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| <StructureSection load='2j1n' size='450' side='right' scene='Porin/Cv/1' caption='E. coli Ompc (PDB code [[2j1n]])'>
| | [[Image:Porin wobble.gif|right]][[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). 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. |
| [[Image:Ompc.png|left|300px|thumb|Crystal structure of Porin OmpC trimer from ''E. coli'', [[2j1n]]]]
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| | __TOC__ |
| {{Clear}} | | {{Clear}} |
| [[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 (OmpC, OmpF, Ompg). See more details in<br />
| | == Function == |
| | The function on a porin depends on the size and lining of the channel. |
| | *'''OprB''' is a carbohydate-selective porin<ref>PMID:7768797</ref>. |
| | *'''OprF''' protects ''Pseudomonas aeruginosa'' against macrophage clearance<ref>PMID:33432030</ref>. |
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| | *'''Maltoporin''' (LamB) facilitates the diffusion of maltodextrin across the membrane<ref>PMID:12003940</ref>. |
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| | *'''Chitoporin''' (Chitp) facilitates the diffusion of chitooligosaccharides across the outer membrane of some bacteria<ref>PMID:23447539</ref>. |
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| | *'''Voltage-Dependent Anion Channel (VDAC)''' are ion channel Omps found in outer mitochondrial membrane<ref>PMID:16787253</ref>. In ''Pseudomonas aeruginosa'' the porin gene products are named OprD, OprE, OprK, OprP, etc. and OpdC, OpdH, etc. |
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| | For discussion of specific porins, see<br /> |
| | *[[Mycobacterium tuberculosis ArfA Rv0899]] for OmpA type<br /> |
| *[[Osmoporin OmpC (E. coli)]]<br /> | | *[[Osmoporin OmpC (E. coli)]]<br /> |
| *[[OmpF]]<br /> | | *[[OmpF]]<br /> |
| | *[[Molecular Playground/OmpG]]<br /> |
| *[[Molecular Playground/OmpG2]]<br /> | | *[[Molecular Playground/OmpG2]]<br /> |
| *[[Osmoporin OmpK36 (K. pneumoniae)]]<br /> | | *[[Osmoporin OmpK36 (K. pneumoniae)]]<br /> |
| '''Voltage-Dependent Anion Channel (VDAC)''' is ion channel Omp found in outer mitochondrial membrane. In Pseudomonas aeruginosa the porin gene products are named OprD, OprK, OprP. The images at the left and at the right correspond to one representative porin structure, ''i.e.'' 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
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| <scene name='1a0s/Hidrophobic/1'>seen</scene> 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 <scene name='1a0s/Hidrophobic1/1'>see</scene> the hole 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).
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| __NOTOC__
| | == Structure == |
| === Gating and conduction of <scene name='Journal:JBSD:3/Cv/7'>nano-channel forming proteins</scene>, a computational approach <ref>doi 10.1080/07391102.2012.712460</ref>=== | | <StructureSection load='' size='450' side='right' scene='41/411405/Membrane/1' caption='E. coli OmpC is a trimeric transmembrane protein with a porin fold (PDB code [[2j1n]])'> |
| The functional units of the living systems are cells whose internal physico-chemical conditions needed for optimum function are different from that of the external medium and are maintained by hydrophobic membrane barrier and reconstituted water filled nano-pore forming proteins. The structure of these channels dictates their function to some extent and makes them to open or close in response to various conditions in the surrounding medium including pH, temperature, ionic strength, potential difference, osmotic pressure, presence of certain ligands and so on. Due to very complex and sensitive structures of these molecules to the medium and the effect of their native location, lipid Bilayer, different from soluble proteins, the molecular structure of most of membrane proteins have not been worked out at atomic level yet. The discovery of the crystal structure of certain membrane macromolecules have paved the way to understand the mechanism(s) by which they control the traffic of certain molecules through the membrane and the way they respond to the internal and external stimulus and signal transduction.
| | 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>. |
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| | Porin is a <scene name='41/411405/Membrane/1'>transmembrane protein</scene>, 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 hydrophobic 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). |
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| | 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. |
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| In this study, certain nano-channel forming proteins, OmpF, OmpA, alpha-hemolysin and TolC whose structure is known at atomic level were considered to work out the relationship between their molecular structure and regional and overall dynamics. The coordinates of all constituent atoms of the molecules, gathered from x-ray diffraction of molecule 3D crystal were obtained from Protein Data Bank (PDB) and used for calculation and simulation required for biophysical approaches. The extent of motion of different parts of the molecules inferred from Root-Mean-Square Deviation (RMSD) of a number of crystallized molecule whose averaged orientation represent the coordinate of different group is reported as B-factor of the protein in PDB.
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| Here, we used the molecular structure of the biomolecules with known 3D structure at atomic level as well as the B-factor to work out regional and global dynamics through theoretical and computational approaches in nonzero slowest modes of vibration. Based on equipartition theorem a criterion was defined to measure the extent of motion in exposed loops and turns on extracellular and cytosolic parts of the membrane channels as well as their channel forming parts acting as a membrane gate and extended along the hydrophobic core of the membrane.
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| The results obtained here were consistent with both experimental data obtained from voltage clamp studies of the reconstituted single channel in planner bilayer as well as theoretical approaches based on Molecular Dynamics (MD) and HOLE programs that show the molecular motions and the geometry of the channel lumen respectively. We noticed large motions in the intramembrane beta-barrel channel forming domains in TolC and alpha-hemolysin that possess large extracellular loops. However, there was less motion identified in the channel forming intramembrane parts of <scene name='Journal:JBSD:3/Cv/9'>OmpF</scene> and OmpA, and the major motion recognized in the external loops.
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| Furthermore, we noticed that there is a <scene name='Journal:JBSD:3/Cv/5'>conducting path (mini-channel) located between the L3 loop and the channel barrel wall </scene>(mini-channel) located between the L3 loop and the channel barrel wall that is in contact with membrane core. This path is different than the main known conducting path of the channel that is partially constricted by L3 loop. The conduction of the mini-channel is mainly governed by the flexibility of the L3 loop as well as the adjacent barrel wall. Thus, it might represent the effects of lateral pressure of the membrane on the channel conductivity.
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| The approach and algorithm used here requires less CPU power and time than MD, and makes it possible to conduct molecular studies of large molecules with known atomic structure at shorter time.
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| </StructureSection>
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| __NOTOC__
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| == 3D structures of Porin ==
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| Updated on {{REVISIONDAY2}}-{{MONTHNAME|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}
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| [[2xe5]], [[2xe1]], [[2xe2]], [[2xe3]], [[2j1n]] – EcOmpC – ''Escherichia coli''<br />
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| [[3k19]], [[3k1b]], [[2zfg]], [[1omf]], [[2omf]], [[1opf]], [[3poq]], [[3pou]], [[3pox]], [[4jfb]], [[4lse]], [[4lsf]], [[4lsh]], [[4lsi]] – EcOmpF<br />
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| [[3nb3]] – EcOmpA + EcOmpC - EM<br />
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| [[3upg]], [[3uu2]] – OmpC – ''Salmonella enterica''<br />
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| [[1hxt]], [[1hxu]], [[1hxx]], [[1bt9]], [[1gfm]], [[1gfn]], [[1gfo]], [[1gfp]], [[1gfq]], [[1mpf]] – EcOmpF (mutant)<br />
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| [[2iwv]], [[2iww]], [[2f1c]] - EcOmpG<br />
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| [[2x9k]] - EcOmpG (mutant)<br />
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| [[2wjq]], [[2wjr]] – EcOmp NANC<br />
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| [[1pho]] - EcOmp<br />
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| [[3a2r]] – NmOmpB – ''Neisseria meningitides''<br />
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| [[3sy9]] – PaOpdC – ''Pseudomonas aeruginosa''<br />
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| [[2odj]], [[3sy7]], [[4foz]] – PaOprD<br />
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| [[3szd]] - PaOpdF<br />
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| [[3t20]] – PaOpdH<br />
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| [[2qtk]], [[2y2x]], [[3sys]] – PaOpdK<br />
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| [[3t0s]] - PaOpdL<br />
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| [[2y0k]], [[2y0l]], [[3szv]] – PaOpdO<br />
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| [[3syb]] – PaOpdP<br />
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| [[3t24]] - PaOpdQ<br />
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| [[3jty]] – Omp – ''Pseudomonas fluorescens''<br />
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| [[2v9u]] – MsOmp rim domain – ''Mycobacteria smegmatis''<br />
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| [[1uun]] – MsOmp (mutant)<br />
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| [[2fgr]] - DaOmp32 - ''Delftia acidovorans''<br />
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| [[1a0s]], [[1mpr]] - StOmp - ''Salmonella typhimurium''<br />
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| [[3nsg]] - StOmpF<br />
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| [[2prn]], [[1bh3]], [[3prn]], [[5prn]], [[6prn]], [[7prn]], [[8prn]] – RbOmp (mutant) - ''Rhodopseudomonas blastica''<br />
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| [[1prn]] - RbOmp<br />
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| [[1osm]] – OmpK36 – ''Klebsiella pneumoniae''<br />
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| [[2por]], [[3por]] – Omp – ''Rhodobacter capsulatus''<br />
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| [[4aui]] – Omp – ''Neisseria gonorrheae''<br />
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| [[4gey]], [[4gf4]] – Omp B – ''Pseudomonas putida''
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| ==Porin + polypeptides ==
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| [[2j4u]] - EcOmpC + lactotransferrin fragment<br />
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| [[2zld]] - EcOmpF + colicin E3<br />
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| [[3o0e]] - EcOmpF + colicin peptide<br />
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| [[1h6s]] - RbOmp + inserted sequence
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| ==Porin + various compounds==
| | 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. |
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| [[3hw9]], [[3hwb]] - EcOmpF + ions <br /> | | [[Image:Porin tunnels sliced.gif]] |
| [[3fyx]] - Ec~OmpF + dibenzo-18-crown-6<br />
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| [[4gcp]], [[4gcq]], [[4gcs]] – EcOmpF + antibiotic<br />
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| [[1af6]], [[1mpq]], [[1mpm]], [[1mpn]], [[1mpo]] - EcOmp LAMB + sugars<br />
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| [[3a2s]], [[3a2t]] - NmOmpB + sugars<br />
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| [[3a2u]] - NmOmpB + AMPPNP<br />
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| [[2o4v]] - PaOprP + phosphate<br />
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| [[2fgq]] - DaOmp32 + malate<br />
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| [[1e54]] - Omp32 + sulfate - ''Comamonas acidovorans''<br />
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| [[1oh2]], [[1a0t]] - StOmp + sucrose
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| | == 3D structures of Porin == |
| | [[Porin 3D structures]] |
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| | </StructureSection> |
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| == Voltage-Dependent Anion Channel == | | ==Acknowledgement== |
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| | 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]]). |
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| [[2jk4]] – hVDAC-1 – human<br />
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| [[2k4t]] - hVDAC-1 - NMR<br />
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| [[3emn]] – VDAC-1 - mouse<br />
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| ==References== | | ==References== |