User:Nikhil Malvankar/Geobacter pilus structure and function: Difference between revisions

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==Molecular Tour==
==Molecular Tour==
<StructureSection size='[250,500]' side='right' caption='' scene='83/834714/Filament/1'>
<StructureSection size='[250,500]' side='right' caption='' scene='83/834714/Filament/1'>
Previously, pili of ''Geobacter sulfurreducens'' were thought to be composed of PilA-N, a 61-amino acid protein<ref>PMID: 25736881 </ref><ref>PMID: 31608018 </ref>. In addition to pili, electrically conductive nanowires composed of linear polymers of cytochromes OmcS and OmcZ have been reported<ref>PMID: 30951668</ref><ref>PMID: 31925024</ref>.
Previously, pili of ''Geobacter sulfurreducens'' were thought to be composed of PilA-N, a 61-amino acid protein<ref>PMID: 25736881 </ref><ref>PMID: 31608018 </ref>. In addition to pili, electrically conductive nanowires composed of linear polymers of cytochromes OmcS and OmcZ have been reported<ref name="nw1">PMID: 30951668</ref><ref name="nw2">PMID: 31925024</ref>.


Our electron cryomicroscopic structure of ''Geobacter sulfurreducens'' pili reveals them to be composed of a core of '''<font color='#e87000'>PilA-N</font>''' coated with an outer surface layer of '''<font color='00a0a0'>PilA-C</font>''' (104 amino acids; <scene name='83/834714/Filament/1'>restore initial scene)</scene>. Here is a <scene name='83/834714/Filament/2'>cutaway view</scene> (front half hidden). The C-termini of '''<font color='#e87000'>PilA-N</font>''' <scene name='83/834714/Filament/3'>protrude into sockets</scene> in '''<font color='00a0a0'>PilA-C</font>'''.
Our electron cryomicroscopic structure of ''Geobacter sulfurreducens'' pili reveals them to be composed of a core of '''<font color='#e87000'>PilA-N</font>''' coated with an outer surface layer of '''<font color='00a0a0'>PilA-C</font>''' (104 amino acids; <scene name='83/834714/Filament/1'>restore initial scene)</scene>. Here is a <scene name='83/834714/Filament/2'>cutaway view</scene> (front half hidden). The C-termini of '''<font color='#e87000'>PilA-N</font>''' <scene name='83/834714/Filament/3'>protrude into sockets</scene> in '''<font color='00a0a0'>PilA-C</font>'''.


The filament is assembled from <scene name='83/834714/Dimer/3'>heterodimers</scene>. Dimer <scene name='83/834714/Dimer/2'>secondary structure</scene>: '''<font color='#e87000'>PilA-N</font>''' consists of two alpha helices, while '''<font color='00a0a0'>PilA-C</font>''' includes a 3-stranded beta sheet. The C-terminal protrusion of '''<font color='#e87000'>PilA-N</font>''' is <scene name='83/834714/Flaps/4'>held between two flaps</scene> (darker) of '''<font color='00a0a0'>PilA-C</font>'''. The flaps have almost no contact with each other. They are held in place by apolar contacts and hydrogen bonds with the C-terminal protrusion of '''<font color='#e87000'>PilA-N</font>'''. These flaps might be open before '''<font color='#e87000'>PilA-N</font>''' arrives to form a dimer, reminiscent of the flaps of HIV protease<ref>PMID: 16418268</ref>.
The filament is assembled from <scene name='83/834714/Dimer/3'>heterodimers</scene>. Dimer <scene name='83/834714/Dimer/2'>secondary structure</scene>: '''<font color='#e87000'>PilA-N</font>''' consists of two alpha helices, while '''<font color='00a0a0'>PilA-C</font>''' includes a 3-stranded beta sheet. The C-terminal protrusion of '''<font color='#e87000'>PilA-N</font>''' is <scene name='83/834714/Flaps/4'>held between two flaps</scene> (darker) of '''<font color='00a0a0'>PilA-C</font>'''. The flaps have almost no contact with each other. They are held in place by apolar contacts and hydrogen bonds with the C-terminal protrusion of '''<font color='#e87000'>PilA-N</font>'''. These flaps might be open before '''<font color='#e87000'>PilA-N</font>''' arrives to form a dimer, reminiscent of the flaps of HIV protease<ref>PMID: 16418268</ref>.
As detailed in the journal publication, the pili studied here are 50-fold less conductive than the nanowires composed of cytochromes<ref name="nw1" /><ref name="nw2" />.




Revision as of 04:30, 9 February 2020

Interactive 3D Complement in Proteopedia

Structure of novel pili evolved for extracellular translocation of microbial nanowires

Yangqi Gu, Vishok Srikanth, Ruchi Jain, Aldo I. Salazar-Morales, J. Patrick O'Brien, Sophia M. Yi, Rajesh K. Soni, Fadel A. Samatey, Sibel Ebru Yalcin, and Nikhil S. Malvankar. (journal article link here) (2020). (DOI link here)

Molecular TourMolecular Tour

Previously, pili of Geobacter sulfurreducens were thought to be composed of PilA-N, a 61-amino acid protein[1][2]. In addition to pili, electrically conductive nanowires composed of linear polymers of cytochromes OmcS and OmcZ have been reported[3][4].

Our electron cryomicroscopic structure of Geobacter sulfurreducens pili reveals them to be composed of a core of PilA-N coated with an outer surface layer of PilA-C (104 amino acids; . Here is a (front half hidden). The C-termini of PilA-N in PilA-C.

The filament is assembled from . Dimer : PilA-N consists of two alpha helices, while PilA-C includes a 3-stranded beta sheet. The C-terminal protrusion of PilA-N is (darker) of PilA-C. The flaps have almost no contact with each other. They are held in place by apolar contacts and hydrogen bonds with the C-terminal protrusion of PilA-N. These flaps might be open before PilA-N arrives to form a dimer, reminiscent of the flaps of HIV protease[5].

As detailed in the journal publication, the pili studied here are 50-fold less conductive than the nanowires composed of cytochromes[3][4].


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Notes & ReferencesNotes & References

  1. ↑ Malvankar NS, Vargas M, Nevin K, Tremblay PL, Evans-Lutterodt K, Nykypanchuk D, Martz E, Tuominen MT, Lovley DR. Structural basis for metallic-like conductivity in microbial nanowires. MBio. 2015 Mar 3;6(2):e00084. doi: 10.1128/mBio.00084-15. PMID:25736881 doi:http://dx.doi.org/10.1128/mBio.00084-15
  2. ↑ Lovley DR, Walker DJF. Geobacter Protein Nanowires. Front Microbiol. 2019 Sep 24;10:2078. doi: 10.3389/fmicb.2019.02078. eCollection , 2019. PMID:31608018 doi:http://dx.doi.org/10.3389/fmicb.2019.02078
  3. ↑ 3.0 3.1 Wang F, Gu Y, O'Brien JP, Yi SM, Yalcin SE, Srikanth V, Shen C, Vu D, Ing NL, Hochbaum AI, Egelman EH, Malvankar NS. Structure of Microbial Nanowires Reveals Stacked Hemes that Transport Electrons over Micrometers. Cell. 2019 Apr 4;177(2):361-369.e10. doi: 10.1016/j.cell.2019.03.029. PMID:30951668 doi:http://dx.doi.org/10.1016/j.cell.2019.03.029
  4. ↑ 4.0 4.1 Filman DJ, Marino SF, Ward JE, Yang L, Mester Z, Bullitt E, Lovley DR, Strauss M. Cryo-EM reveals the structural basis of long-range electron transport in a cytochrome-based bacterial nanowire. Commun Biol. 2019 Jun 19;2(1):219. doi: 10.1038/s42003-019-0448-9. PMID:31925024 doi:http://dx.doi.org/10.1038/s42003-019-0448-9
  5. ↑ Hornak V, Okur A, Rizzo RC, Simmerling C. HIV-1 protease flaps spontaneously open and reclose in molecular dynamics simulations. Proc Natl Acad Sci U S A. 2006 Jan 24;103(4):915-20. doi:, 10.1073/pnas.0508452103. Epub 2006 Jan 17. PMID:16418268 doi:http://dx.doi.org/10.1073/pnas.0508452103
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