Porin

From Proteopedia

proteopedia linkproteopedia linkPorin or Outer Membrane Proteins (Omps) act as channels which allow passive diffusion of sugars, ions and amino acids. They are beta barrel proteins which traverse the cell membrane. In E. coli they are named according to their genes: C, F, G, etc. (OmpC, OmpF, OmpG). While porins all share a common fold, the detailed makeup and the shape of the inside of the barrel (the channel) determines which molecules pass through the porin and which are retained.

Contents 1 Function 2 Structure 3 Acknowledgement 4 References

Function

The function on a porin depends on the size and lining of the channel.

• OprB is a carbohydate-selective porin^[1].
• OprF protects Pseudomonas aeruginosa against macrophage clearance^[2].

• Maltoporin (LamB) facilitates the diffusion of maltodextrin across the membrane^[3].

• Chitoporin (Chitp) facilitates the diffusion of chitooligosaccharides across the outer membrane of some bacteria^[4].

• Voltage-Dependent Anion Channel (VDAC) are ion channel Omps found in outer mitochondrial membrane^[5]. In Pseudomonas aeruginosa the porin gene products are named OprD, OprE, OprK, OprP, etc. and OpdC, OpdH, etc.

For discussion of specific porins, see

• Mycobacterium tuberculosis ArfA Rv0899 for OmpA type
  
• Osmoporin OmpC (E. coli)
  
• OmpF
  
• Molecular Playground/OmpG
  
• Molecular Playground/OmpG2
  
• Osmoporin OmpK36 (K. pneumoniae)
  

Structure

One representative porin structure is the crystal structure osmoporin OmpC from Escherichia coli (2j1n). OmpC has three beta-barrels associated to form a tight trimer [6]. Porin is a transmembrane protein, as can be seen from the hydrophobic ring around the protein, this makes it possible to submerge in the lipid bilayer (hydrophobic amino acids are sandybrown, hydrophilic ones are cyan). As you can see the channel in the protein is made of mainly hydrophilic chains thus making it possible for the sugar to pass through (these scenes were created by Nádori Gergely). The channels have wide openings on either side with a tighter bottleneck in the middle, as illustrated in the interactive view visualizing channels with pseudoatoms. In an alternative visualization, channels are shown as surfaces, slabbed on both sides of the bottleneck for better visibility. Finally, the animation below shows a view perpendicular to the membrane, slicing through different layers of the porin structure with the solvent accessible surface shown in tan. The channels appear narrower in this animation than in the interactive scene because the animation shows the solvent accessible surface while the interactive view shows the molecular surface. 3D structures of Porin Porin 3D structures

spinqualitylabelsall models E. coli OmpC is a trimeric transmembrane protein with a porin fold (PDB code 2j1n) Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image

Acknowledgement

The scene showing channels as pseudoatoms is from a page (User:Eric_Martz/Sandbox_19) made by Eric Martz. Eric also helped creating the surface rendition of the channels (technical details here: Image:Tunnels.jvxl).

References

1. ↑ Wylie JL, Worobec EA. The OprB porin plays a central role in carbohydrate uptake in Pseudomonas aeruginosa. J Bacteriol. 1995 Jun;177(11):3021-6. PMID:7768797 doi:10.1128/jb.177.11.3021-3026.1995
2. ↑ Moussouni M, Berry L, Sipka T, Nguyen-Chi M, Blanc-Potard AB. Pseudomonas aeruginosa OprF plays a role in resistance to macrophage clearance during acute infection. Sci Rep. 2021 Jan 11;11(1):359. PMID:33432030 doi:10.1038/s41598-020-79678-0
3. ↑ Van Gelder P, Dumas F, Bartoldus I, Saint N, Prilipov A, Winterhalter M, Wang Y, Philippsen A, Rosenbusch JP, Schirmer T. Sugar transport through maltoporin of Escherichia coli: role of the greasy slide. J Bacteriol. 2002 Jun;184(11):2994-9. PMID:12003940
4. ↑ Suginta W, Chumjan W, Mahendran KR, Schulte A, Winterhalter M. Chitoporin from Vibrio harveyi, a channel with exceptional sugar specificity. J Biol Chem. 2013 Apr 19;288(16):11038-46. PMID:23447539 doi:10.1074/jbc.M113.454108
5. ↑ Shoshan-Barmatz V, Israelson A, Brdiczka D, Sheu SS. The voltage-dependent anion channel (VDAC): function in intracellular signalling, cell life and cell death. Curr Pharm Des. 2006;12(18):2249-70. PMID:16787253
6. ↑ Basle A, Rummel G, Storici P, Rosenbusch JP, Schirmer T. Crystal structure of osmoporin OmpC from E. coli at 2.0 A. J Mol Biol. 2006 Oct 6;362(5):933-42. Epub 2006 Aug 3. PMID:16949612 doi:10.1016/j.jmb.2006.08.002