View source for User:Ke Xiao/Geobacter pilus models

[[Interactive_3D_Complement_in_Proteopedia|Interactive 3D Complement in Proteopedia]]<br>
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<span style="border: 2px solid #a1a1a1; border-radius: 6px;padding:35px 50px 20px 30px;background: linear-gradient(#b0d0ff, #ffffff);"><span style="font-size:250%;">Scientific Reports</span>
<span style="padding: 0px 0px 0px 100px;color:#808080;font-size:120%;">an online, open access journal: [http://www.nature.com/srep nature.com/srep]</span></span>

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<span style="font-size:160%;line-height:130%;"><b>Low energy atomic models suggesting a pilus structure that could account for electrical conductivity of ''Geobacter sulfurreducens'' pili.</b></span>
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<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]'''.
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''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])-->
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==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'>
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Click the ''green links'' below to change the molecular scene.
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===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>.

===Monomer Chains===

This ARC-1 model contains 21 chains of pilA<ref>Each chain contains the 61 C-terminal amino acids of [http://www.uniprot.org/uniprot/Q74D23 UniProt Q74D23].</ref> of ''Geobacter sulfurreducens''. The 21 chains were restrained to have <scene name='69/699340/Arc-1_no_hydrogen/2'>identical conformations</scene>. Amino acids 3-50 are <scene name='69/699340/Arc-1_no_hydrogen/3'>alpha-helical, with a slight bend at Pro22</scene>. 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:
* <scene name='69/699340/2m7g_mdl1_vs_arc1_chaink/1'>Compare main chain traces</scene>: '''<font color="#006000">2m7g model 1</font>, <font color="magenta">ARC-1 chain K</font>'''.
* <scene name='69/699340/2m7g_mdl1_vs_arc1_chaink/2'>Compare sidechains</scene>.

===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<ref name="xiao1" /><ref name="malvankar2015" />.

Each pilA chain contains <scene name='69/699340/Arc-1_no_hydrogen/9'>six aromatic amino acids</scene>. In the pilus assembly, <scene name='69/699340/Arc-1_no_hydrogen/10'>half of the aromatic rings form a helical chain in the core, while the other half are near the surface</scene>.

The aromatic <scene name='69/699340/Arc-1_no_hydrogen/11'>rings in the core are closely packed</scene>. The core aromatic rings are <scene name='69/699340/Arc-1_no_hydrogen/13'>Phe1, Phe24 and Tyr27</scene>.

===Salt Bridges===
80% of the 50 lowest-energy models have a [[Salt bridges|salt bridge]] between Arg41 and Asp39 in different chains.
* <scene name='69/699340/Arc-1_no_hydrogen/14'>Salt bridges stabilize the pilus</scene> (Arg41:Asp39, sidechain nitrogens and oxygens).
* <scene name='69/699340/Arc-1_no_hydrogen/15'>Single salt bridge between chains J and K</scene>.

===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 <scene name='69/699340/Arc-1_no_hydrogen/18'>just one atom per protein monomer chain</scene> (alpha carbon of Phe51). Then these chain-marking-atoms are <scene name='69/699340/Arc-1_no_hydrogen/20'>connected with with rods</scene>, 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.

<table cellpadding="4" border="1">
<tr><td>
Pilus
</td><td>
Chains/Turn (Angle)
</td><td>
Image
</td></tr><tr><td>
''Geobacter sulfurreducens'' (type IVa, 61 amino acids, theoretical model ARC-1, 2016)<ref name="xiao1" />
</td><td>
<span style="font-size:170%;">'''6.4''' (56.0&deg;)</span>
</td><td>
[[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>
''Pseudomonas aeruginosa'' (type IVa, 150 amino acids, fiber diffraction, 2004)<ref>PMID: 15100690</ref>
</td><td>
<span style="font-size:170%;">'''4.0''' (90&deg;)</span>
</td><td>
[[Image:CPT-Pa-end.png|175px]]
</td></tr><tr><td>
''Vibrio cholerae'' (type '''IVb''', 198 amino acids, cryo-EM, 2012)<ref>PMID: 22361030</ref>
</td><td>
<span style="font-size:170%;">'''3.7''' (96.8&deg;)</span>
</td><td>
[[Image:CPT-Vc2012-end.png|175px]]
</td></tr><tr><td>
''Neisseria gonorrhoeae'' (type IVa, 165 amino acids, cryo-EM [[2hil]], 2006)<ref>PMID: 16949362</ref>
</td><td>
<span style="font-size:170%;">'''3.6''' (100.8&deg;)</span>
</td><td>
[[Image:CPT-Ng-2hil-end.png|175px]]
</td></tr></table>

</StructureSection>
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{{Theoretical_model}}
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==Download==

===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]

===Animations for Powerpoint===
{| class="wikitable"
|-
| [[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).
|-
| [[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).
|}

==See Also==
* [http://geobacter.org Geobacter.Org]

==Notes & References==
<references />