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Pilus Model
The theoretical Geobacter sulfurreducens pilus model shown here, called ARC-1[1] (restore initial scene), is representative of a cluster of 50 low-energy models with an arrangement of aromatic rings consistent with X-ray diffraction data[2]. Unlike the docking of crystallographic models into electron density from cryo-electron microscopy[3][4], these models have chemically realistic interactions between subunit chains. Energy minimization produced subunit interactions with shape complementarity, non-covalent bonds, and very few atomic clashes[5].
Monomer Chains
This ARC-1 model contains 21 chains of pilA[6] of Geobacter sulfurreducens. The 21 chains were restrained to have identical conformations. Amino acids 3-50 are alpha-helical, with a slight bend at Pro22. Modeling was initiated with model 1 of NMR ensemble 2m7g of Geobacter sulfurreducens. The monomers in ARC-1 are only slightly different from the initial conformation:
Stacked Aromatic Rings
The ARC-1 model (and others of its cluster) are the first chemically realistic pilus models that can account for the electrical conductivity of these pili in terms of a core of stacked aromatic rings. These models are consistent with multiple lines of experimental evidence including X-ray diffraction suggesting stacked aromatics[1][2].
Each pilA chain contains six aromatic amino acids. In the pilus assembly, half of the aromatic rings form a helical chain in the core, while the other half are near the surface.
The aromatic rings in the core are closely packed. The core aromatic rings are Phe1, Phe24 and Tyr27.
Salt Bridges
80% of the 50 lowest-energy models have a salt bridge between Arg41 and Asp39 in different chains.
Monomers Per Turn
The ARC-1 model has 6.4 monomer chains per turn (56.0 degrees rotation between monomers). This is more chains/turn than some previous type IV pilus models. Among the 50 models with lowest energy in the cluster including ARC-1, chains/turn ranged from 5.0 to 7.6.
To visualize chains/turn, we show just one atom per protein monomer chain (alpha carbon of Phe51). Then these chain-marking-atoms are connected with with rods, and the resulting helix is viewed from one end. When counting the chains/turn, bear in mind that the first and last (to complete one turn) count as 1/2 chain each.
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Pilus
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Chains/Turn (Angle)
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Image
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Geobacter sulfurreducens (type IVa, 61 amino acids, theoretical model ARC-1, 2016)[1]
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6.4 (56.0°)
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Klebsielle oxytoca (type IVa, 137 amino acids A0A0E0WUQ8, theoretical model, 2010)[7]
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4.3 (84.7°)
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Pseudomonas aeruginosa (type IVa, 150 amino acids, fiber diffraction, 2004)[8]
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4.0 (90°)
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Vibrio cholerae (type IVb, 198 amino acids, cryo-EM, 2012)[9]
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3.7 (96.8°)
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Neisseria gonorrhoeae (type IVa, 165 amino acids, cryo-EM 2hil, 2006)[10]
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3.6 (100.8°)
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- ↑ 1.0 1.1 1.2 Xiao K, Malvankar NS, Shu C, Martz E, Lovley DR, Sun X. Low Energy Atomic Models Suggesting a Pilus Structure that could Account for Electrical Conductivity of Geobacter sulfurreducens Pili. Sci Rep. 2016 Mar 22;6:23385. doi: 10.1038/srep23385. PMID:27001169 doi:https://dx.doi.org/10.1038/srep23385
- ↑ 2.0 2.1 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:https://dx.doi.org/10.1128/mBio.00084-15
- ↑ Craig L, Volkmann N, Arvai AS, Pique ME, Yeager M, Egelman EH, Tainer JA. Type IV pilus structure by cryo-electron microscopy and crystallography: implications for pilus assembly and functions. Mol Cell. 2006 Sep 1;23(5):651-62. PMID:16949362 doi:10.1016/j.molcel.2006.07.004
- ↑ Craig L, Taylor RK, Pique ME, Adair BD, Arvai AS, Singh M, Lloyd SJ, Shin DS, Getzoff ED, Yeager M, Forest KT, Tainer JA. Type IV pilin structure and assembly: X-ray and EM analyses of Vibrio cholerae toxin-coregulated pilus and Pseudomonas aeruginosa PAK pilin. Mol Cell. 2003 May;11(5):1139-50. PMID:12769840
- ↑ The chemical realism of these theoretical energy-minimized models contrasts with models where empirical monomer structures are docked into cryo-electron microscopic electron density maps. Those are unrealistic in details of subunit interactions, lacking shape complementarity and having many atomic clashes. See "Initial Model Outputs" in the publication for details.
- ↑ Each chain contains the 61 C-terminal amino acids of UniProt Q74D23.
- ↑ Campos M, Francetic O, Nilges M. Modeling pilus structures from sparse data. J Struct Biol. 2011 Mar;173(3):436-44. doi: 10.1016/j.jsb.2010.11.015. Epub 2010 , Nov 27. PMID:21115127 doi:https://dx.doi.org/10.1016/j.jsb.2010.11.015
- ↑ 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:https://dx.doi.org/10.1038/nrmicro885
- ↑ Li J, Egelman EH, Craig L. Structure of the Vibrio cholerae Type IVb Pilus and stability comparison with the Neisseria gonorrhoeae type IVa pilus. J Mol Biol. 2012 Apr 20;418(1-2):47-64. doi: 10.1016/j.jmb.2012.02.017. Epub 2012, Feb 21. PMID:22361030 doi:https://dx.doi.org/10.1016/j.jmb.2012.02.017
- ↑ Craig L, Volkmann N, Arvai AS, Pique ME, Yeager M, Egelman EH, Tainer JA. Type IV pilus structure by cryo-electron microscopy and crystallography: implications for pilus assembly and functions. Mol Cell. 2006 Sep 1;23(5):651-62. PMID:16949362 doi:10.1016/j.molcel.2006.07.004
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