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

Line 1:

~~The paper describing these models is~~ in ~~press in ''Scientific Reports''.~~

[[Interactive_3D_Complement_in_Proteopedia|Interactive 3D Complement in Proteopedia]]

{{Clear}}

~~Interactive 3D scenes and the model for download are ready to display here~~, ~~together with the journal publication link and DOI, as soon as the corresponding publication appears online in ''~~Scientific Reports''.

Scientific Reports

an online, open access journal: [http://www.nature.com/srep nature.com/srep]

~~If you arrived~~ at ~~this page~~ from a ~~link~~ in the ~~paper~~ in ''~~Scientific Reports~~'' by Xiao ''~~et al~~.'', ~~please inform~~ '''~~emartz@microbio~~.~~umass~~.~~edu~~''' and ~~the content will be released here ASAP~~. ~~Thank you~~.

{{Clear}}

Low energy atomic models suggesting a pilus structure that could account for electrical conductivity of ''Geobacter sulfurreducens'' pili.

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]'''.

''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])

__NOTOC__

==Molecular Tour==

__TOC__

Click the ''green links'' below to change the molecular scene.

</center>

===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>.

===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>: '''2m7g model 1, ARC-1 chain K'''.

* <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.

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>

'''6.4''' (56.0°)

</td><td>

[[Image:CPT-Gs-Xiao-end.png|175px]]

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

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

</td><td>

'''4.0''' (90°)

</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>

'''3.7''' (96.8°)

</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>

'''3.6''' (100.8°)

</td><td>

[[Image:CPT-Ng-2hil-end.png|175px]]

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

</StructureSection>

<hr>

==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===

* [[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).

==See Also==

* [http://geobacter.org Geobacter.Org]

==Notes & References==

@@ Line 1: / Line 1: @@
-The paper describing these models is in press in ''Scientific Reports''.
+[[Interactive_3D_Complement_in_Proteopedia|Interactive 3D Complement in Proteopedia]]<br>
+{{Clear}}<br>
-Interactive 3D scenes and the model for download are ready to display here, together with the journal publication link and DOI, as soon as the corresponding publication appears online in ''Scientific Reports''.
+<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>
-If you arrived at this page from a link in the paper in ''Scientific Reports'' by Xiao ''et al.'', please inform '''emartz@microbio.umass.edu''' and the content will be released here ASAP. Thank you.
+{{Clear}}<br>
+<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>
+<br>
+<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])
+<!--[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__
+==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'>
+__TOC__
+<center>
+<span style="border: 2px solid #ffff00; border-radius: 5px;padding:3px 8px 3px 8px;background: #ffffa0;">
+Click the ''green links'' below to change the molecular scene.
+</span>
+</center>
+===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===
+% 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>
+''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>
+<!--####################################-->
+<br>
+{{Theoretical_model}}
+<hr><br>
+==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===
+* [[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).
+==See Also==
+* [http://geobacter.org Geobacter.Org]
+==Notes & References==
+<references />