Porin: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
← Older editNewer edit →
Karsten Theis (talk | contribs)
Macro
4,174 edits
No edit summary
Karsten Theis (talk | contribs)
Macro
4,174 edits
No edit summary
Line 1: Line 1:
<StructureSection load='' size='350' side='right' scene='Porin/Cv/1' caption='E. coli OmpC is a trimeric transmembrane protein with a porin fold (PDB code [[2j1n]])'>
<StructureSection load='' size='450' side='right' scene='Porin/Cv/1' caption='E. coli OmpC is a trimeric transmembrane protein with a porin fold (PDB code [[2j1n]])'>
__TOC__
__TOC__
{{Clear}}
{{Clear}}
Line 21: Line 21:
== Structure ==
== Structure ==


One representative porin structure is the crystal structure osmoporin OmpC from ''Escherichia coli'' ([[2j1n]]). OmpC has three beta-barrels associated to form a <scene name='Porin/Cv/2'>tight trimer</scene> <ref>PMID:16949612</ref>. Porin is a transmembrane protein, as can be seen from the <jmol><jmolLink><script>script "/scripts/1a0s/Hidrophobic/1.spt"; ppdiaCaptionCmd = "changeCaption('Hydrophobic residues (shown in tan) are prevalent where the protein comes in contact with the hydrophbic layer of the double-layer membrane, while other parts of the surface are hydrophilic (hydrophilic residues, ordered water molecules and calcium ions shown in skyblue). Shown here is the sucrose-specific porin (PDB-ID 1a0s) in its trimeric quaternary structure.','white','black');";javascript @ppdiaCaptionCmd;</script><text>hydrophobic ring</text></jmolLink></jmol> 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 <scene name='1a0s/Hidrophobic1/1'>see</scene> 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 <scene name='99/995028/Pacupp/2'>visualizing channels</scene> with pseudoatoms. In an alternative visualization, channels are shown as <scene name='41/411405/Channels/3'>surfaces</scene>, 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.
One representative porin structure is the crystal structure osmoporin OmpC from ''Escherichia coli'' ([[2j1n]]). OmpC has three beta-barrels associated to form a <scene name='Porin/Cv/2'>tight trimer</scene> <ref>PMID:16949612</ref>. Porin is a transmembrane protein, as can be seen from the <jmol><jmolLink><script>script "/scripts/1a0s/Hidrophobic/1.spt"; ppdiaCaptionCmd = "changeCaption('Hydrophobic residues (shown in tan) are prevalent where the protein comes in contact with the hydrophbic layer of the double-layer membrane, while other parts of the surface are hydrophilic (hydrophilic residues, ordered water molecules and calcium ions shown in skyblue). Shown here is the sucrose-specific porin (PDB-ID 1a0s) in its trimeric quaternary structure.','white','black');";javascript @ppdiaCaptionCmd;</script><text>hydrophobic ring</text></jmolLink></jmol> 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 <scene name='1a0s/Hidrophobic1/1'>see</scene> 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 <scene name='99/995028/Pacupp/2'>visualizing channels</scene> with pseudoatoms. In an alternative visualization, channels are shown as <scene name='41/411405/Channels/3'>surfaces</scene>, 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.


[[Image:Porin 2j1n channels.gif]]
[[Image:Porin 2j1n channels.gif]]
Line 29: Line 39:


</StructureSection>
</StructureSection>
==Acknowledgement==
The scene showing channels as pseudoatoms is from a page ([[User:Eric_Martz/Sandbox_19]]) made by Eric Martz.


==References==
==References==

Revision as of 16:56, 19 September 2023

Function

Porin 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).

Voltage-Dependent Anion Channel (VDAC) are ion channel Omps found in outer mitochondrial membrane[1]. In Pseudomonas aeruginosa the porin gene products are named OprD, OprE, OprK, OprP, etc. and OpdC, OpdH, etc.

Maltoporin (LamB) facilitates the diffusion of maltodextrin across the membrane[2].

Chitoporin (Chitp) facilitates the diffusion of chitooligosaccharides across the outer membrane of some bacteria[3].

See more details in

Structure

One representative porin structure is the crystal structure osmoporin OmpC from Escherichia coli (2j1n). OmpC has three beta-barrels associated to form a [4]. Porin is a transmembrane protein, as can be seen from the 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 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 with pseudoatoms. In an alternative visualization, channels are shown as , 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.

3D structures of Porin

Porin 3D structures


E. coli OmpC is a trimeric transmembrane protein with a porin fold (PDB code 2j1n)

Drag the structure with the mouse to rotate

AcknowledgementAcknowledgement

The scene showing channels as pseudoatoms is from a page (User:Eric_Martz/Sandbox_19) made by Eric Martz.


ReferencesReferences

  1. ↑ 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
  2. ↑ 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
  3. ↑ 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
  4. ↑ 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

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Alexander Berchansky, Michal Harel, Jaime Prilusky, Joel L. Sussman, Karsten Theis
Retrieved from "https://proteopedia.openfox.io/wiki/index.php?title=Porin&oldid=3871769"