1.F.1 The Synaptosomal Vesicle Fusion Pore (SVF-Pore) Family

Many substances (neurotransmitters, proteins, complex carbohydrates, small molecules such as ATP) in eukaryotes are sequestered in vesicles which then fuse with the plasma membrane releasing to the extracellular medium the intravesicular contents. The vesicles can then either reform or remain associated with the plasma membrane. In the latter case, the lipids flow from the vesicle into the plasma membrane. SNARE (Soluble NSF Attachment protein Receptor) transmembrane domains catalyze lipid flipping as well as membrane fusion. Langer and Langosch (2011) have shown that lipid flippase activity is not essential for membrane fusion.  In fact, Zhou et al. (2013) provided evidence that the transmembrane domains of SNARES are not required for membrane fusion.  This suggests that these proteins function as power engines to bring the membranes together (Rizo and Xu 2013).  The SNARE complex in mammalian neurosecretory cells is composed of the proteins synaptobrevin 2 (also called VAMP2), syntaxin, and SNAP-25 (plays a key role in vesicle fusion.  At least in neurosecretory cells, fusion pore formation may be directly accomplished by conformational changes in the SNARE complex via movement of the transmembrane domains (Fang and Lindau 2014).  The fusion pore may be a hybrid structure composed of both lipids and proteins (Bao et al. 2015). Fusion pores have been reviewed (Sharma and Lindau 2018), and some of these proteins contain intrinsically disordered regions (Aneskievich et al. 2021).

.Fusion has been shown to initiate by formation of a pore complex of various pore sizes (He et al., 2006). Fusion of a vesicle with the cell membrane opens a pore that releases neurotransmitters to the extracellular space. The pore can either dilate fully so that the vesicle collapses completely, or close rapidly to generate 'kiss-and-run' (reversible) fusion. The size of the pore determines the release rate. At synapses, the size of the fusion pore may vary. By recording fusion pore kinetics during single vesicle fusion, He et al. (2006) found both full collapse and 'kiss-and-run' fusion at calyx-type synapses. For full collapse, the initial fusion pore conductance (G_p) is usually >375 pS and increases rapidly at ≥299 pS ms^–1. 'Kiss-and-run' fusion is seen as a brief capacitance flicker (<2 s) with G_p >288 pS for most flickers, but within 15-288 pS for the remaining flickers. Large G_p (>288 pS) might discharge transmitter rapidly and thereby cause rapid synaptic currents, whereas small G_p might generate slow and small synaptic currents. Thus, 'kiss-and-run' fusion occurs at synapses and can generate rapid postsynaptic currents. The results of He et al. (2006) suggest that various fusion pore sizes help to control the kinetics and amplitude of synaptic currents. SNARE assembly and disassembly have also been studied by Jena (2008).

The crystal structure at 2.4 Å resolution for the SNARE ([soluble N-ethyl-maleimide-sensitive fusion (NSF) protein] attachment protein receptor) complex involved in synaptic exocytosis has been reported (Sutton et al., 1998). Additionally, lipid-bound synaptobrevin has been solved by NMR (Ellena et al., 2009). The core fusion complex contains syntaxin-1A, synaptobrevin-II (= VAMPII) and SNAP25B. The structure reveals a highly twisted, parallel 4-helix bundle with leucine zipper-like layers at the center of the synaptic fusion complex. Within these layers is an ionic layer of an arg and 3 gln residues from each of the four α-helices. These residues are highly conserved in the SNARE family. The regions flanking the leucine zipper-like layers contain a hydrophobic core. The surface of the synaptic fusion complex possesses distinct hydrophilic, hydrophobic and charged regions important for fusion (Ernest and Brunger, 2003; Sutton et al., 1998).

Proteins known to be associated with SNARE complexes, conserved from yeast to humans, include: (1) syntaxin-1A (STX1A), (2) synaptobrevin I (VAMPI), (3) synaptobrevin-II (VAMPII), (4) SNAP25B (cytoplasmic membrane protein), (5) SNAP23, (6) syntaxin 4A (STX4A), (7) VAMP8, (8) snapin, and (9) NSF (N-ethyl maleimide-sensitive fusion) protein. Fusion-competent SNARE complexes may consist of 3 Q-SNAREs and 1 R-SNARE (Fasshauser et al., 1998). Synaptotagmin IV modulates vesicle size and fusion pores in PC12 cells (Zhang et al., 2010). Williams et al. (2009) have proposed a model in which the positively charged VAMP and syntaxin juxtamembrane regions facilitate fusion by bridging the negatively charged vesicle and plasma membrane leaflets. There are many isoforms of the synaptobrevins.  

During exocytosis, the fusion pore expands to allow release of neurotransmitters and hormones to the extracellular space. Many proteins have been implicated in vesicle fusion. Myosin II has been shown to participate in the transport of vesicles, and in the final phases of exocytosis, it affects the kinetics of catecholamine release in adrenal chromaffin cells. The fusion pore is controlled by myosin II which acts as a molecular motor, acting on fusion pore expansion by hindering its dilation when it lacks the phosphorylation sites (Neco et al., 2008). Fang et al., 2008 have proposed that SNARE/lipid complexes form proteolipid fusion pores and that SNAP-25, together with several other proteins, controls fusion pore opening and conductance.  Fusion pore flux directly contributes to miniature excitatory postsynaptic current (mEPSC) rise-time, and variations in fusion pores account for differences among neuron responses (Jackson et al. 2024).

Stein et al., (2009) reported the X-ray structure of the neuronal SNARE complex, consisting of rat syntaxin 1A, SNAP-25 and synaptobrevin 2, with the carboxy-terminal linkers and transmembrane regions at 3.4 A resolution (Stein et al., 2009). The structure shows that assembly proceeds beyond the already known core SNARE complex, resulting in a continuous helical bundle that is further stabilized by side-chain interactions in the linker region. The results suggest that the final phase of SNARE assembly is directly coupled to membrane merger with helical extension of the neuronal SNARE complex into the membrane (Stein et al., 2009).

In chromaffin cells, Ca²⁺ binding to synaptotagmin-1 and -7 triggers exocytosis by promoting fusion pore opening and fusion pore expansion. Synaptotagmins contain two C2 domains that both bind Ca²⁺ and contribute to exocytosis. Segovia et al. (2010) used patch amperometry measurements in WT and synaptotagmin-7-mutant chromaffin cells to analyze the role of Ca²⁺ binding to the two synaptotagmin-7 C2 domains in exocytosis. They showed that Ca²⁺ binding to the C2A domain suffices to trigger fusion pore opening, but that the resulting fusion pores are unstable and collapse, causing a dramatic increase in kiss-and-run fusion events. Thus, synaptotagmin-7 controls fusion pore dynamics during exocytosis via a push-and-pull mechanism in which Ca²⁺ binding to both C2 domains promotes fusion pore opening, but the C2B domain is selectively essential for continuous expansion of an otherwise unstable fusion pore.

Synaptotagmin-1 (syt1) is a vesicle-localized transmembrane protein with two cytoplasmic C2 domains, C2A and C2B thatis the major Ca²⁺ sensor for fast neurotransmitter release. The C2A and the C2B domains each bind Ca²⁺, which enables them to interact with membranes, causing membrane fusion. Ca²⁺ -dependent and -independent interactions between syt1 with SNAREs have been demonstrated.  Between the tandem Ca²⁺-binding C2 domains (C2AB) and the single transmembrane α-helix is a highly charged 60-residue- long linker. Lai et al. 2013 found that the linker region of Syt1 is essential for its two signature functions: Ca2+-independent vesicle docking and Ca2+-dependent fusion pore opening. The linker contains the basic amino acid-rich N-terminal region and the acidic amino acid-rich C-terminal region. When the charge segregation was disrupted, fusion pore opening was slowed, whereas docking was unchanged. Intramolecular disulfide cross- linking between N- and C-terminal regions of the linker or deletion of 40 residues from the linker reduced docking while enhancing pore opening. The results suggest that the electrostatically bipartite linker region may facilitate pore opening.

The fusion of two membranes is believed to occur through a hemifusion intermediate. Ca²⁺ binding by syt1 is mediated by a series of conserved aspartate residues that line pockets on one end of each of the C2A and C2B domains. Martens et al. (2007) used a syt1 construct lacking the transmembrane domain but having the double C2 domain module (C2AB). Ca²⁺ binding allowed the C2A and C2B domains to interact with negatively charged phospholipids such as phosphatidylserine and phosphatidylinositol-4,5-bisphosphate. This interaction resulted in the insertion of four loops (two from each of the C2 domains) into the lipid bilayer. M173, F234, V304, and I367, located on the tips of the membrane-binding loops, penetrate to a third of the lipid monolayer depth. This kind of hydrophobic-loop insertion generates a tendency for the monolayer to bend to relieve the tension created by the insertion. If syt1 contributes to spontaneous membrane curvature, the closer the membrane curvature is to that preferentially produced by syt1, the stronger the syt1 affinity for membrane binding should be. Conversely, addition of syt1 to initially flat membranes should induce a positive curvature.

The Ca²⁺ sensor required for fast fusion is synaptotagmin-1. The activation energy of bilayer-bilayer fusion is very high (≈40 k_BT). Martens et al., (2007) found that, in response to Ca²⁺ binding, synaptotagmin-1 could promote SNARE-mediated fusion by inducing high positive curvature in target membranes upon C2-domain membrane insertion. Thus, synaptotagmin-1 triggers the fusion of docked vesicles by local Ca²⁺-dependent buckling of the plasma membrane together with the zippering of SNAREs.

Ngatchou et al. (2010) showed that the ability of synaptobrevin II (sybII) to support exocytosis is inhibited by addition of one or two residues to the sybII C terminus depending on their energy of transfer from water to the membrane interface, following a Boltzmann distribution. These results suggest that following stimulation, the SNARE complex pulls the C terminus of sybII deeper into the vesicle membrane. Ngatchou et al. (2010) proposed that this movement disrupts the vesicular membrane continuity, leading to fusion pore formation. Thus, fusion pore formation begins with molecular rearrangements at the intravesicular membrane leaflet and not between the apposed cytoplasmic leaflets.

Bulk endocytosis is a process by which nerve terminals retrieve large amounts of synaptic vesicle membrane during periods of strong stimulatory intensity. The process is rapidly activated and is most probably calcium dependent in a similar manner to synaptic vesicle exocytosis (Clayton et al., 2007). However the relationships of these two processes to each other are not well defined.

Shi et al. (Shi et al., 2012) used lipid bilayer nanodiscs as fusion partners; their rigid protein framework prevents dilation and reveals properties of the fusion pore induced by SNARE. They found that although only one SNARE per nanodisc is required for maximal rates of bilayer fusion, efficient release of content on the physiologically relevant time scale of synaptic transmission required three or more SNARE complexes (SNAREpins) and the native transmembrane domain of vesicle-associated membrane protein 2 (VAMP2). They suggested that several SNAREpins simultaneously zippering their SNARE transmembrane helices within the freshly fused bilayers provide a radial force that prevents the nascent pore from resealing during synchronous neurotransmitter release.  VAMP2 is involved in the targeting and/or fusion of transport vesicles to their target membrane and also modulates the gating characteristics of the delayed rectifier voltage-dependent potassium channel KCNB1. The intracellular periodontal pathogen, P. gingivalis, exploits a recycling pathway involving VAMP2 to exit from infected cells (Takeuchi et al. 2016).

SNARE proteins (1.F.1) and fusogenic viral membrane proteins (1.G.1) represent the major classes of integral membrane proteins that mediate fusion of eukaryotic lipid bilayers. Although both subclasses have different primary structures, they share a number of basic architectural features. The fusogenic function of representative fusion proteins is influenced by the primary structure of the single transmembrane domain (TMD) and the region linking it to the soluble assembly domains. Neumann and Langosch (2011) demonstrated conserved overall and/or site-specific enrichment of β-branched residues and Gly within the TMDs, underrepresentation of Gly and Pro in regions flanking the TMD N-terminus, and overrepresentation of the same residue types in C-terminal flanks of SNAREs and viral fusion proteins. The basic Lys and Arg residues are enriched within SNARE N-terminal flanking regions. These observations suggest evolutionary conservation of key structural features of fusion proteins. Ca²⁺-triggered release of neurotransmitters and hormones depends on soluble N-ethylmaleimide- sensitive factor attachment protein receptors (SNAREs) to drive the fusion of the vesicle and plasma membranes. The formation of the SNARE complex by the vesicle SNARE synaptobrevin 2 (syb2) and the two plasma membrane SNAREs syntaxin (syx) and SNAP-25 draws the two membranes together, but the events that follow membrane juxtaposition. The SNAREs syx and syb2 have TMSs that exert force on the lipid bilayers. The TMD of syx influences fusion pore flux in a manner that suggests it lines the nascent fusion pore through the plasma membrane. The TMS of syb2 traverses the vesicle membrane and is the most likely partner to syx in completing a proteinaceous fusion pore through the vesicle membrane (Chang et al. 2015). The syb2 TMS is involved in fusion pore formation during catecholamine exocytosis in mouse chromaffin cells. Fusion pore flux was sensitive to the size and charge of TMS residues near the N terminus; fusion pore conductance was altered by substitutions at these sites. Unlike syx, the syb2 residues that influence fusion pore permeation fell along two alpha-helical faces of its TMD, rather than one. Thus, the syb2 TMS is important in nascent fusion pores, but in a very different structural arrangement from that of the syx TMS. 

The initial, nanometer-sized connection between the plasma membrane and a hormone- or neurotransmitter-filled vesicle -the fusion pore- can flicker open and closed repeatedly before dilating or resealing irreversibly. Single flickering pores connect v-SNARE (232 aas, 1 C-terminal TMS)-reconstituted nanodiscs to cells ectopically expressing cognate, 'flipped' t-SNAREs (513 aas, 1 C-terminal TMS). Conductance through single, voltage-clamped fusion pores directly reported sub-millisecond pore dynamics. Pore currents fluctuated, transiently returned to baseline multiple times, and disappeared ~6 s after initial opening, as if the fusion pore fluctuated in size, flickered, and resealed. Interactions between v- and t-SNARE transmembrane domains (TMDs) promote, but are not essential for pore nucleation. TMD modifications designed to disrupt v- and t-SNARE TMD zippering prolonged pore lifetimes dramatically (Wu et al. 2016). 

Conformational flexibility of the single C-terminal synaptobrevin-2 TMS is essential for efficient Ca²⁺-triggered exocytosis and actively promotes membrane fusion as well as fusion pore expansion. Introduction of helix-stabilizing leucine residues within the TMS region spanning the vesicle's outer leaflet strongly impairs exocytosis and decelerates fusion pore dilation, but increasing the number of helix-destabilizing, ss-branched valine or isoleucine residues within the TMS restores normal secretion while accelerating fusion pore expansion beyond the rate found for the wild type protein. Thus, the synaptobrevin-2 TMS catalyzes the fusion process by its structural flexibility, actively setting the pace of fusion pore expansion (Dhara et al. 2016).

Through atomistic molecular dynamics simulations, transient pore formation, induced by close contact of two apposed bilayers occurs (Bu et al. 2016). Close contacts give rise to a high local transmembrane voltage that induces transient pore formation. Through simulations on two apposed bilayers fixed at a series of given distances, the process in which two bilayers approaching to each other under the pulling force from fusion proteins for membrane fusion was mimicked. Close contact induced fusion pore formation. Bu et al. 2016 showed that the transmembrane voltage increases with the decrease of the distance between the bilayers, and below a critical distance, depending on the lipid composition, the local transmembrane voltage can be sufficiently high to induce formation of transient pores. The size of these pores is approximately 1~2 nm in diameter, which is large enough to allow passing of neurotransmitters. Resealing of the membrane pores, resulting from the neutralization of the transmembrane voltage by ions through the pores, was then observed. The membrane tension can either prolong the lifetime of transient pores or cause them to dilate for full collapse.

Membrane composition and protein-lipid interactions influence the likelihood of the nascent fusion pore forming. Hastoy et al. 2017 related these factors to the hypothesis that fusion pore expansion is affected in type-2 diabetes via changes in disease-related gene transcription and alterations in the circulating lipid profile.  Zipping of SNARE complexes pulls the polar C-terminal residues of the synaptobrevin 2 and syntaxin 1A transmembrane domains to form a hydrophilic core between the two distal leaflets, inducing fusion pore formation. Restricted SNARE mobility is required for rapid fusion pore formation, but removal of the restriction is required for fusion pore expansion (Sharma and Lindau 2018).

Membrane fusion requires tethers, SNAREs of R, Qa, Qb, and Qc families, and chaperones of the SM, Sec17/SNAP, and Sec18/NSF families. SNAREs have N-domains, SNARE domains that zipper into 4-helical RQaQbQc coiled coils, a short juxtamembrane (Jx) domain, and (often) a C-terminal transmembrane anchor. Orr et al. 2022 reconstituted fusion with purified components from yeast vacuoles (TC# 1.F.1.1.2), where the HOPS protein combines tethering and SM functions. The vacuolar Rab, lipids, and R-SNARE activate HOPS to bind Q-SNAREs and catalyze trans-SNARE associations. With SNAREs initially disassembled, as they are on the organelle, R- and Qa-SNAREs require their physiological juxtamembrane (Jx) regions for fusion. Swap of the Jx domain between the R- and Qa-SNAREs blocks fusion after SNARE association in trans. This block is bypassed by either Sec17, which drives fusion without requiring complete SNARE zippering, or transmembrane-anchored Qb-SNARE in complex with Qa. The abundance of the trans-SNARE complex is not the sole fusion determinant, as it is unaltered by Sec17, Jx swap, or the Qb-transmembrane anchor. The sensitivity of fusion to Jx swap in the absence of a Qb transmembrane anchor is inherent to the SNAREs, because it remains when a synthetic tether replaces HOPS (Orr et al. 2022).

The transport reaction catalyzed in response to fusion pore opening is:

neurotransmitter (intravesicular) → neurotransmitter (extracellular)