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

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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]'''.

<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])

</span>

__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.

</td></tr></table>

==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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</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>

</td><td>

</td></tr><tr><td>

''Pseudomonas aeruginosa'' (type IVa, 150 amino acids, fiber diffraction, 2004)<ref>PMID: 15100690</ref>

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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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|-

| [[Image:Model128-1-24-27-orange-greentrace-animation-250px.gif]]

| Low resolution, ARC-1 model (smoothed green backbone traces) with aromatic rings of residues 1, 24, and 27 in orange. [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).

|}

@@ 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]'''.
 <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])-->
 </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'>
@@ Line 24: / Line 27: @@
 ===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 63: / Line 66: @@
 </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>
@@ Line 93: / 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===
@@ Line 98: / Line 108: @@
 |-
 | [[Image:Model128-1-24-27-orange-greentrace-animation-250px.gif]]
-| Low resolution, ARC-1 model (smoothed green backbone traces) with aromatic rings of residues 1, 24, and 27 in orange. [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).
 |}