User:Nikhil Malvankar/Geobacter pilus
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Interactive 3D Complement in Proteopedia
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Structural basis for metallic-like conductivity in microbial nanowires.
Nikhil S. Malvankar, Madeline Vargas, Kelly Nevin, Pier-Luc Tremblay, Kenneth Evans-Lutterodt, Dmytro Nykypanchuk, Eric Martz, Mark T. Tuominen, Derek R. Lovley. mBio 6(2):e00084-15 (2015). (doi:10.1128/mBio.00084-15)
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CAVEAT: The homology model described here was published in 2015. In 2019, cryo-EM structures of highly conductive Geobacter nanowires were found to be composed of the cytochrome OmcS[1][2]. This called into question whether highly conductive pilus nanowires composed of the protein pilA exist. |
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Molecular Tour
Geobacter Pilin MonomersTwo pilin monomer models (restore initial scene) were utilized. First, we made a homology model templated on the X-ray crystallographic structure of the pilin of Pseudomonas aeruginosa[3]. This model is colored in amino-to-carboxy rainbow coloring:
Second, we utilized model 5 of the NMR ensemble of Geobacter sulfurreducens pilin[4]. NMR model 5 is colored magenta. Amino acid sidechains are shown only for aromatics. The models are virtually identical for residues 1-32[5], except for the differing sidechain rotamer positions of Phe1. The models are similarly alpha helical from residues 33-51. Residues 52-61 vary in conformation in the NMR ensemble, while for residues 52-60 in the homology model, the template is unlikely to be appropriate since Pseudomonas has a substantial domain from 52-144 while Geobacter pilin ends at 61. Thus, while one can be confident that residues 1-51 are alpha helical, the conformation of residues 52-61 is uncertain. Geobacter Pilus ModelsWe constructed a model of the pilus of ''Geobacter sulfurreducens'', templated on a model of the Pseudomonas aeruginosa pilus[6]. Nineteen copies of the pilin monomer were fitted to the 19 monomers in the template ("magic fit", a sequence-guided structural alignment, Swiss-Model, RMSD for alpha carbons, 1.52 Å). Alternatively, the NMR structure of Geobacter sulfurreducens pilin 2m7g was used as a monomer. Results with this pilus model were similar and are not shown. A Conductive Pathway Of AromaticsIn the homology-modeled pilus, the distances between aromatic sidechain rings (Phe and Tyr) are consistent with X-ray fiber diffraction results that suggest pi-orbital stacking as an electrically conductive pathway. In particular, F1, F24 and Y27 form a plausible conductive pathway. Our homology model is approximate. The exact positions of the aromatic sidechains will certainly be different in the true pilus structure. The X-ray fiber diffraction results presented in the paper argue strongly for 3.2 Å spacing between aromatic rings in the actual pilus structure. It is not excluded that Y57 (which protrudes from the pilus shaft in our model) could fold into the pilus shaft so as to participate in a conductive pathway.
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Download
Pilus Model
- Click to download Geobacter sulfurreducens pilus homology model templated on Pseudomonas pilus model.
Animations for Powerpoint
Click images to see them full size, or to download them.
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Pilus Assembly Simulation
- Pilus Model, Rocking
- Aromatic rings (yellow) in pilus model
See Also
Notes & References
- ↑ 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
- ↑ 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
- ↑ A Geobacter sulfurreducens pilin (pilA) homology model was constructed by Swiss-Model, templated on the X-ray crystallographic structure of Pseudomonas aeruginosa pilin (1oqw, chain A). This model represents residues 1-60 of the mature pilin protein (length 61 amino acids: residues 30-90 of Q74D23), sequence FTLIELLIVVAIIGILAAIAIPQFSAYRVKAYNSAASSDLRNLKTALESAFADDQTYPPES. This monomer includes six aromatic residues, F1, F24, Y27, Y32, F51 and Y57.
- ↑ We employed the NMR structure of Geobacter sulfurreducens pilin, 2m7g. We employed model 5 of this 18-conformer ensemble because model 5 had the best clash score and MolProbity score.
- ↑ The Geobacter sequence is identical to the template Pseudomonas sequence in 22 of the first 23 residues. Residues 24-50 have 26% sequence identity.
- ↑ Craig L, Pique ME, Tainer JA. Type IV pilus structure and bacterial pathogenicity. Nat Rev Microbiol. 2004 May;2(5):363-78. PMID:15100690 doi:http://dx.doi.org/10.1038/nrmicro885
