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[[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>
 
{{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, accepted (2016).
<!--[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='' 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, 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>.
 
</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===
* Aromatic rings (yellow) in pilus model
 
==See Also==
* [http://geobacter.org Geobacter.Org]
 
==Notes & References==
<references />

Revision as of 17:40, 13 March 2016

Interactive 3D Complement in Proteopedia


Scientific Reports an online, open access journal: nature.com/srep


Low energy atomic models suggesting a pilus structure that could account for electrical conductivity of Geobacter sulfurreducens pili.
Ke Xiao, Nikhil S. Malvankar, Chuanjun Shu, Eric Martz, Derek R. Lovley, and Xiao Sun.
Scientific Reports, accepted (2016).

Molecular TourMolecular Tour

Click the green links below to change the molecular scene.

Pilus Model

The theoretical Geobacter sulfurreducens pilus model shown here, called ARC-1[1] (), is representative of a cluster of 50 low-energy models with an arrangement of aromatic rings consistent with X-ray diffraction data[2]. Unlike the docking of crystallographic models into electron density from cryo-electron microscopy[3][4], 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[5] of Geobacter sulfurreducens. The 21 chains were restrained to have . Amino acids 3-50 are . 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:

  • : 2m7g model 1, ARC-1 chain K.
  • .

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[1][2].

Each pilA chain contains . In the pilus assembly, .

The aromatic . The core aromatic rings are .

Salt Bridges

80% of the 50 lowest-energy models have a salt bridge between Arg41 and Asp39 in different chains.

  • (Arg41:Asp39, sidechain nitrogens and oxygens).
  • .


Drag the structure with the mouse to rotate


Theoretical Model: The protein structure described on this page was determined theoretically, and hence should be interpreted with caution.


DownloadDownload

Pilus ModelPilus Model

Animations for PowerpointAnimations for Powerpoint

  • Aromatic rings (yellow) in pilus model

See AlsoSee Also

Notes & ReferencesNotes & References

  1. ↑ 1.0 1.1 Xiao et al., Scientific Reports, accepted, 2016.
  2. ↑ 2.0 2.1 Malvankar NS, Vargas M, Nevin K, Tremblay PL, Evans-Lutterodt K, Nykypanchuk D, Martz E, Tuominen MT, Lovley DR. Structural basis for metallic-like conductivity in microbial nanowires. MBio. 2015 Mar 3;6(2):e00084. doi: 10.1128/mBio.00084-15. PMID:25736881 doi:http://dx.doi.org/10.1128/mBio.00084-15
  3. ↑ Craig L, Volkmann N, Arvai AS, Pique ME, Yeager M, Egelman EH, Tainer JA. Type IV pilus structure by cryo-electron microscopy and crystallography: implications for pilus assembly and functions. Mol Cell. 2006 Sep 1;23(5):651-62. PMID:16949362 doi:10.1016/j.molcel.2006.07.004
  4. ↑ Craig L, Taylor RK, Pique ME, Adair BD, Arvai AS, Singh M, Lloyd SJ, Shin DS, Getzoff ED, Yeager M, Forest KT, Tainer JA. Type IV pilin structure and assembly: X-ray and EM analyses of Vibrio cholerae toxin-coregulated pilus and Pseudomonas aeruginosa PAK pilin. Mol Cell. 2003 May;11(5):1139-50. PMID:12769840
  5. ↑ Each chain contains the 61 C-terminal amino acids of UniProt Q74D23.
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