User:Nikhil Malvankar/Geobacter pilus: Difference between revisions

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Structural basis for metallic-like conductivity in microbial nanowires.

Nikhil S. '''Malvankar''', Madeline '''Vargas''', Kelly '''Nevin''', Pier-Luc '''Tremblay''', Kenneth '''Evans-Lutterodt''', Dmytro '''Nykypanchuk''', Eric '''Martz''', Mark T. '''Tuominen''', Derek R. '''Lovley'''. ''mBio 6 ~~in press~~ (2015).

Nikhil S. '''[[Malvankar]]''', Madeline '''Vargas''', Kelly '''Nevin''', Pier-Luc '''Tremblay''', Kenneth '''Evans-Lutterodt''', Dmytro '''Nykypanchuk''', Eric '''[[User:Eric Martz|Martz]]''', Mark T. '''Tuominen''', Derek R. '''[http://www.micro.umass.edu/faculty-and-research/derek-lovley Lovley]'''. [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])

CAVEAT: The homology model described here was published in 2015. 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==

===Geobacter Pilin Monomers===

Two pilin monomer models (<scene name='59/595215/2_gs_pilin_models/2'>restore initial scene</scene>) were utilized. First, we made a homology model templated on the X-ray crystallographic structure of the pilin of ''Pseudomonas aeruginosa''<ref>A ''Geobacter sulfurreducens'' pilin (pilA) homology model was constructed by Swiss-Model, templated on the X-ray crystallographic structure of ''Pseudomonas aeruginosa'' pilin ([[1oqw]], chain A). This model represents residues 1-60 of the mature pilin protein (length 61 amino acids: residues 30-90 of [http://www.uniprot.org/uniprot/~~D7AIT1 D7AIT1~~]), sequence {{Yelspan|F}}TLIELLIVVAIIGILAAIAIPQ{{Yelspan|F}}SA{{Yelspan|Y}}RVKA{{Yelspan|Y}}NSAASSDLRNLKTALESA{{Yelspan|F}}ADDQT{{Yelspan|Y}}PPES. This monomer includes six {{Yelspan|aromatic residues}}, F1, F24, Y27, Y32, F51 and Y57.</ref>. This model is colored in amino-to-carboxy rainbow coloring:

Two pilin monomer models (<scene name='59/595215/2_gs_pilin_models/2'>restore initial scene</scene>) were utilized. First, we made a homology model templated on the X-ray crystallographic structure of the pilin of ''Pseudomonas aeruginosa''<ref>A ''Geobacter sulfurreducens'' pilin (pilA) homology model was constructed by Swiss-Model, templated on the X-ray crystallographic structure of ''Pseudomonas aeruginosa'' pilin ([[1oqw]], chain A). This model represents residues 1-60 of the mature pilin protein (length 61 amino acids: residues 30-90 of [http://www.uniprot.org/uniprot/Q74D23 Q74D23]), sequence {{Yelspan|F}}TLIELLIVVAIIGILAAIAIPQ{{Yelspan|F}}SA{{Yelspan|Y}}RVKA{{Yelspan|Y}}NSAASSDLRNLKTALESA{{Yelspan|F}}ADDQT{{Yelspan|Y}}PPES. This monomer includes six {{Yelspan|aromatic residues}}, F1, F24, Y27, Y32, F51 and Y57.</ref>. This model is colored in amino-to-carboxy rainbow coloring:

Second, we utilized model 5 of the NMR ensemble of ''Geobacter sulfurreducens'' pilin<ref>We employed the NMR structure of ''Geobacter sulfurreducens'' pilin, [[2m7g]]. We employed model 5 of this 18-conformer ensemble because model 5 had the best clash score and [[MolProbity]] score.</ref>.

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</StructureSection>

<hr>

<hr>

==Download==

===Pilus Model===

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* [[:Image:Geobacter pilus assembled rocking.gif|Pilus Model, Rocking]]

* [[:Image:Geobacter pilus aromatics rotating.gif|Aromatic rings (yellow) in pilus model]]

==See Also==

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

==Notes & References==

@@ Line 11: / Line 11: @@
 [[Image:Blank-white-30x460px.png]]<br>
 <span style="font-size:160%"><b>Structural basis for metallic-like conductivity in microbial nanowires.</b></span><br><br>
-<span style="font-size:120%">Nikhil S. '''Malvankar''', Madeline '''Vargas''', Kelly '''Nevin''', Pier-Luc '''Tremblay''', Kenneth '''Evans-Lutterodt''', Dmytro '''Nykypanchuk''', Eric '''Martz''', Mark T. '''Tuominen''', Derek R. '''Lovley'''. ''mBio 6 in press (2015). </span>
+<span style="font-size:120%">Nikhil S. '''[[Malvankar]]''', Madeline '''Vargas''', Kelly '''Nevin''', Pier-Luc '''Tremblay''', Kenneth '''Evans-Lutterodt''', Dmytro '''Nykypanchuk''', Eric '''[[User:Eric Martz|Martz]]''', Mark T. '''Tuominen''', Derek R. '''[http://www.micro.umass.edu/faculty-and-research/derek-lovley Lovley]'''. [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>
+<table class="wikitable" style="background-color:#ffffa0;"><tr><td>
+CAVEAT: The homology model described here was published in 2015. 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='[250,500]' side='right' caption='Geobacter pilus homology model' scene='59/595215/2_gs_pilin_models/2'>
 ===Geobacter Pilin Monomers===
-Two pilin monomer models (<scene name='59/595215/2_gs_pilin_models/2'>restore initial scene</scene>) were utilized. First, we made a homology model templated on the X-ray crystallographic structure of the pilin of ''Pseudomonas aeruginosa''<ref>A ''Geobacter sulfurreducens'' pilin (pilA) homology model was constructed by Swiss-Model, templated on the X-ray crystallographic structure of ''Pseudomonas aeruginosa'' pilin ([[1oqw]], chain A). This model represents residues 1-60 of the mature pilin protein (length 61 amino acids: residues 30-90 of [http://www.uniprot.org/uniprot/D7AIT1 D7AIT1]), sequence {{Yelspan|F}}TLIELLIVVAIIGILAAIAIPQ{{Yelspan|F}}SA{{Yelspan|Y}}RVKA{{Yelspan|Y}}NSAASSDLRNLKTALESA{{Yelspan|F}}ADDQT{{Yelspan|Y}}PPES. This monomer includes six {{Yelspan|aromatic residues}}, F1, F24, Y27, Y32, F51 and Y57.</ref>. This model is colored in amino-to-carboxy rainbow coloring:
+Two pilin monomer models (<scene name='59/595215/2_gs_pilin_models/2'>restore initial scene</scene>) were utilized. First, we made a homology model templated on the X-ray crystallographic structure of the pilin of ''Pseudomonas aeruginosa''<ref>A ''Geobacter sulfurreducens'' pilin (pilA) homology model was constructed by Swiss-Model, templated on the X-ray crystallographic structure of ''Pseudomonas aeruginosa'' pilin ([[1oqw]], chain A). This model represents residues 1-60 of the mature pilin protein (length 61 amino acids: residues 30-90 of [http://www.uniprot.org/uniprot/Q74D23 Q74D23]), sequence {{Yelspan|F}}TLIELLIVVAIIGILAAIAIPQ{{Yelspan|F}}SA{{Yelspan|Y}}RVKA{{Yelspan|Y}}NSAASSDLRNLKTALESA{{Yelspan|F}}ADDQT{{Yelspan|Y}}PPES. This monomer includes six {{Yelspan|aromatic residues}}, F1, F24, Y27, Y32, F51 and Y57.</ref>. This model is colored in amino-to-carboxy rainbow coloring:
 {{Template:ColorKey_Amino2CarboxyRainbow}}
 Second, we utilized model 5 of the NMR ensemble of ''Geobacter sulfurreducens'' pilin<ref>We employed the NMR structure of ''Geobacter sulfurreducens'' pilin, [[2m7g]]. We employed model 5 of this 18-conformer ensemble because model 5 had the best clash score and [[MolProbity]] score.</ref>.
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 </StructureSection>
-<br><hr><br>
+<br>
+{{Theoretical_model}}
+<hr><br>
 ==Download==
 ===Pilus Model===
@@ Line 42: / Line 48: @@
 * [[:Image:Geobacter pilus assembled rocking.gif|Pilus Model, Rocking]]
 * [[:Image:Geobacter pilus aromatics rotating.gif|Aromatic rings (yellow) in pilus model]]
+==See Also==
+* [http://geobacter.org Geobacter.Org]
 ==Notes & References==
 <references />