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

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__NOTOC__

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.

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==Molecular Tour==

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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 "Initial Model Outputs" 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 "Initial Model Outputs" in [http://www.nature.com/articles/srep23385 the publication] for details.</ref>.

===Monomer Chains===

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===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]

*[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===

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 </span>
 __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== <!--####################################-->
 <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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 ===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===
@@ Line 99: / Line 102: @@
 ===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]
+*[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===