User:Ke Xiao/Geobacter pilus models

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Scientific Reports an online, open access journal: nature.com/srep

Low energy atomic models suggesting a pilus structure that could account for electrical conductivity of Geobacter sulfurreducens pili.
Ke Xiao, Nikhil S. Malvankar, Chuanjun Shu, Eric Martz, Derek R. Lovley, and Xiao Sun.
Scientific Reports 6:23385, March 2016: nature.com/articles/srep23385. (DOI: 10.1038/srep23385)

Molecular Tour

1 Pilus Model
2 Monomer Chains
3 Stacked Aromatic Rings
4 Salt Bridges
5 Monomers Per Turn

Click the green links below to change the molecular scene.

Pilus Model

The theoretical Geobacter sulfurreducens pilus model shown here, called ARC-1^[1] (), 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 . Amino acids 3-50 are . 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:

: 2m7g model 1, ARC-1 chain K.
.

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 . In the pilus assembly, .

The aromatic . The core aromatic rings are .

Salt Bridges

80% of the 50 lowest-energy models have a salt bridge between Arg41 and Asp39 in different chains.

(Arg41:Asp39, sidechain nitrogens and oxygens).
.

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 (alpha carbon of Phe51). Then these chain-marking-atoms are , 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.

Pilus	Chains/Turn (Angle)	Image
Geobacter sulfurreducens (type IVa, 61 amino acids, theoretical model ARC-1, 2016)^[1]	6.4 (56.0°)
Klebsielle oxytoca (type IVa, 137 amino acids A0A0E0WUQ8, theoretical model, 2010)^[7]	4.3 (84.7°)
Pseudomonas aeruginosa (type IVa, 150 amino acids, fiber diffraction, 2004)^[8]	4.0 (90°)
Vibrio cholerae (type IVb, 198 amino acids, cryo-EM, 2012)^[9]	3.7 (96.8°)
Neisseria gonorrhoeae (type IVa, 165 amino acids, cryo-EM 2hil, 2006)^[10]	3.6 (100.8°)

Theoretical Model: The protein structure described on this page was determined theoretically, and hence should be interpreted with caution.

Download

Pilus Model

Click to download Geobacter sulfurreducens pilus model ARC-1

Animations for Powerpoint

	Low resolution, ARC-1 model (smoothed green backbone traces) with aromatic rings of residues Phe1, Phe24, and Tyr27 in orange. DOWNLOAD HIGH RESOLUTION ANIMATION (19 MB).
	Low resolution, ARC-1 model with spacefilling (van der Waals) atoms, each chain a different color. DOWNLOAD HIGH RESOLUTION ANIMATION (29 MB).
	Low resolution, ARC-1 model with translucent spacefilling atoms. Aromatic rings of Phe1, Phe24, and Tyr27 are opaque. Each chain is a different color. DOWNLOAD HIGH RESOLUTION ANIMATION (28 MB).

Notes & References

↑ ^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:http://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:http://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:http://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:http://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:http://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

Proteopedia Page Contributors and Editors (what is this?)

Eric Martz

Retrieved from "http://52.214.119.220/wiki/index.php/User:Ke_Xiao/Geobacter_pilus_models"

@@ Line 24: / Line 24: @@
 ===Pilus Model===
-The theoretical ''Geobacter sulfurreducens'' pilus model shown here, called ''ARC-1''<ref name="xiao1">Xiao et al., ''Scientific Reports'', March 2016: [http://www.nature.com/articles/srep23385 nature.com/articles/srep23385].</ref> (<scene name='69/699340/Arc-1_no_hydrogen/1'>restore initial scene</scene>), is representative of a cluster of 50 low-energy models with an arrangement of aromatic rings consistent with X-ray diffraction data<ref name="malvankar2015">PMID: 25736881</ref>. Unlike the docking of crystallographic models into electron density from cryo-electron microscopy<ref>PMID: 16949362</ref><ref>PMID: 12769840</ref>, 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<ref>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 &quot;Initial Model Outputs&quot; in [http://www.nature.com/articles/srep23385 the publication] for details.</ref>.
+The theoretical ''Geobacter sulfurreducens'' pilus model shown here, called ''ARC-1''<ref name="xiao1">PMID: 27001169</ref> (<scene name='69/699340/Arc-1_no_hydrogen/1'>restore initial scene</scene>), is representative of a cluster of 50 low-energy models with an arrangement of aromatic rings consistent with X-ray diffraction data<ref name="malvankar2015">PMID: 25736881</ref>. Unlike the docking of crystallographic models into electron density from cryo-electron microscopy<ref>PMID: 16949362</ref><ref>PMID: 12769840</ref>, 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<ref>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 &quot;Initial Model Outputs&quot; in [http://www.nature.com/articles/srep23385 the publication] for details.</ref>.
 ===Monomer Chains===

User:Ke Xiao/Geobacter pilus models

From Proteopedia

Revision as of 20:50, 28 March 2016

Molecular Tour

Contents

Pilus Model

Monomer Chains

Stacked Aromatic Rings

Salt Bridges

Monomers Per Turn

Download

Pilus Model

Animations for Powerpoint

See Also

Notes & References

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