User:Ke Xiao/Geobacter pilus models: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
← Older edit
Eric Martz (talk | contribs)
ConfirmAccount, Editor, Tester, Administrators
27,351 edits
No edit summary
Eric Martz (talk | contribs)
ConfirmAccount, Editor, Tester, Administrators
27,351 edits
No edit summary
 
(6 intermediate revisions by the same user not shown)
Line 10: Line 10:
<span style="font-size:120%; line-height:160%;">Ke '''[[User:Ke_Xiao|Xiao]]''', Nikhil S. '''[[User:Nikhil_Malvankar|Malvankar]]''', Chuanjun '''[https://www.researchgate.net/profile/Chuanjun_Shu Shu]''', Eric '''[[User:Eric Martz|Martz]]''', Derek R. '''[http://www.micro.umass.edu/faculty-and-research/derek-lovley Lovley]''', and Xiao '''[http://www.lmbe.seu.edu.cn/chenyuan/xsun/mainpage.htm Sun]'''.
<span style="font-size:120%; line-height:160%;">Ke '''[[User:Ke_Xiao|Xiao]]''', Nikhil S. '''[[User:Nikhil_Malvankar|Malvankar]]''', Chuanjun '''[https://www.researchgate.net/profile/Chuanjun_Shu Shu]''', Eric '''[[User:Eric Martz|Martz]]''', Derek R. '''[http://www.micro.umass.edu/faculty-and-research/derek-lovley Lovley]''', and Xiao '''[http://www.lmbe.seu.edu.cn/chenyuan/xsun/mainpage.htm Sun]'''.
<br>
<br>
''Scientific Reports'', March 2016: [http://www.nature.com/articles/srep23385 nature.com/articles/srep23385].  ([http://dx.doi.org/10.1038/srep23385 DOI: 10.1038/srep23385])
''Scientific Reports'' '''6''':23385, March 2016: [http://www.nature.com/articles/srep23385 nature.com/articles/srep23385].  ([http://dx.doi.org/10.1038/srep23385 DOI: 10.1038/srep23385])
<!--[http://mbio.asm.org/content/6/2/e00084-15.abstract mBio 6(2):e00084-15] (2015). ([http://dx.doi.org/10.1128/mBio.00084-15 doi:10.1128/mBio.00084-15])-->
<!--[http://mbio.asm.org/content/6/2/e00084-15.abstract mBio 6(2):e00084-15] (2015). ([http://dx.doi.org/10.1128/mBio.00084-15 doi:10.1128/mBio.00084-15])-->
</span>
</span>
__NOTOC__
__NOTOC__
<table class="wikitable" style="background-color:#ffffa0;"><tr><td>
CAVEAT: The theoretical model described here was published in 2016. In 2019, [[cryo-EM]] structures of highly conductive ''Geobacter'' nanowires were found to be composed of the cytochrome OmcS<ref name="wang-gu">PMID:30951668</ref><ref name="filman">PMID:31925024</ref>. This called into question whether highly conductive pilus nanowires composed of the protein pilA exist.
</td></tr></table>
==Molecular Tour== <!--####################################-->
==Molecular Tour== <!--####################################-->
<StructureSection size='[300,600]' side='right' caption='Drag with mouse to rotate. Zoom with mouse wheel, or shift+drag.' scene='69/699340/Arc-1_no_hydrogen/1'>
<StructureSection size='[300,600]' side='right' caption='Drag with mouse to rotate. Zoom with mouse wheel, or shift+drag.' scene='69/699340/Arc-1_no_hydrogen/1'>
Line 24: Line 27:


===Pilus Model===
===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===
===Monomer Chains===
Line 63: Line 66:
</td><td>
</td><td>
[[Image:CPT-Gs-Xiao-end.png|175px]]
[[Image:CPT-Gs-Xiao-end.png|175px]]
</td></tr><tr><td>
''Klebsielle oxytoca'' (type IVa, 137 amino acids [http://www.uniprot.org/uniprot/A0A0E0WUQ8 A0A0E0WUQ8], theoretical model, 2010)<ref>PMID: 21115127</ref>
</td><td>
<span style="font-size:170%;">'''4.3''' (84.7&deg;)</span>
</td><td>
</td></tr><tr><td>
</td></tr><tr><td>
''Pseudomonas aeruginosa'' (type IVa, 150 amino acids, fiber diffraction, 2004)<ref>PMID: 15100690</ref>
''Pseudomonas aeruginosa'' (type IVa, 150 amino acids, fiber diffraction, 2004)<ref>PMID: 15100690</ref>
Line 93: Line 102:
===Pilus Model===
===Pilus Model===
*Click to download [http://proteopedia.org/wiki/images/8/8e/Geobacter_sulfurreducens_pilus_model_ARC-1.pdb Geobacter sulfurreducens pilus model ARC-1]
*Click to download [http://proteopedia.org/wiki/images/8/8e/Geobacter_sulfurreducens_pilus_model_ARC-1.pdb Geobacter sulfurreducens pilus model ARC-1]
*[http://bioinformatics.org/firstglance/fgij/fg.htm?mol=http://proteopedia.org/wiki/images/8/8e/Geobacter_sulfurreducens_pilus_model_ARC-1.pdb Explore pilus model in FirstGlance in Jmol].


===Animations for Powerpoint===
===Animations for Powerpoint===
Line 99: Line 109:
| [[Image:Model128-1-24-27-orange-greentrace-animation-250px.gif]]
| [[Image:Model128-1-24-27-orange-greentrace-animation-250px.gif]]
| Low resolution, ARC-1 model (<font color="green">'''smoothed green backbone traces'''</font>) with <font color="#d08000">'''aromatic rings of residues Phe1, Phe24, and Tyr27 in orange'''</font>. [http://bioinformatics.org/molvis/gifs/model128-1-24-27-orange-greentrace-animation.gif DOWNLOAD HIGH RESOLUTION ANIMATION] (19 MB).
| Low resolution, ARC-1 model (<font color="green">'''smoothed green backbone traces'''</font>) with <font color="#d08000">'''aromatic rings of residues Phe1, Phe24, and Tyr27 in orange'''</font>. [http://bioinformatics.org/molvis/gifs/model128-1-24-27-orange-greentrace-animation.gif DOWNLOAD HIGH RESOLUTION ANIMATION] (19 MB).
|-
| [[Image:Model128-1-24-27-path-solid-animation-250px.gif]]
| Low resolution, ARC-1 model with spacefilling (van der Waals) atoms, each chain a different color. [http://bioinformatics.org/molvis/gifs/model128-1-24-27-path-solid-animation.gif DOWNLOAD HIGH RESOLUTION ANIMATION] (29 MB).
|-
| [[Image:Model128-1-24-27-path-translucent-animation-250px.gif]]
| Low resolution, ARC-1 model with translucent spacefilling atoms. Aromatic rings of Phe1, Phe24, and Tyr27 are opaque. Each chain is a different color. [http://bioinformatics.org/molvis/gifs/model128-1-24-27-path-translucent-animation.gif DOWNLOAD HIGH RESOLUTION ANIMATION] (28 MB).
|}
|}


Latest revision as of 01:26, 9 August 2021

Interactive 3D Complement in Proteopedia


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)

CAVEAT: The theoretical model described here was published in 2016. 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.

Molecular TourMolecular Tour

Click the green links below to change the molecular scene.

Pilus Model

The theoretical Geobacter sulfurreducens pilus model shown here, called ARC-1[3] (), is representative of a cluster of 50 low-energy models with an arrangement of aromatic rings consistent with X-ray diffraction data[4]. Unlike the docking of crystallographic models into electron density from cryo-electron microscopy[5][6], 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[7].

Monomer Chains

This ARC-1 model contains 21 chains of pilA[8] 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[3][4].

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)[3]

6.4 (56.0°)

Klebsielle oxytoca (type IVa, 137 amino acids A0A0E0WUQ8, theoretical model, 2010)[9]

4.3 (84.7°)

Pseudomonas aeruginosa (type IVa, 150 amino acids, fiber diffraction, 2004)[10]

4.0 (90°)

Vibrio cholerae (type IVb, 198 amino acids, cryo-EM, 2012)[11]

3.7 (96.8°)

Neisseria gonorrhoeae (type IVa, 165 amino acids, cryo-EM 2hil, 2006)[12]

3.6 (100.8°)


Drag with mouse to rotate. Zoom with mouse wheel, or shift+drag.

Drag the structure with the mouse to rotate


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


DownloadDownload

Pilus ModelPilus Model

Animations for PowerpointAnimations 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).

See AlsoSee Also

Notes & ReferencesNotes & References

  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
  2. ↑ 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
  3. ↑ 3.0 3.1 3.2 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
  4. ↑ 4.0 4.1 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
  5. ↑ 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
  6. ↑ 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
  7. ↑ 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.
  8. ↑ Each chain contains the 61 C-terminal amino acids of UniProt Q74D23.
  9. ↑ 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
  10. ↑ 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
  11. ↑ 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
  12. ↑ 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
Retrieved from "https://proteopedia.openfox.io/wiki/index.php?title=User:Ke_Xiao/Geobacter_pilus_models&oldid=3435347"