1.B.1 The General Bacterial Porin (GBP) Family
OMP porins are present in the outer membranes of Gram-negative bacteria, mitochondria and plastids. They catalyze the energy-independent facilitation of small (Mr of <1000 Da) molecules across the outer membranes of bacteria and organelles with variable degrees of selectivity. The structurally characterized members of this functional superfamily usually consist of homotrimeric proteins with subunits that are of 250-450 amino acyl residues in length. The high resolution three-dimensional structures of several of these proteins are known. These proteins include OmpC, OmpF and PhoP of E. coli. They form 16-stranded antiparallel β-barrel structures with all β-strands hydrogen-bonded to their nearest neighbors along the chain. Each trimer consists of three channels, each with the β-barrel perpendicular to the plane of the membrane. Polypeptide loops lining the inner barrel wall restrict the channel width, thereby defining the diffusion properties of the pore. Some porins are cation-selective, others are anion-selective and still others are selective for specific compounds (e.g., sugars, nucleotides, phosphate, pyrophosphate). Sequence comparisons and three-dimensional structural analyses suggest that many of the families described under category 1.B are related (see porin superfamilies in TCDB and (Reddy and Saier 2016). Outer membrane porins have been reviewed (Masi et al. 2019; Vergalli et al. 2019). Hermansen et al. 2022 have summarized the knowledge of beta-barrel structure and folding and give an overview of their functions, evolution, and potential as drug targets. Larger porins can be made from smaller porins using a loop-to-hairpin mechanism (Dhar et al. 2023). Gating of beta-barrel protein pores, porins and channels has been reviewed (Mayse and Movileanu 2023). Structural bioinformatic studies of bacterial outer membrane beta-barrel porins have been conducted (Sajeev-Sheeja et al. 2023).
β-barrel membrane proteins perform a variety of functions, such as mediating non-specific, passive transport of ions and small molecules, selectively passing molecules like maltose and sucrose, and can form voltage dependent anion channels. Understanding the structural features of β-barrel membrane proteins and detecting them in genomic sequences are challenging tasks in structural and functional genomics. With the survey of experimentally known amino acid sequences and structures, the characteristic features of amino acid residues in β-barrel membrane proteins and novel parameters for understanding their folding and stability have been described by Gromiha and Suwa (2007). Statistical methods and machine learning techniques discriminate β-barrel membrane proteins from other folding types of globular and membrane proteins. Different methods including hydrophobicity profiles, rule based approach, amino acid properties, neural networks, hidden Markov models etc., predict membrane spanning segments of β-barrel membrane proteins. Discrimination techniques for detecting β-barrel membrane proteins in genomic sequences are discussed by Gromiha and Suwa (2007).
Vibrio furnissii possesses an outer membrane porin that is induced by β1,4-N-acetyl glucosamine (GlcNAc) oligomers of two to six sugar units, hydrolysis products of chitinase action on chitin (Keyhani et al., 2000). This porin is required for growth on (GlcNAc)3, and it transports acetylated chitobiose analogues, suggesting that it is specific for these oligosaccharides. It forms a subfamily (TC #1.B.1.7.1) of the GBP family. Another porin, OmpP2 of Haemophilus influenzae (TC # 1.B.1.3.2), shows specificity for nicotinamide-derived nucleotide substrates (Andersen et al., 2003).
Gram-negative Legionella pneumophila produces a siderophore (legiobactin) that promotes lung infection. lbtA and lbtB are required for the synthesis and secretion of legiobactin. An iron-repressed gene (lbtU) is directly upstream of the lbtAB-containing operon. LbtU is an outer membrane protein consisting of a 16-stranded transmembrane β-barrel, multiple extracellular domains, and short periplasmic tails. Although replicating normally, lbtU mutants, like lbtA mutants, were impaired for growth on iron-depleted media and would not take up Fe3+ legiobactin. It is the Legionella siderophore receptor.
The generalized transport reaction catalyzed by porins is:
Solute (out) Solute (in)