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, accepted (2016).

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==Molecular Tour== <!--####################################-->

<StructureSection size='[300,600]' side='right' caption='' 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, accepted, 2016.</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.

===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>.

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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===

* Aromatic rings (yellow) in pilus model

==See Also==

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

==Notes & References==

<references />