Structural Research of Monomeric/Dimeric Beta-Barrel Membrane Proteins
Inquiry
Beta-barrel membrane proteins are a class of proteins that are embedded in the lipid bilayer of the cell membrane and play a vital role in the transport of various molecules across the membrane. These proteins consist of multiple β-strands that form a cylindrical shape with a central pore and can exist as monomers or form dimers or higher-order oligomers in the membrane.
Recent advances in structural biology techniques have enabled the determination of the high-resolution structures of several beta-barrel membrane proteins in their monomeric and dimeric forms. For example, the dynamic NMR structures of AlkL, a protein that plays a role in transporting hydrophobic molecules across the membrane, revealed a β-barrel structure with hydrophobic residues lining the inside of the barrel. The crystal structure of OmpF, a protein that forms a dimeric structure in the membrane, showed that the dimerization is mediated by hydrogen bonds and van der Waals interactions between the β-strands.
Figure 1. NMR structure and dynamics of AlkL. (Schubeis T, et al., 2020)
| Protein | Organism | Method | Resolution | PDB Entry ID |
| TolC outer membrane protein (expressed in E. coli) | Escherichia coli | X-ray diffraction | 2.10 Å | 1EK9 |
| TolC outer membrane protein, ligand blocked | Escherichia coli | X-ray diffraction | 2.75 Å | 1TQQ |
| TolC outer membrane protein (Y362F, R367E), partially open state (expressed in E. coli) | Escherichia coli | X-ray diffraction | 3.20 Å | 2VDE |
| TolC outer membrane protein in a nanodisc with colicin E1 fragment (expressed in E. coli) | Escherichia coli | Cryo-EM single particle analysis | 3.09 Å | 6WXH |
| TolC outer membrane protein in complex with KlebC (expressed in E. coli) | Klebsiella quasipneumoniae | Cryo-EM single particle analysis | 3.20 Å | 7NG8 |
| CmeC bacterial multi-drug efflux transporter outer membrane channel (expressed in E. coli) | Campylobacter jejuni | X-ray diffraction | 2.37 Å | 4MT4 |
| VceC outer membrane protein (expressed in E. coli) | Vibrio cholerae | X-ray diffraction | 1.80 Å | 1YC9 |
| OprM drug discharge outer membrane protein (expressed in Pseudomonas aeruginosa) | Pseudomonas aeruginosa | X-ray diffraction | 2.56 Å | 1WP1 |
| OprM drug discharge outer membrane protein (expressed in E. coli) | Pseudomonas aeruginosa | X-ray diffraction | 2.40 Å | 3D5K |
| OprN drug discharge outer membrane protein, I4 space group (expressed in E. coli) | Pseudomonas aeruginosa | X-ray diffraction | 2.70 Å | 5AZO |
| OprJ drug discharge outer membrane protein (expressed in E. coli) | Pseudomonas aeruginosa | X-ray diffraction | 3.10 Å | 5AZS |
| ST50 discharge outer membrane protein (expressed in E. coli) | Salmonella enterica | X-ray diffraction | 2.98 Å | 5BUN |
| CusC heavy metal discharge outer membrane protein | Escherichia coli | X-ray diffraction | 2.30 Å | 3PIK |
| CusC heavy metal discharge outer membrane protein (expressed in E. coli) | Escherichia coli | X-ray diffraction | 2.09 Å | 4K7R |
| apo BtuB cobalamin transporter (expressed in E. coli) | Escherichia coli | X-ray diffraction | 2.00 Å | 1NQE |
| BtuB with bound colicin E3 R-domain (expressed in E. coli) | Escherichia coli | X-ray diffraction | 2.75 Å | 1UJW |
| apo BtuB by in meso crystallization (expressed in E. coli) | Escherichia coli | X-ray diffraction | 1.95 Å | 2GUF |
| BtuB in complex with TonB (expressed in E. coli) | Escherichia coli | X-ray diffraction | 2.10 Å | 2GSK |
| BtuB with bound colicin E2 R-domain (expressed in E. coli) | Escherichia coli | X-ray diffraction | 3.50 Å | 2YSU |
| apo BtuB V10R1 spin-labeled (expressed in E. coli) | Escherichia coli | X-ray diffraction | 2.44 Å | 3M8B |
| Colicin I receptor Cir in complex with Colicin Ia binding domain (expressed in E. coli) | Escherichia coli | X-ray diffraction | 2.50 Å | 2HDI |
| OmpA (expressed in E. coli) | Escherichia coli | X-ray diffraction | 2.50 Å | 1BXW |
| OmpA (expressed in E. coli) | Escherichia coli | X-ray diffraction | 1.65 Å | 1QJP |
| OmpA (expressed in E. coli) | Escherichia coli | Solution NMR | / | 1G90 |
| OmpA (expressed in E. coli) | Escherichia coli | Solution NMR | / | 2GE4 |
| OmpA with four shortened loops (expressed in E. coli) | Escherichia coli | Solution NMR | / | 2JMM |
| OmpA (expressed in E. coli) | Klebsiella pneumoniae | Solution NMR | / | 2K0L |
| OmpT outer membrane protease (expressed in E. coli) | Escherichia coli | X-ray diffraction | 2.60 Å | 1I78 |
| Pla Plasminogen activator (native 1) (expressed in E. coli) | Yersinia pestis | X-ray diffraction | 1.85 Å | 2X55 |
| OmpW outer membrane protein (expressed in E. coli) | Escherichia coli | X-ray diffraction | 2.70 Å | 2F1V |
| OmpW outer membrane protein (expressed in E. coli) | Escherichia coli | Solution NMR | / | 2MHL |
| AlkL passive importer of hydrophobic molecules in DMPC lipid bilayer (expressed in E. coli) | Pseudomonas oleovorans | Solid-state NMR | / | 6QWR |
| CarO outer membrane protein, isoform 1 (expressed in E. coli) | Acinetobacter baumannii | X-ray diffraction | 2.70 Å | 4RL9 |
| OprF outer membrane protein, N-terminal β-barrel domain (expressed in E. coli) | Pseudomonas aeruginosa | X-ray diffraction | 1.60 Å | 4RLC |
| OprG outer membrane protein (expressed in E. coli) | Pseudomonas aeruginosa | X-ray diffraction | 2.40 Å | 2X27 |
| OprH, outer membrane protein H (expressed in E. coli) | Pseudomonas aeruginosa | Solution NMR | / | 2LHF |
| OmpX (expressed in E. coli) | Escherichia coli | X-ray diffraction | 1.90 Å | 1QJ8 |
| OmpX (expressed in E. coli) | Escherichia coli | Solution NMR | / | 1ORM |
| OmpX (expressed in E. coli) | Escherichia coli | Solution NMR | / | 1Q9F |
| OmpX in optimized nanodiscs (expressed in E. coli) | Escherichia coli | Solution NMR | / | 2M06 |
| Ail adhesion protein (expressed in E. coli) | Yersinia pestis | X-ray diffraction | 1.80 Å | 3QRA |
| Ail adhesion protein, decylphosphocholine micelles (expressed in E. coli) | Yersinia pestis | Solution NMR | / | 2N2M |
| Ail adhesion protein (expressed in E. coli) | Yersinia pestis | Solution NMR | / | 5VJ8 |
| TtoA Outer Membrane Protein (OMP) (expressed in Thermus thermophilus) | Thermus thermophilus | X-ray diffraction | 2.80 Å | 3DZM |
| OmpLA (PldA) outer membrane phospholipase A monomer (expressed in E. coli) | Escherichia coli | X-ray diffraction | 2.17 Å | 1QD5 |
| OmpLA (PldA) outer membrane phospholipase A monomer with Ca++ (expressed in E. coli) | Escherichia coli | X-ray diffraction | 2.60 Å | 1FW2 |
| OmpLA (PldA) active-site mutant (N156A), pH 6.1 (expressed in E. coli) | Escherichia coli | X-ray diffraction | 2.50 Å | 1ILZ |
| OpcA adhesin protein | Neisseria meningitidis | X-ray diffraction | 2.03 Å | 1K24 |
| OpcA adhesin protein (expressed in E. coli) | Neisseria meningitidis | X-ray diffraction | 1.95 Å | 2VDF |
| NspA surface protein (expressed in E. coli) | Neisseria meningitidis | X-ray diffraction | 2.55 Å | 1P4T |
| NanC Porin, model for KdgM porin family (expressed in E. coli) | Escherichia coli | X-ray diffraction | 1.80 Å | 2WJR |
| PagL LPS 3-O-deacylase (expressed in E. coli) | Pseudomonas aeruginosa | X-ray diffraction | 2.00 Å | 2ERV |
| LpxR lipid A deacylase (expressed in E. coli) | Salmonella enterica | X-ray diffraction | 1.90 Å | 3FID |
| PagP outer membrane palimitoyl transferease (expressed in E. coli) | Escherichia coli | Solution NMR | / | 1MM4 |
| PagP outer membrane palimitoyl transferease (expressed in E. coli) | Escherichia coli | X-ray diffraction | 1.90 Å | 1THQ |
| PagP outer membrane palimitoyl transferease crystallized from SDS/Co-solvent (expressed in E. coli) | Escherichia coli | X-ray diffraction | 1.40 Å | 3GP6 |
| FadL long-chain fatty acid transporter (expressed in E. coli) | Escherichia coli | X-ray diffraction | 2.60 Å | 1T16 |
| FadL long-chain fatty acid transporter A77E/S100R mutant (expressed in E. coli) | Escherichia coli | X-ray diffraction | 2.50 Å | 3DWN |
| FadL long-chain fatty acid transporter D348R mutant (expressed in E. coli) | Escherichia coli | X-ray diffraction | 2.60 Å | 3PGR |
| FadL homologue long-chain fatty acid transporter (expressed in E. coli) | Pseudomonas aeruginosa | X-ray diffraction | 2.20 Å | 3DWO |
| YebT lipid transporter, domains 1-4 (expressed in E. coli) | Escherichia coli | Cryo-EM single particle analysis | 3.10 Å | 6KZ3 |
| FauA alcaligin outer membrane transporter (expressed in E. coli) | Bordetella pertussis | X-ray diffraction | 2.33 Å | 3EFM |
| TodX hydrocarbon transporter (expressed in E. coli) | Pseudomonas putida | X-ray diffraction | 2.60 Å | 3BS0 |
| TbuX hydrocarbon transporter (expressed in E. coli) | Ralstonia pickettii | X-ray diffraction | 3.20 Å | 3BRY |
| Tsx nucleoside transporter (apoprotein) (expressed in E. coli) | Escherichia coli | X-ray diffraction | 3.01 Å | 1TLY |
| FhuA, Ferrichrome-iron receptor without ligand | Escherichia coli | X-ray diffraction | 2.74 Å | 1BY3 |
| FhuA (expressed in E. coli) | Escherichia coli | X-ray diffraction | 2.50 Å | 2FCP |
| FhuA-AW140-LPS (expressed in E. coli) | Escherichia coli | X-ray diffraction | 2.50 Å | 1QFG |
| FhuA in complex with albomycin (expressed in E. coli) | Escherichia coli | X-ray diffraction | 3.10 Å | 1QKC |
| FhuA in complex with lipopolysaccharide and rifamycin CGP4832 (expressed in E. coli) | Escherichia coli | X-ray diffraction | 2.90 Å | 1FI1 |
| FhuA in complex withTonB (expressed in E. coli) | Escherichia coli | X-ray diffraction | 3.30 Å | 2GRX |
| FhuA in complex with lasso peptide microcin J25 (MccJ25) (expressed in E. coli) | Escherichia coli | X-ray diffraction | 2.30 Å | 4CU4 |
| FhuA in complex with the superinfection exclusion lipoprotein Llp (expressed in E. coli) | Escherichia coli | X-ray diffraction | 3.37 Å | 8A60 |
| FyuA siderophore transporter (expressed in E. coli) | Yersinia pestis | X-ray diffraction | 3.20 Å | 4EPA |
| FepA, Ferric enterobactin receptor | Escherichia coli | X-ray diffraction | 2.40 Å | 1FEP |
| Fiu Ferric-Catecholate import receptor, open C222(1) crystal form (expressed in E. coli) | Escherichia coli | X-ray diffraction | 2.10 Å | 6BPN |
| FecA, siderophore transporter (expressed in E. coli) | Escherichia coli | X-ray diffraction | 2.00 Å | 1KMO |
| FecA, siderophore transporter (no ligand) (expressed in E. coli) | Escherichia coli | X-ray diffraction | 2.50 Å | 1PNZ |
| FecA, siderophore transporter periplasmic signalling domain (expressed in E. coli) | Escherichia coli | Solution NMR | / | 2D1U |
| PiuA siderophore receptor (expressed in E. coli) | Pseudomonas aeruginosa | X-ray diffraction | 1.90 Å | 5FOK |
| PiuD siderophore receptor (expressed in E. coli) | Pseudomonas aeruginosa | X-ray diffraction | 2.30 Å | 5NEC |
| PiuA siderophore receptor (expressed in E. coli) | Acinetobacter baumannii | X-ray diffraction | 1.94 Å | 5FP1 |
| PirA siderophore receptor (expressed in E. coli) | Pseudomonas aeruginosa | X-ray diffraction | 2.97 Å | 5FP2 |
| PirA siderophore receptor (expressed in E. coli) | Acinetobacter baumannii | X-ray diffraction | 2.83 Å | 5FR8 |
| HasR heme-uptake receptor in complex with HasA hemophore and heme (expressed in E. coli) | Serratia marcescens | X-ray diffraction | 2.70 Å | 3CSL |
| ShuA heme-uptake receptor in complex with HasA hemophore and heme (expressed in E. coli) | Shigella dysenteriae | X-ray diffraction | 2.60 Å | 3FHH |
| FptA pyochelin siderophore transporter | Pseudomonas aeruginosa | X-ray diffraction | 2.00 Å | 1XKW |
| FptA pyochelin siderophore transporter (expressed in Pseudomonas fluorescens) | Pseudomonas fluorescens | X-ray diffraction | 3.26 Å | 3QLB |
| FpvA, Pyoverdine receptor (expressed in Pseudomonas aeruginosa) | Pseudomonas aeruginosa | X-ray diffraction | 3.60 Å | 1XKH |
| FpvA, Pyoverdine receptor (apo form) (expressed in Pseudomonas aeruginosa) | Pseudomonas aeruginosa | X-ray diffraction | 2.77 Å | 2O5P |
| FpvA, Full-length structure bound to iron-pyoverdine (expressed in Pseudomonas aeruginosa) | Pseudomonas aeruginosa | X-ray diffraction | 2.73 Å | 2IAH |
| AlgE alginate export protein (expressed in E. coli) | Pseudomonas aeruginosa | X-ray diffraction | 2.30 Å | 3RBH |
| AlgE alginate export protein (expressed in E. coli) | Pseudomonas aeruginosa | X-ray diffraction | 1.90 Å | 4AFK |
| AlgE alginate export protein at 100 K (expressed in E. coli) | Pseudomonas aeruginosa | X-ray diffraction | 2.90 Å | 4XNL |
| AlgK–AlgX alginate export protein complex (expressed in E. coli) | Pseudomonas putida | X-ray diffraction | 2.46 Å | 7ULA |
| P pilus usher translocation domain, PapC130-640 (expressed in E. coli) | Escherichia coli | X-ray diffraction | 3.20 Å | 2VQI |
| P pilus usher translocation domain, PapC146-637 (expressed in E. coli) | Escherichia coli | X-ray diffraction | 3.15 Å | 3FIP |
| P pilus FimD usher bound to FimC:FimH substrate (expressed in E. coli) | Escherichia coli | X-ray diffraction | 2.80 Å | 3RFZ |
| P pilus FimD usher in complex with FimC:FimF:FimG:FimH (expressed in E. coli) | Escherichia coli | X-ray diffraction | 3.80 Å | 4J3O |
| P pilus assembly intermediate (FimD-FimC-FimF-FimG-FimH), conformer 1 (expressed in E. coli) | Escherichia coli | Cryo-EM single particle analysis | 4.00 Å | 6E14 |
| P pilus tip assembly intermediate PapC-PapD-PapK-PapF-PapG (expressed in E. coli) | Escherichia coli | Cryo-EM single particle analysis | 7.60 Å | 7LHI |
| Transferrin binding protein A (TbpA) in complex with human transferrin (expressed in E. coli) | Neisseria meningitidis | X-ray diffraction | 2.60 Å | 3V8X |
| Wzi outer-membrane lectin | Escherichia coli | X-ray diffraction | 2.64 Å | 2YNK |
| Opa60 for receptor-mediated engulfment, EXPLOR refined (expressed in Neisseria gonorrhoeae) | Neisseria gonorrhoeae | Solution NMR | / | 2MLH |
| CsgG bacterial amyloid secretion channel (expressed in E. coli) | Escherichia coli | X-ray diffraction | 3.59 Å | 4UV3 |
| CsgG bacterial amyloid secretion channel (expressed in E. coli) | Escherichia coli | X-ray diffraction | 3.10 Å | 4Q79 |
| CsgG-CsgF complex involved in curli biogenesis (expressed in E. coli) | Escherichia coli | Cryo-EM single particle analysis | 2.94 Å | 6LQH |
| CsgG-CsgF complex involved in curli biogenesis (expressed in E. coli) | Escherichia coli | Cryo-EM single particle analysis | 3.38 Å | 6L7A |
| CsgG-CsgF complex involved in curli biogenesis (expressed in E. coli) | Escherichia coli | Cryo-EM single particle analysis | 3.40 Å | 6SI7 |
| FusA plant-ferredoxin receptor (expressed in E. coli) | Pectobacterium atrosepticum | Cryo-EM single particle analysis | 3.20 Å | 4ZGV |
| Omp33 outer membrane protein (expressed in E. coli) | Acinetobacter baumannii | X-ray diffraction | 2.10 Å | 6GIE |
| FrpB TonB-dependent iron transporter (expressed in E. coli) | Neisseria meningitidis | X-ray diffraction | 2.40 Å | 4AIP |
| FhuE TonB-dependent transporter (expressed in E. coli) | Escherichia coli | X-ray diffraction | 2.00 Å | 6E4V |
| YncD TonB-dependent transporter (expressed in E. coli) | Escherichia coli | X-ray diffraction | 2.96 Å | 6V81 |
| PfeA ferric enterobactin receptor, apo form (expressed in E. coli) | Pectobacterium atrosepticum | X-ray diffraction | 2.12 Å | 5M9B |
| PfeA ferric enterobactin receptor in complex with TCV (expressed in E. coli) | Pseudomonas aeruginosa | X-ray diffraction | 2.57 Å | 5NC3 |
| BcsC cellulose synthase outer membrane channel (expressed in E. coli) | Escherichia coli | X-ray diffraction | 1.85 Å | 6TZK |
| ZnuD zinc transporter (expressed in E. coli) | Neisseria meningitidis | X-ray diffraction | 3.20 Å | 4RDT |
| MtrE Outer Membrane Channel (expressed in E. coli) | Neisseria gonorrhoeae | X-ray diffraction | 3.29 Å | 4MT0 |
| LetB lipophilic Envelope-spanning Tunnel B, model 1 (expressed in E. coli) | Escherichia coli | Cryo-EM single particle analysis | 3.46 Å | 6V0C |
| PcoB copper transporter (expressed in E. coli) | Escherichia coli | X-ray diffraction | 2.00 Å | 7PGE |
Table 1. Structural Research of Beta-Barrel Membrane Proteins: Monomeric/Dimeric.
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References
- Budiardjo S J, et al. Colicin E1 opens its hinge to plug TolC. Elife. 2022, 11: e73297.
- Schubeis T, et al. A β-barrel for oil transport through lipid membranes: Dynamic NMR structures of AlkL. Proceedings of the National Academy of Sciences. 2020, 117(35): 21014-21021.
- Isom G L, et al. LetB structure reveals a tunnel for lipid transport across the bacterial envelope. Cell. 2020, 181(3): 653-664. e19.
