008). Other substrates transported (but less well) include 4-nitrobenzoate, caproate, octanoate, carbenicillin, cefoxitin, tetracycline antibiotics, and carbapenem antibioitics (imipenem and meropenem) (Eren et al., 2012). Molecular dynamic simulations and mutant analyses have been reported (Wang et al. 2012).
|1.B.25.1.9||OpdP glycine-glutamate-selective porin (Tamber et al., 2006)||
Cyclodextrin (high affinity)/linear malto-oligosaccharide (low affinity) porin, CymA (Orlik et al. 2003). Electroosmosis influences the transport efficiency of cyclodextrins through the CymA pore (Bhamidimarri et al. 2016).
HopQ of 632 aas
LamB (MalL) maltoporin (maltose–maltoheptose). Also catalyzes the uptake of antibiotics (Lin et al. 2014). LamB preferentially binds maltodextrins from the periplasmic side, and thus, sugar binding and uptake are asymmetric (Mulvihill et al. 2019).
Oligosaccharide porin, ScrY (transports sucrose, raffinose and maltooligo-saccharides) (Kim et al. 2002). The 3-d structure known (PDB ID 1A0S). Sucrose translocation through the pore showed two main energy barriers within the constriction region of ScrY. Three asparate residues are key residues, opposing the passage of sucrose, all located within the L3 loop (Sun et al. 2016).
Omp85 outer membrane OMP translocase, YaeT. The high resolution 3-d structure of the N. gonorrhoea orthologue has been solved (Noinaj et al. 2013).
Protective surface antigen D15 precursor. The high resolution 3-d structure of the H. ducreyi orthologue has been solved (Noinaj et al. 2013).
Outer membrane biogenesis complex (Wu et al., 2005). YaeT (BamA) may serve as an outer membrane ""receptor"" for the CdiA/CdiB 2-partner secretion system that mediates direct cell-cell contact-dependent growth inhibition (Aoki et al., 2008). High-resolution structures of crystal forms of BamA POTRA4-5 from E. coli has been reported (Zhang et al., 2011; Sinnige et al. 2014). Solid-state NMR on BamA, a large multidomain integral membrane protein, revealed dynamic conformational states (Renault et al., 2011). In contrast to the N-terminal periplasmic polypeptide-transport-associated (POTRA) domains, the C-terminal transmembrane β-barrel domain of BamA is mechanically much more stable. Exposed to mechanical stress, this β-barrel stepwise unfolds β-hairpins until unfolding has been completed. The mechanical stabilities of β-barrel and β-hairpins are thereby modulated by the POTRA domains, the membrane composition and the extracellular lid closing the β-barrel. The NMR structure of SmpA (OmlA) is also known (Vanini et al. 2006). The periplasmic region of BamA is firmly attached to the β-barrel and does not experience fast global motion around the angle between POTRA 2 and 3, but the barrel is flexible (Sinnige et al. 2014). It appears that the BAM complex does not catalyze insertion and assembly of all out membrane (α- and β-)porins (Dunstan et al. 2015). YfgL shows significant sequence similarity (e-9) with YxaL/K of Bacillus subtilis. The E. coli periplasmic chaperones, Skp and SurA, and BamA, the central subunit of the BAM complex, have been examined with respect to the folding kinetics of a model OMP (tOmpA) (Schiffrin et al. 2017), showing that prefolded BamA promotes the release of tOmpA from Skp, despite the nM affinity of the Skp for tOmpA. This activity is located in the BamA β-barrel domain, but is greater when full-length BamA is present, indicating that both the beta-barrel and POTRA domains are required for maximal activity. By contrast, SurA is unable to release tOmpA from Skp, providing direct evidence against a sequential chaperone model. BamA has a greater catalytic effect on tOmpA folding in thicker bilayers, suggesting that BAM catalysis involves lowering the kinetic barrier imposed by the hydrophobic thickness of the membrane (Schiffrin et al. 2017). While BamA is the primary translocator, TamB is involved in folding and maturation of autotransporters (Babu et al. 2018).
TamA (YftM) of 577 aas; has a 16 transmembrane β-stranded β-barrel with 3 PORTRA domains. The 2.3 Å crystal structure is known revealing that the barrel is closed by a lid-loop (Gruss et al. 2013). The C-terminal β-strand of the barrel forms an unusual inward kink, which weakens the lateral barrel wall and creates a gate for substrate access to the lipid bilayer. TamA is an Omp85 homologue that may function in autotransporter biogenesis together with TamB (TC# 1.B.22.1.2) and OMP85 (Selkrig et al. 2012). The TAM complex likely evolved from an original combination of BamA and TamB, with a later gene duplication event of BamA, giving rise to an additional Omp85 sequence that evolved to be TamA in Proteobacteria and TamL in Bacteroidetes/Chlorobi (Heinz et al. 2015). Possibly TamB nucleates folding of the passenger domain while TamA/B-BamA interact to catalyze β-domain membrane insertion and pore enlargement to facmilitate translocation of partially folded autotransporters (M. Babu et al., unpublished hypothesis).
The Sorting and Assembly Machinery (SAM) complex consists of three proteins that assemble as a 1:1:1 complex to fold beta-barrel proteins and insert them into the mitochondrial outer membrane. Diederichs et al. 2020 reported cryoEM structures of the SAM complex from Myceliophthora thermophila, which show that Sam50 forms a 16-stranded transmembrane beta-barrel with a single polypeptide-transport-associated (POTRA) domain extending into the intermembrane space. Sam35 and Sam37 are located on the cytosolic side of the outer membrane, with Sam35 capping Sam50, and Sam37 interacting extensively with Sam35. Sam35 and Sam37 each adopt a GST-like fold, with no functional, structural, or sequence similarity to their bacterial counterparts. Structural analyses showed how the Sam50 beta-barrel opens a lateral gate to accommodate its substrates (Diederichs et al. 2020).
The oligogalacturonate-specific porin, KdgM. The 3-D structure is known at 1.9 Å resolution (Hutter et al. 2014). KdgM folds into a 12-stranded antiparallel beta-barrel with a circular cross-section defining a transmembrane pore with a minimal radius of 3.1 Å. Most loops that face the cell exterior in vivo are disordered but nevertheless mediate contact between densely packed membrane-like layers in the crystal. The channel is lined by two tracks of arginine residues facing each other across the pore, a feature that is conserved within the KdgM family and is likely to facilitate the diffusion of acidic oligosaccharides (Hutter et al. 2014).
The N-acetylneuraminic acid-inducible, anion selective porin, NanC (Condemine et al., 2005). A crystal structure (3.3 Å resolution) is available (2WJQ; Wirth et al., 2009). It forms a 28 Å high 12 stranded β barrel like the autotransporter, NalP. The pore is lined by basic residues (conserved in other KdgM family members) allowing diffusion of acidic oligosaccharides (Wirth et al., 2009). Single channels of NanC at pH 7.0 have: (1) conductance 100 to 800 pS in 100 mM: KCl to 3 M: KCl), (2) anion over cation selectivity, and (3) two forms of voltage-dependent gating (channel closures above 200 mV). Phosphate interferes with channel conductance (Giri et al. 2012).
SusD protein of 570 aas and 1 N-terminal TMS (Joglekar et al. 2018).
SusD of 502 aas and 1 N-terminal TMS.
Outer membrane maltooligosaccharide uptake protein, SusE, of 387 aas and 1 N-terminal TMS. It forms a complex with the SusC porin (TC# 1.B.14.6.1), the SusD porin (TC# 1.B.38.1.10), the SusF porin (TC# 1.B.38.4.2) and SusG (α-amylase; TC# 8.A.9.1.3) in the outer membrane (Foley et al. 2018). The complex binds starch and maltooligosaccharides (Cho and Salyers 2001).
Outer membrane protein, SusF, of 485 aas and 1 N-terminal TMS. The protein has an N-terminal DUF5115 domain followed by two C-terminal CBM-SusEF-like domains. SusF mediates starch-binding (or maltooligosaccharde-binding) before transport into the periplasm for further degradation. SusE and SusF do not constitute the major starch-binding proteins in the starch degradative pathway. SusF has lower affinity for starch compared to SusE (Shipman et al. 2000). The 3-d structure of the complex has been determined (Cameron et al. 2012). The SusCDEFG complex in the outer membrane is described in more detail in TC# 1.B.38.4.1 (Foley et al. 2018).
OCT plasmid-encoded AlkL outer membrane cation-selective porin, (probably transports alkanes) (van Beilen et al., 1992). Has been used for the uptake of dodecanoic acid methyl ester (DAME) in E. coli for the production of 12-aminododecanoic acid methyl ester (ADAME), a building block for the high-performance polymer Nylon 12 (Ladkau et al. 2016).
The anaerobically induced outer membrance porin, OprG. Transports small neutral amino acids (Kucharska et al. 2015). The 3-d structure is available (Touw et al. 2010). Essential for normal biofilm formation (Ritter et al. 2012). It is an eight-stranded β-barrel monomer that is too narrow to accommodate even the smallest transported amino acid, glycine, raising the question of how OprG facilitates amino acid uptake (Sanganna Gari et al. 2018). Pro-92 of OprG is important for amino acid transport, with a P92A substitution inhibiting transport and the NMR structure of this variant revealing that this substitution produces structural changes in the barrel rim and restricts loop motions. OprG assembles into oligomers in the OM whose subunit interfaces could form a transport channel, and conformational changes in the barrel-loop region may be crucial for its activity (Sanganna Gari et al. 2018).
Outer membrane porin, OmpW, of 212 aas. Mediates transport of quaternary cationic ammonium compounds (Beketskaia et al. 2014). It is involved in anaerobic carbon and energy metabolism, mediating the transition from aerobic to anaerobic lifestyles (Xiao et al. 2016).
|1.B.40.1.1||YadA consists of 3 domains: an adhesion head, a stalk involved in serum resistance, and an anchor that forms a pore for auto-transport (Grosskinsky et al., 2007).||
|1.B.41.1.1||Outer mycolate membrane porin, PorB||
LPS export porin complex, LptBCFG-A-DE, consists of LptD (Omp; OmpA; 784 aas)-LptE (RlpB; 193 aas; O.M. lipoprotein)-LptA (KdsD; YhbN; OstA small; 185 aas periplasmic chaparone protein)-LptB (KdsC; YhbG; 241 aas cytoplasmic ABC-type ATPase)-LptC (YrbK, 199aas;1 N-terminal TMS)- LptFG, part of the ABC transporter. LptDE (1:1 stoichiometry) comprise a two-protein β-barrel-lipoprotein complex in the outer membrane that assembles and exports LPS (Chng et al., 2010). After LPS (or a precursor) is transported across the inner membrane by MsbA (3.A.1.106.1), this seven component system translocates LPS from the outer surface of the inner membrane to the outer surface of the outer membrane using ATP hydrolysis to sequentially energize transfer from one binding site to another in several steps (Freinkman et al. 2012; Okuda et al. 2012; Sherman et al. 2014). LPS interacts with LptC and LptA sequentially before being passed to the LptD outer membrane porin, anchored by the LptE lipoprotein on the inner surface of the outer membrane. LptF and LptG are the transmembrane consituents of the ABC pump, and LptB is the ATPase of an ABC-like system that energizes the transport using several ATP molecules (Okuda et al. 2012; Sherman et al. 2014). LptC interconnects the LptBFG ABC system with the periplasmic LptA protein via its large periplasmic domain (Villa et al. 2013). LptDE form a complex in the outer membrane which inserts LPS into this membrane. The 3-D strcture of the complex shows that the LptE lipoprotein inserts into the 26 stranded barrel of LptD as a plug. The first two strands of LptD contain prolines and are therefore distorted, possibly creating a portal for lateral diffusion of LPS into the outer leaflet of the outer membrane (Qiao et al. 2014). The 3-d structure of the Pseudomonas aeruginosa LptA, LptH, has been solved at 2:75 Å resolution revealing a β-jellyroll fold similar to that in LptD (Bollati et al. 2015). Direct interaction of LptB and LptC has been demonstrated (Martorana et al. 2016). A specific binding site in the LptB ATPase for the coupling helices of the transmembrane LptFG complex
is responsible for coupling ATP hydrolysis by LptB with LptFG
function to achieve LPS extraction (Simpson et al. 2016). After biosynthesis, bacterial lipopolysaccharides (LPS) are transiently anchored to the outer leaflet of the inner membrane (IM). The ABC transporter LptB2FG extracts LPSs from the IM and transports them to the outer membrane. Luo et al. 2017 reported the crystal structure of nucleotide-free LptB2FG from P. aeruginosa. It shows that LPS transport proteins LptF and LptG each contain a TM domain (TMD), a periplasmic beta-jellyroll-like domain and a coupling helix that interacts with LptB on the cytoplasmic side. The LptF and LptG TMDs form a large outward-facing V-shaped cavity in the IM. Mutational analyses suggested that LPS may enter the central cavity laterally, via the interface of the TMD domains of LptF and LptG, and is expelled into the beta-jellyroll-like domains upon ATP binding and hydrolysis by LptB. These studies suggest a mechanism for LPS extraction by LptB2FG that is distinct from those of classical ABC transporters that transport substrates across the IM (Luo et al. 2017). Transport involves a stable association between the inner (LptBFG) and outer (LptDE)
membrane components, supporting a mechanism in which
lipopolysaccharide molecules are pushed one after the other across a protein bridge (LptCA) that connects the inner
and outer membranes (Sherman et al. 2018). The ABC transporter, LptB2FG, which tightly associates with LptC, extracts lipopolysaccharide out of the inner membrane.Li et al. 2019 characterized the structures of LptB2FG and LptB2FGC in nucleotide-free and vanadate-trapped states, using single-particle cryo-electron microscopy. These structures resolve the bound lipopolysaccharide, reveal transporter-lipopolysaccharide interactions with side-chain details and uncover how the capture and extrusion of lipopolysaccharide are coupled to conformational rearrangements of LptB2FGC. LptC inserts its TMS between the two transmembrane domains of LptB2FG, which represents a previously unknown regulatory mechanism for ABC transporters. These results suggest a role for LptC in achieving efficient lipopolysaccharide transport, by coordinating the action of LptB2FG in the inner membrane and Lpt protein interactions in the periplasm (Li et al. 2019). cryo-EM structures of LptB2FG alone and complexed with LptC are known, revealing conformational changes between these states. Two functional transmembrane arginine-containing loops interact with bound AMP-PNP which induces an inward rotation and shift of the transmembrane helices of LptFG and LptC to tighten the cavity, with the closure of two lateral gates, to eventually expel LPS into the bridge (Tang et al. 2019). The ABC transporter, LptB2FGC extracts LPS from the inner membrane and places it onto a periplasmic protein bridge. Lundstedt et al. 2020 showed that residue E86 of LptB is essential for coupling the function of this ATPase to that of its membrane partners, LptFG, at the step where ATP binding drives the closure of the LptB dimer and the collapse of the LPS-binding cavity in LptFG that moves LPS to the Lpt periplasmic bridge consisting of LptC, A and D (from inside to out) and then to the outer membrane insertase, LptE. Defects caused by changing residue E86 are suppressed by mutations altering either the LPS structure or TMSs in LptG. These suppressors fix defects in the coupling helix of LptF, but not of LptG. These observations support a transport mechanism in which the ATP-driven movements of LptB and those of the substrate-binding cavity in LptFG are bi-directionally coordinated through the rigid-body coupling, with LptF's coupling helix being important in coordinating cavity collapse with LptB dimerization (Lundstedt et al. 2020). The TMS of LptC participates in LPS extraction by the LptB2 FGC transporter (Wilson and Ruiz 2022).
Treponema porin, TP0453 of 287 aas. May be involved in ligand transport, altering membrane permeability at acidic pH (4.0 to 5.5) (Luthra et al. 2011). Incubation of the non-lipidated form with lipid vesicles increases their permeability (Hazlett et al. 2005).
The lipoprotein insertase, LolAB, of Gram-negative bacteria
The 36 β-stranded outer membrane porin, CsgG with auxiliary subunits, CsgE and CsgF (Goyal et al. 2014; PMID# 25219853).
Outer membrane phosphate-selective porin OprP (PorP) of 440 aas. Binds and transports a variety of mono, di- and trivalent anions (Benz et al. 1993). An arginine in the pore determines the anion selectivity (Modi et al. 2013). Residues involved in anion affinity and a preference for Pi versus P2 have been identified (Modi et al. 2015). Both monomeric and trimeric OprP are belived to maintain their anion selectivity (Niramitranon et al. 2016). The phosphonic-acid antibiotic fosfomycin is highly permeable through the OprO and OprP channels (Citak et al. 2018).
Pyrophosphate-selective porin OprO (Hancock et al. 1992). The residue basis for the selectivity of P2 over Pi has been determined and involves two residues (Modi et al. 2015). The phosphonic-acid antibiotic fosfomycin is highly permeable through the OprO and OprP channels (Citak et al. 2018).
Attachment GIII (G3P) capsid protein precursor of 434 aa
|1.B.54.1.1||γ-Intimin (Eae protein) (934 aas; Wentzel et al., 2001)||
|1.B.54.1.2||Invasin 985aas (Gal-Mor et al., 2008) (crystal structure of the c-terminal passenger domain has been solved; Hamburger et al., 1999)||
The ZirS/T (ZirS (276 aas)) is the putative exoprotein passenger domain, but it shows no sequence similarity to passenger domains of other Int/Inv family members. ZirT (660 aas) is the outer membrane β-barrel postulated transporter (Gal-Mor et al., 2008).
The β-barrel porin with a superhelical domain containing tetratricopeptide repeats, PgaA or YcdS; exports (deacetylated) poly β-1,6-N-acetyl glucosamine (PGA), a biofilm adhesin that may also play a role in immune evasion (Itoh et al., 2008; Cerca and Jefferson 2008).
Cellulose synthase operon, protein C of 1157 aas and up to 18 C-terminal (720 - 1157 aas) β-strands with a single N-terminal α-TMS, BcsC or YhjL (Zogaj et al. 2001). Translocation across the outer membrane occurs through the BcsC porin, which extends into the periplasm via 19 tetra-tricopeptide repeats (TPR). Acheson et al. 2019 presented the crystal structure of a truncated BcsC, encompassing the last TPR repeat and the complete outer membrane channel domain, revealing a 16-stranded, β barrel pore architecture. The pore is blocked by an extracellular gating loop, while the extended C terminus inserts deeply into the channel and positions a conserved Trp residue near its extracellular exit. The channel is lined with hydrophilic and aromatic residues suggesting a mechanism for facilitated cellulose diffusion based on aromatic stacking and hydrogen bonding (Acheson et al. 2019).
Weakly anion-selective OmpA porin. Can exist in two distinct conductance states (Arora et al. 2000). May function in the transport of phenylpropanoids (resveratrol, naringenin and rutin) (Zhou et al. 2014). Three membrane-bound folding intermediates of OmpA were discovered in folding studies with dioleoylphosphatidylcholine bilayers. A highly synchronized mechanism of secondary and tertiary structure formation, applicable to this and other β-barrel membrane proteins has been described (Kleinschmidt 2006).
OmpA of 210 aas. The 3-d structure has been solved by NMR (Renault et al. 2010), and its dynamics have been examined (Renault et al. 2009).
OmpF (OprF) porin. The N-terminal domain has pore activity (Saint et al. 2000). The protein can exist in multiple conformations of variable conductivities (Nestorovich et al. 2006). Factors affecting its one-domain open conformer have been studied by Sugawara et al. (2010). OprF is a complement component C3 receptor (Mishra et al. 2015) and is a target of antibacterial drugs (Maccarini et al. 2017). OprF assumes dual conformations and is involved in solute transport, cell envelope integrity, biofilm formation and pathogenesis (Cassin and Tseng 2019).
Omp38; OmpA of 356 aas and 1 N-terminal TMSs. It is a selective antibiotic transporting porin (Iyer et al. 2018; Jyothisri et al. 1999) and induces apoptosis in human cell lines through caspase-dependent and AIF-dependent pathways. Purified Omp38 enters host cells and localizes to the mitochondria, which presumably leads to a release of proapoptotic molecules such as cytochrome c and AIF (apoptosis-inducing factor) (Choi et al. 2005).
OmpATb (ArfA). The central domain (residues 73-220) has been reported to exhibit channel activity (Molle et al., 2006). Its expression is dependent on small single TMS membrane proteins which are encoded in a single operon with it (Veyron-Churlet et al., 2011). The rv0899 gene, encoding OmpATb, is part of an operon (rv0899-rv0901) that is required for fast ammonia secretion, pH neutralization, and growth of M. tuberculosis in acidic environments (Song et al. 2011). Homologues are widespread in bacteria with functions in nitrogen metabolism, adaptation to nutrient poor environments, and/or establishing symbiosis with host organisms (Marassi, 2011). The high resolution 3-d structure is known, revealing two independent domains separated by a proline-rich hinge region.The C-terminal domain (OmpATb(198-326)) revealed a module structurally related to other OmpA-like proteins from Gram-negative bacteria, but the N-terminal domain(73-204), which forms channels in planar lipid bilayers, exhibits a fold, which belongs to the α+β sandwich class fold. It exists in a major monomeric form and a minor oligomeric form yielding rings able to insert into phospholipid membranes (Yang et al. 2011).
Outer membrane porin precursor, OmpX (8 TM β-strands). The NMR structures in lipid bilayers has been solved (Mahalakshmi et al., 2007; Mahalakshmi and Marassi, 2008; Fernández et al. 2004). Expression of the encoding gene is induced by acid or base compared to pH 7 (Stancik et al. 2002).
The attachment inversion locus (Ail) (Bartra et al., 2007). Membrane-bound proteins, Ail and OmpF, are involved in the adsorption of T7-related bacteriophage (Zhao et al. 2013).
Porin of 224 aas and 8 beta strands, TtoA (Estrada Mallarino et al. 2015). The crystal structure is known (3DZM) (Nesper et al. 2008). The 2.8 Å structure reveals a transmembrane 8 stranded β-barrel, an extracellular cation-binding region and an external 5-β stranded sheet (Brosig et al. 2009).
The CarO porin is slightly cation-selective and can be mutated to give rise to imipenem-resistance (Zhu et al. 2019). It is of 243 aas (Siroy et al. 2005) and plays a role in cabapenum resistance (Fonseca et al. 2013) as well as MDR (Yang et al. 2015). It has been implicated in the uptake of ornithine as well as carbapenem antibiotics. Zahn et al. 2015 reported crystal structures of three isoforms of CarO. The structures show a monomeric eight-stranded barrel lacking an open channel. CarO has a substantial extracellular domain resembling a glove that contains all the divergent residues between the different isoforms. A6XB80 is another isoform with 77% identity to the one listed here in TCDB. Overexpression of carO is associated with carbapenem resistance (AlQumaizi et al. 2022).
PorI (OpmA) porin. Forms channels that allow the passive diffusion of small hydrophilic solutes up to an exclusion limit of about 600 Da. The 3-d structure is known (PDB ID 1PRN).
The outer membrane β-barrel protein, OmpL32 (Eshghi et al. 2012).
Blue multi-copper oxidase of 516 aas, CueO. CueO is involved in copper tolerance under aerobic conditions. It features the four typical copper atoms that act as electron transfer (T1) and dioxygen reduction (T2, T3; trinuclear) sites. In addition, it displays a methionine- and histidine-rich insert that includes a helix that blocks physical access to the T1 site (Cortes et al. 2015). It catalyzes oxidation of Mn2+ (Su et al. 2014). Also referred to as copper efflux oxidase (Kataoka et al. 2013).
VDAC1 or VDAC porin of 283 aas, which is > 99% identical to human (P21796) and mouse (60932) VDAC1. Mammals possess three VDACs (VDAC1, 2 and 3) encoded by three genes, but they are all similar in sequence (~60-70% identical) (Messina et al., 2011). The 3-d structure of the human VDAC1 is known (PDB ID 2JK4; Bayrhuber et al. 2008). Reviewed by Shoshan-Barmatz et al. 2015. VDAC1 is found both in mitochondria and the plasma membrane (Lawen et al. 2005) where it may cause cytoplasmic ATP loss.. It may be involved in cancer (Shoshan-Barmatz et al. 2017) and Alzheimer's disease (AD) (Shoshan-Barmatz et al. 2018). Along with its low toxicity profile and high antioxidant activity, the gallic acid derivative, AntiOxBEN3, strongly inhibits calcium-dependent mitochondrial permeability transition pore (mPTP) opening (Teixeira et al. 2018). VDAC dimerization plays a role in mitochondrial metabolic regulation and apoptosis in response to cytosolic acidification during cellular stress, and E73 is involved (Bergdoll et al. 2018). Inhibiting VDAC1 overproduction and plasma membrane insertion in β-cells preserves insulin secretion in diabetes (Zhang et al. 2018). βII and βIII-tubulin, bound to VDAC, regulate VDAC permeability (Puurand et al. 2019). This VDAC porin interacts with carrier precursors arriving in the intermembrane space and recruits TIM22 complexes, thus ensuring efficient transfer of the precursors to the inner membrane translocase (Ellenrieder et al. 2019). A method has been develped to determine the number of VDAC1 channels (and other integral membrane proteins) in nanodiscs under various assembly conditions (Häusler et al. 2020). Stable low-conducting states of human VDAC1 predominantly take place from disordered events and do not result from the displacement of a voltage sensor or a significant change in the pore. Conductance jumps reveal entropy as a key factor for VDAC gating (Preto et al. 2022).
19 β-stranded barrel translocase across the outer membrane, Tom40 (Pfam Porin 3 Superfamily).
The pellicle exporting porin of 1193 aas and 1 N-terminal α-helical TMS with up to 48 β-strands, PelB. The porin is in the N-terminal domain while the 19 predicted periplasmic TPRs are C-terminal. These repeats bind PelA, a periplasmic hydrolase (see the family description and Marmont et al. 2017). PelA and PelB together form a modification and secretion complex essential for Pel polysaccharide-dependent biofilm formation in P. aeruginosa (Marmont et al. 2017).
Fatty acid outer membrane porin. Gated by high affinity ligand (fatty acid) binding which causes conformational changes in the N-terminus that open up a channel for substrate diffusion (Lepore et al., 2011). May function in the transport of phenylpropanoids (resveratrol, naringenin and rutin) (Zhou et al. 2014).
|1.B.9.2.3||The 14 TMS hydrocarbon porin, TbuX. The crystal structure is known. (3BRY_A) (Hearn et al., 2008).||
Colicin Ia. Residues lining the channel have been identified (Kienker et al. 2008).
Pore-forming pyocin S5 of 498 aas, PyoS5. Active against several P. aeruginosa clinical isolates where it causes membrane damage and leakage (Ling et al. 2010). Uses the ferripyochelin (FptA) receptor (Elfarash et al. 2014). A PyoS5 immunity protein prevents cell damage (Rasouliha et al. 2013).
Colicin E1 of 522 aas and 1 C-terminal TMS. Ho et al. (2011) suggested a membrane topological model with a circular arrangement of helices 1-7 in a clockwise direction from the extracellular side and membrane interfacial association of helices 1, 6, 7, and 10 around the central transmembrane hairpin formed by helices 8 and 9. ColE1 induces lipid flipping, consistent with the toroidal (proteolipidic) pore model of channel formation (Sobko et al. 2010). The mechanism of channel integration involving the transition of the soluble to membrane-bound form has been presented (Lugo et al. 2016). Colicin E1 uses BtuB as receptor and possibly, the outer membrane TolC protein as the translocator (Cramer et al. 2018). Colicin E1 adopts a closed-channel state at positive transmembrane potentials, correlating with a large tilt angle of alpha-helical TMSs. When the transmembrane potential becomes negative, it inserts into the lipid bilayer with a low tilt angle for the TMSs. Insertion, driven by the negative potential, generates the channel with the open and closed states interconverting reversibly (Su et al. 2019).
Colicin A. The role of the hydrophobic helical hairpin of the pore-forming domain has been elucidated (Bermejo et al. 2013). Acidic conditions promote membrane insertion (Pulagam and Steinhoff 2013).
Colicin B. Its structural stability and interactions have been studied (Ortega et al. 2001).
|1.C.1.3.3||Colicin N (OmpF is the receptor and translocator (Baboolal et al., 2008)).||
|1.C.1.3.4||Colicin S4 (crystal structure known (3FEW_X; Arnold et al., 2009))||
Colicin E2 or E9 (Mosbahi et al., 2002). Colicin E2 is still in contact with its receptor and import machinery when its nuclease domain enters the cytoplasm (Duche, 2007). Colicin E3 is almost identical to Colicin E3 (RNAase). The crystal structure of Colicin E3 with bound BtuB and with the N-terminal translocation (T) domain of E3 and E9 (DNAase) inserted into the OM OmpF porin has been solved (Cramer et al. 2018) revealing: (I) Details of the initial interaction of the colicin central receptor (R)- and N-terminal T-domain with OM receptors/translocators. (II) Features of the translocon include: (a) high-affinity (K d ≈ 10-9 M) binding of the E3 receptor-binding R-domain E3 to BtuB; (b) insertion of disordered colicin N-terminal domain into the OmpF trimer; (c) binding of the N-terminus, documented for colicin E9, to the TolB protein on the periplasmic side of OmpF. Reinsertion of the colicin N-terminus into the second of the three pores in OmpF implies a colicin anchor site on the periplasmic side of OmpF. (III) Studies on the insertion of nuclease colicins into the cytoplasmic compartment imply that translocation proceeds via the C-terminal catalytic domain, proposed here to insert through the unoccupied third pore of the OmpF trimer, consistent with in vitro occlusion of OmpF channels by the isolated E3 C-terminal domain (Cramer et al. 2018).
Pyocin-S2, Pys2 of 689 aas. Causes breakdown of chromosomal DNA as well as complete inhibition of lipid synthesis in sensitive cells. Prevents biofilm formation in vitro and in vivo (Smith et al. 2012). Binds the FpvA receptor (Elfarash et al. 2012). It forms pores though which the toxin enters the cytoplasm (Parret and De Mot 2000).
The alpha-PFT, Haemolysin E, HlyE or ClyA of 536 aas. A peptide derived from the putative transmembrane domain in the tail region of hemolysin E (aas 88-120) assembles in phospholipid membrane and exhibits lytic activity to human red blood cells (Yadav et al., 2009). Residues important for insertion and activity have been identified (Ludwig et al., 2010). An unusual assembly pathway has been proposed (see family description; Fahie et al. 2013). The pore can be blocked by PAMAM dendrimers (Mandal et al. 2016). The C-terminus directs pore formation and function (Sathyanarayana et al. 2016). Similar in structure to Cry6Aa (TC# 1.C.41.2.1) although sequence similarity could not be discerned (Dementiev et al. 2016 and unpublished results). The C-terminal domain is not directly involved in the pore structure, but is not a passive player in pore formation as it plays important roles in mediating the transition through intermediary steps leading to successful pore formation in a membrane (Sathyanarayana et al. 2016). Transmembrane oligomeric intermediates or "arcs" probably form stable proteolipidic complexes consisting of protein arcs with toroidal lipids lining the free edges (Desikan et al. 2017). High-resolution cryo-EM structures revealed that ClyA pore complexes can exist as oligomers of a tridecamer and a tetradecamer, at estimated resolutions of 3.2 Å and 4.3 Å, respectively. The 2.8 A cryo-EM structure of a dodecamer dramatically improves the existing structural model. Structural analysis indicates that protomers from distinct oligomers resemble each other, and neighboring protomers adopt a conserved interaction mode. A stabilized intermediate state of ClyA during the transition process from soluble monomers to pore complexes was identified. Even without the formation of mature pore complexes, ClyA can permeabilize membranes and allow leakage of particles less than ~400 Daltons. In addition, ClyA forms pore complexes in the presence of cholesterol within artificial liposomes (Peng et al. 2019). The mechanism of pore formation has been reviewed (Sathyanarayana et al. 2020). Maurya et al. 2022 described how to monitor the nanopore assembly of bacterial pore-forming toxin Cytolysin A (ClyA) on crowded lipid membranes with single-molecule photobleaching analysis.
The heterokaryon incompatibility prion/amyloid protein, HET-s (Seuring et al., 2012).
The vegetative insecticidal protein, Vip2Ac (462 aas)
Exoenzyme T, ExoT of 453 aas. 74% identical to ExoS (TC# 1.C.106.4.1). ExoS and ExoT properties have been reviewed (Barbieri and Sun 2004). ExoT causes apoptosis in the target cell (Wood et al. 2015).
Antimicrobial dermcidin, DCD. Based on 3-d structural data, dermcidin forms an architecture of high-conductance transmembrane channels, composed of zinc-connected trimers of antiparallel helix pairs. Molecular dynamics simulations elucidated the unusual membrane permeation pathway for ions and showed adjustment of the pore to various membranes (Song et al. 2013). DCD assembles in solution into a hexameric pre-channel complex before targeting the membrane and integration, the complex follows a deviation of the barrel stave model (Zeth and Sancho-Vaello 2017). The tilt angle and the conductance is determined by the membrane thickness and the cholesterol composition (Song et al. 2019). A soluble 48 residue fragment has been structurally characterized (PDB: 2KSG_A). Membrane interactions and pore formation have been investigated for α-helical AMPs leading to the formulation of three basic mechanistic models: the barrel stave, toroidal, and carpet models. Human cathelicidin (LL-37) and dermcidin (DCD) are α-helical, and their structures have been solved at atomic resolution. DCD assembles in solution into a hexameric pre-channel complex before actual membrane targeting and integration steps occur, and the complex follows a deviation of the barrel stave model (Zeth and Sancho-Vaello 2017).
Bifunctional adenylate cyclase-haemolysin toxin precursor, CyaA. Although homologous, HlyA (1.C.11.1.3) and CyaA exhibit different modes of permeabilization (Fiser and Konopásek 2009). A pore model comprising three alpha2-loop-alpha3 hairpins suggested that Gly530XXGly533XXXGly537 in TMS2 could function in toxin oligomerization (Juntapremjit et al. 2015). Structural integrity of TMSs 1, 2, 3 and 5, but not 4, is important for haemolytic activity, particularly for transmembrane helices 2 and 3 that might form the pore (Powthongchin and Angsuthanasombat 2009). CyaA forms small cation-selective membrane pores that permeabilize cells for potassium efflux, contributing to cytotoxicity of CyaA and eventually provoking colloid-osmotic cell lysis (Wald et al. 2016). The toxin penetrates myeloid phagocytes expressing the complement receptor 3 and delivers into the cytosol its N-terminal adenylate cyclase enzyme domain (~400 residues). In parallel, the ~1300 residue-long RTX hemolysin moiety of CyaA permeabilizes target cell membranes for efflux of cytosolic potassium ions (Svedova et al. 2016). Positively-charged side-chains substituted at positions Gln574 and Glu581 in the pore-lining alpha3 enhance hemolytic activity and ion-channel opening, mimicing the highly-active RTX (repeat-in-toxin) cytolysins (Kurehong et al. 2017). Residues 529 to 549 participate in membrane penetration and pore-forming activity (Roderova et al. 2019). Two distinct conformers of CyaA appear to accomplish its two parallel activities within target cell membranes. The translocating conformer would deliver the N-terminal adenylyl cyclase domain into the cytosol of cells, while the pore precursor conformer would assemble into oligomeric cation-selective pores and permeabilize cellular membrane. Both toxin activities involve a membrane-interacting 'AC-to-Hly-linking segment' (residues 400 to 500). Two clusters of negatively charged residues within this linking segment (Glu419 to Glu432 and Asp445 to Glu448) regulate the balance between the AC domain translocating and pore-forming capacities of CyaA as a function of the calcium concentration (Sukova et al. 2020). Four cholesterol-recognition motifs in the pore-forming and translocation domains of CyaA are essential for invasion of eukaryotic cells and lysis of erythrocytes (Amuategi et al. 2022).
The PNC-37 (32 aas) pore-forming peptide derived from the Mdm-2 binding domain of the p53 tumor-supressor protein which is selectively cytotoxic to cancer cells. The 3-d structure is known from NMR anayses (Sookraj et al. 2010). PNC-27 binds to HDM-2 in a 1:1 stoichiometry to induce pore-formation, and the pores are lined by PNC-27 bound to HDM-2 at the membrane surface with the PNC-27 leader sequence lining the pores (Sarafraz-Yazdi et al. 2022).
Dendritic cell natural killer lectin group receptor 1, DNGR-1, of 238 aas and 1 N-terminal TMS. It is also called C-type lectin domain family 9 member A (Cle9a). It functions as an endocytic receptor on a small subset of myeloid cells specialized for the uptake and processing of material from dead cells (Sancho et al. 2009). It recognizes filamentous form of actin in association with particular actin-binding domains of cytoskeletal proteins, including spectrin, exposed when cell membranes are damaged. It mediates the cross-presentation of dead-cell associated antigens in a Syk-dependent manner (Sancho et al. 2009; ). DNGR-1 is a receptor expressed by certain dendritic cell (DC) subsets and by DC precursors in the mouse. It possesses a C-type lectin-like domain (CTLD) followed by a poorly characterized neck region coupled to a transmembrane region and short intracellular tail. The CTLD of DNGR-1 binds F-actin exposed by dead cell corpses and causes the receptor to signal and potentiate cross-presentation of dead cell-associated antigens by DCs.The neck region of DNGR-1 is an integral receptor component that senses receptor progression through the endocytic pathway and has evolved to maximize extraction of antigens from cell corpses (Hanč et al. 2016).
NKG2-D type II protein of 216 aas and 1 central TMS. Functions as an activating and costimulatory receptor involved in immunosurveillance upon binding to various cellular stress-inducible ligands displayed at the surface of autologous tumor cells and virus-infected cells. Provides both stimulatory and costimulatory innate immune responses on activated killer (NK) cells, leading to cytotoxic activity (Zafirova et al. 2011). It stimulates perforin-mediated elimination of ligand-expressing tumor cells; signaling involves calcium influx, culminating in the expression of TNF-alpha (Zuo et al. 2017).
Regenerating islet-derived protein 3α, RegIIIα or Reg3A. Also called Proliferation-induced Protein 34, PAP or HIP of 157 aas. It is a C-type intestinal lectin and forms hexameric pores in Gram-positive bacterial membranes. The 3-d x-ray structure is known (Mukherjee et al. 2014). Lipopolysaccharides inhibit pore formation, and hence, Gram-negative bacteria are usually not susceptible to its killing action (Mukherjee et al. 2014).
ADIPOR2 of 387 aas and 7 TMSs. It may funtion in promoting cholesterol efflux together with ADIPOR1 and adiponectin (Hafiane et al. 2019).
The adiponectin receptor 1 or ADIPOQ, an essential hormone secreted by adipocytes that regulates glucose and lipid metabolism (Tanabe et al. 2015; Yamauchi et al. 2003. Required for normal glucose and fat homeostasis and for maintaining a normal body weight. ADIPOQ-binding activates a signaling cascade that leads to increased AMPK activity, and ultimately to increased fatty acid oxidation, increased glucose uptake and decreased gluconeogenesis. Has high affinity for globular adiponectin and low affinity for full-length adiponectin. The 3-d structure revealed ceramidase activity for both ADIPOR1 and ADIPOR2; however, the two structures are substantially different (Vasiliauskaité-Brooks et al. 2017). It may function with adiponectin to stimulate cholesterol efflux via ABCA1 (Hafiane et al. 2019). The Tyr-Pro dipeptide may function as an AdipoR1 agonist (Lee et al. 2021).
Moricin of 66 aas and 1 TMS is processed to the active 42 aas peptide. The 3-d solution structure has been solved (1KV4).
Moricin of 67 aas; known to increase permeability of and disrupt cytoplasmic membranes (Hara and Yamakawa 1995).
Moricin of 67 aas
Ostreolysin A6, OlyA6 of 138 aas
Perfringolysin O, PFO. In the formation of the pore forming toxin, the elongated toxin monomer binds stably to the membrane in an "end-on" orientation, with its long axis approximately perpendicular to the plane of the membrane bilayer (Ramachandran et al. 2005). This orientation is largely retained, even after monomers associate to form an oligomeric prepore complex. The domain 3 (D3) polypeptide segments that ultimately form transmembrane beta-hairpins remain far above the membrane surface in both the membrane-bound monomer and prepore oligomer. Upon pore formation, these segments enter the bilayer, whereas D1 moves to a position that is substantially closer to the membrane. Therefore, the extended D2 beta-structure that connects D1 to membrane-bound D4 appears to bend or otherwise reconfigure during the prepore-to-pore transition of the perfringolysin O oligomer (Ramachandran et al. 2005). The prepore to pore transition has been visualized by electron microscopy (Dang et al. 2005). Phosphatidylcholine in the outer leaflet increases the cholesterol concentration required to induce PFO binding while phosphatidylethanolamine and phosphatidylserine in the inner leaflet of asymmetric vesicles stabilized the formation of a deeply inserted conformation that does not form pores, even though it contains transmembrane segments (Lin and London 2014). This conformation may represent an important intermediate stage in PFO pore formation. Cholesterol recognition, oligomerization, and the conformational changes involved in pore formation have been reviewed (Johnson and Heuck 2014), and the involvement of the D1 domain in structural transitions leading to pore formation has been studied (Kacprzyk-Stokowiec et al. 2014). Interaction of PFO with cholesterol is sufficient to initiate an irreversible sequence of coupled conformational changes that extend throughout the toxin molecule and induce pore formation (Heuck et al. 2007). Once this transmembrane beta-barrel protein is inserted, PFO assembles into pore-forming oligomers containing 30-50 PFO monomers. These form a pore of up to 300 Å, far exceeding the size of most other proteinaceous pores. Decreasing the length of the β-strands causes the pore to shrink (Lin et al. 2015). Site-directed mutagenesis data combined with binding studies performed with different sterols, and molecular modeling are beginning to shed light on the interaction with cholesterol (Savinov and Heuck 2017). Fine-tuning of the stability of beta-strands by Y181 in perfringolysin O directs the prepore to pore transition (Kulma et al. 2019).
Intermedilysin of 532 aas and 1 N-terminal TMS, ILY or Ply. It binds to membranes containing the human protein CD59 but forms pores only if the membrane contains sufficient cholesterol (Heuck et al. 2007). CD59 is required for the specific coordination of intermedilysin (ILY) monomers and for triggering collapse of an oligomeric prepore. Movement of Domain 2 with respect to Domain 3 of ILY is essential for forming a late prepore intermediate that releases CD59, while the role of cholesterol may be limited to insertion of the TMSs (Boyd et al. 2016). The pore-forming regions are initially folded up on the surfaces of the soluble precursors. To create the transmembrane pores, these regions must extend and refold into membrane-inserted beta-barrels (Tilley and Saibil 2006).
β-Conglycinin α-chain of 639 aas. A pore-forming 20 aa peptide that forms pores in bacterial membranes, 7a16 (FQTLFKNQYGHVRVLQRFNK), was derived from this protein (Xiang et al. 2016).
Glycinin A3 subunit of 516 aas. A pore-forming 20 aa peptide that forms pores in bacterial membranes, G5466 (VFKTHHNAVSSYIKDVFRVI), was derived from this protein (Xiang et al. 2016).
δ-hemolysin of 26 aas and possibly 1 TMS. Lyses red blood cells and other animal cells preferentially to bacteria. Forms dimers on the surfaces of bilayers at low concentrations but pores at higher concentrations (King et al. 2016).
Pore-forming Gasdermin D (Gasdermin-A3, GSDMD, DFNA5L, GSDMDC1, FKSG10) of 484 aas (Ding et al. 2016). GSDMD is activated by inflammasome-activated caspases-1/-4/-5/-11 as well as a caspase-8-mediated pathway during Yersinia infection. These caspases cleave GSDMD to release its functional N-terminal fragment (GSDMD-NT) from its auto-inhibitory C-terminal fragment (GSDMD-CT). GSDMD-NTs bind to acid lipids in mammalian cell membranes and bacterial membranes, oligomerize, and insert into the membranes to form large transmembrane pores. Consequently, cellular contents including inflammatory cytokines are released (e.g., IL-1β), and cells can undergo pyroptosis, a highly inflammatory form of cell death (Xia et al. 2019; Muendlein et al. 2020). As organelles of the innate immune system, inflammasomes activate caspase-1 and other inflammatory caspases that cleave gasdermin D. Caspase-1 also cleaves inactive precursors of the interleukin (IL)-1 family to generate mature cytokines such as IL-1beta and IL-18. Cleaved GSDMD forms transmembrane pores to enable the release of IL-1 and to drive cell lysis through pyroptosis. Cryo-EM structures of the pore and the prepore reveal the different conformations of the two states, as well as membrane-binding elements including a hydrophobic anchor and three positively charged patches. The pore conduit is predominantly negatively charged, but IL-1 precursors have an acidic domain that is proteolytically removed by caspase-1. When permeabilized, unlysed liposomes release positively charged and neutral cargoes faster than negatively charged cargoes of similar sizes, and the pores favor the passage of IL-1beta and IL-18 over that of their precursors (Xia et al. 2021). Gasdermin-A3 oligomers assemble on the membrane surface where they remain attached and mobile. Once inserted into the membrane it grows variable oligomeric stoichiometries and shapes, each able to open transmembrane pores. Molecular dynamics simulations resolved how the membrane-inserted amphiphilic beta-hairpins and the structurally adapting hydrophilic head domains stabilize variable oligomeric conformations and open the pore. Without a vertical collapse, gasdermin pore formation propagates along a set of multiple parallel but connected reaction pathways to ensure a robust cellular response (Mari et al. 2022).
Gasdermin B of 411 aas. Promotes invasioin and metastasis in breast cancer (Hergueta-Redondo et al. 2014).
Two component stonustoxin with alpha and beta subunits, of 703 aas (α-toxin) and 700 aas (β-toxin). See family descriiption for description and references. The two subunits are 47% identical.
Co2+-resistance protein, CorC, of 292 aas and 0 TMSs (Sponder et al. 2010). The E. coli orthologue (P6AE78) is 97% identical to the S. enterica protein.
Cytohemolysin precursor, HlyA (Vibrio cholerae cytolysin, VCC) is a beta-barrel pore-forming toxin (beta-PFT). A cryo-electron microscopic study revealed low resolution structures for different functional forms (Dutta et al., 2009). Crystal structures of the soluble and transmembrane heptamer reveal common features among disparate pore-forming toxins (De and Olson, 2011). The toxin forms transmembrane heptameric β-barrel channels with two lectin activities on the β-prism and the β-trefoil (Rai et al. 2013). A ring of tryptophan residues forms the narrowest constriction in the transmembrane channel reminiscent of the phenylalanine clamp identified in anthrax protective antigen (Krantz et al., 2005). A single point mutation prevents membrane integration and pore formation (Paul and Chattopadhyay 2012). The deletion of the pre-stem segment does not affect membrane binding and pre-pore oligomer formation, but it critically abrogates the functional pore-forming activity of VCC (Paul and Chattopadhyay 2013). The membrane-bound monomer can not form pores (Rai and Chattopadhyay 2014). VCC can be delivered to host cells via extracellular bacterial vesicles (Elluri et al. 2014). Loops within the membrane-proximal region of VCC play critical roles in determining the functional interactions of the toxin with the membrane lipids that allow pore formation (Rai and Chattopadhyay 2015). VCC may interfer with signalling in the target cell as well as form pores (Khilwani and Chattopadhyay 2015). A functional map of the VCC membrane-binding surface has been published (De et al. 2015). Residues involved in oligomerization have been identified (Rai and Chattopadhyay 2016). The multiple membrane interaction mechanisms of VCC have been reviewed (Kathuria and Chattopadhyay 2018). A model of the transmembrane pore has been presented that accounts for some of its properties (Pantano and Montecucco 2006). An overview of the understanding regarding the membrane interaction mechanisms of VCC and their functional implications for the pore-forming activity of the toxin have been reviewed (Kathuria and Chattopadhyay 2018). The specific cholesterol-binding ability of VCC does not appear to dictate its association with the cholesterol-rich micro-domains on human erythrocytes but may be essential for formation of the membrane integraed pore structure (Gupta et al. 2022). Rather, targeting of VCC toward the membrane micro-domains of human erythrocytes possibly acts to facilitate the cholesterol-dependent pore-formation mechanism of the toxin (Cyr 2018). Tyrosine in the hinge region of the pore-forming motif regulates oligomeric beta-barrel pore formation (Mondal et al. 2020). Single-particle cryo-EM was used to characterize the structure of the VCC oligomer in large unilamellar vesicles. The rim domain amino acid residues of VCC interacting with lipid membrane were visualized. Cryo-EM views of lipid bilayer-embedded VCC suggested interesting conformational variabilities, especially in the transmembrane channel, which could have a potential impact on the pore architecture and assist in understanding the pore formation mechanism (Sengupta et al. 2021).
Vibrio vulnificus hemolysin (VVH-A). Consists of three domains: Hemolysin N (residues 1 - 200), Leukocidin (residues 220 - 480) and Ricin (690 - 600).
Magainin precursor of 333 aas and 1 TMS. 3-d structural determinations and simulations show the oligomeric states, transmembrane helices and tilt angles in the various states of the mature Maganin (Pino-Angeles et al. 2016). Forms stable heterooligomers with PglA (TC# 1.C.16.1.5) at lower concentrations of the two peptides than allows each one alone to form pores in which PglA, rather than magainin 2 forms the pore (Strandberg et al. 2016). Mixtures of peptides such as magainin 2 and PGLa, which are stored and secreted naturally as a cocktail, exhibit considerably enhanced antimicrobial activities when investigated together in antimicrobial assays and also in pore forming experiments applied to biophysical model systems. Investigations have revealed that these peptides do not form stable complexes but act by specific lipid-mediated interactions and are influenced by the nanoscale properties of phospholipid bilayers (Juhl et al. 2021).
Cecropin A, B and C precursor. Cecropin A and B form pores, but cecropin P1 doesn't. Insertion and activity are dependent on the lipids present. Can be cation- or anion-selective, or non-selective. The negative pole of the dipole is probably inserted into the membrane first (Efimova et al. 2014).
Melittin major precursor (anion selective). Its bacteriocidal activity against Listeria and its cytotoxicity to animal cells have been studied (Wu et al. 2016). In zwitterionic membranes, melittin forms transmembrane toroidal homomeric pores supported by four to eight peptides. Its ability to diffuse freely in a 1,2-dimyristoyl-SN-glycero-3-phosphocholine membrane leads to dynamic pores of vaious diameters with varying molecularity containing from 4 to peptides/channel (Pino-Angeles and Lazaridis 2018).
Defensin 1, 2 and 3 precursor, also called human neutrophil peptide.
|1.C.19.1.5||Defensin-related cryptdin-4 precursor, Crp4 (structure: 2GW9_A) (Cummings and Vanderlick, 2007).||
Pesticide crystal protein Cry4Ba (δ-endotoxin) (1136aas). Cadherin AgCad1 is the receptor for Cry4Ba (Hua et al., 2008). Asn183 in TMS5 is essential for oligomerizatioin of the protein in the midgut membrane of the insect, and therefore for pore formation and toxicity (Likitvivatanavong et al. 2006). The complete structure of a functional form of the Bacillus thuringiensis Cry4Ba delta-endotoxinhas been solved with nsight into the toxin-induced transmembrane pore architecture (Thamwiriyasati et al. 2022). The 2.0 Å crystal structure revealed a wedge-shaped arrangement of three domains: a well-defined N-terminal domain of eight alpha-helices responsible for pore formation, a three-beta-sheet prism displaying two functional motifs and a C-terminal beta-sandwich domain. Two conserved side-chains-Asn(166) and Tyr(170) in the α4-α5 loop were found to interact directly with phospholipid head groups, leading to pore opening and stability (Thamwiriyasati et al. 2022).
The Cry8Ea1 toxin of 1164 aas. The 2.2-Å crystal structure has been reported (Guo et al. 2009). Cry8Ea1 is specifically toxic to the underground larvae of Holotrichia parallela (Jia et al. 2014).
Class I lantibiotic bacteriocin, Epidermin precursor (has a mersacidin-like Lipid II domain, and forms Lipid II-dependent pores) (Sahl & Bierbaum, 2008). The genetic organization, biosynthesis, modification, excretion, extracellular activation of the modified pre-peptide by proteolytic processing, self-protection of the producer, gene regulation, structure, and mode of actionhave been reviewed (Götz et al. 2014).
Nukacin ISK-1 of 57 aas (Okuda et al., 2008). It is active on Gram-positive bacteria, including Lactobacillus sakei, Leuconostoc mesenteroides and Pediococcus
pentosaceus. The bactericidal activity is based on
depolarization of energized bacterial cytoplasmic membranes, initiated
by the formation of aqueous transmembrane pores (Aso et al. 2004). It is processed and secreted by NukT (TC# 3.A.1.111.7) (Zheng et al. 2017).
|1.C.22.1.6||Plantaricin A precursor||
Bacteriocin protein of 51 aas and 1 TMS
Class IIa bacteriocin Pediocin PA-1 precursor of 62 aas. Class II bacteriocins are unmodified membrane-active peptides that act over a narrow spectrum of target bacteria. They bind a specific receptor protein on the membrane to form a pore, leading to membrane permeabilization and cell death. The specific receptor acts as a docking molecule, not as a structural piece of the pore, if the bacteriocin is anchored to the membrane (Ríos Colombo et al. 2019).
|1.C.24.1.2||Class IIa bacteriocin Sakacin P precursor||
|1.C.24.1.6||Class IIa bacteriocin Leucocin A precursor||
|1.C.24.1.7||Class IIa bacteriocin Carno(bacterio)cin B2 precursor||
|1.C.25.1.1||Class IIb two peptide bacteriocin Lactococcin G (Oppegard et al., 2007)|