Difference between revisions of "Team:NRP-UEA-Norwich/Results/ProteinModeling"

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<h2>PROTEIN MODELING</h2>
 
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<p>Modelling hydrogenases and MtrCAB in Shewanella</p>
 
  
 
<div class="subTitle">Aim</div>
 
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Apart from MtrC (http://www.rcsb.org/pdb/explore/explore.do?structureId=4lm8), the crystal structures of the hydrogenase and Mtr proteins are currently unknown. To help the general public to understand our project in a visual way using virtual reality, on posters and presentations, we decided to model the proteins.
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Apart from <a href="http://www.rcsb.org/pdb/explore/explore.do?structureId=4lm8"> MtrC </a>, the crystal structures of the hydrogenase and Mtr proteins are currently unknown. To help the general public to understand our project in a visual way using virtual reality, on posters and presentations, we decided to model the proteins.
 
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Genbank was used to find the sequence of the gene for each of the proteins. Then this was translated into an amino acid sequence using the web programme (ExPASy). The amino acid sequence was the modelled against different proteins in the Protein Data Bank using Phyre to predict the 3D structure. This 3D model was then aligned with the PDB protein file that it was modelled against to look for any cofactors that may exist in the protein.
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Genbank was used to find the sequence of the gene for each of the proteins. The DNA sequence was translated into an amino acid sequence using the web programme ExPASy. All modelling was carried out using the Phyre2 software, this works by aligning the amino acid sequence of the protein to be modelled against other proteins with solved structures in the Protein Data Bank.  
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For the fumarate reductase FccA and small tetraheme cytochrome (STC), the existing PDB files were used for the figure.
 
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For the FccA and STC, the existing PDB files were used for the figure.
 
 
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<div class="subTitle">Results</div>
 
<div class="subTitle">Results</div>
  
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<img src="https://static.igem.org/mediawiki/2016/8/87/T--NRP-UEA-Norwich--placeholder.jpg" class="showFullSizeImage centerMiddle" />
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<img src="https://static.igem.org/mediawiki/2016/8/87/T--NRP-UEA-Norwich--placeholder.jpg"class="showFullSizeImage centerMiddle" />
  
 
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Although the sequence identity and coverage was low for many of the proteins (see table), the models are the most accurate the group could produce so it was decided to use them.
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Although the sequence identity and coverage was low for many of the proteins (see table), the models are the most accurate possible approximations of these proteins available through homology modelling.
 
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<p class="underline">Table of the models Phyre2 used – organism, pdb file, % identity, % coverage</p>
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<p class="underline">Table 1. Details of the structures Phyre2 used, the proteins used are the most accurate from the Phyre2 software. </p>
  
 
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<span class="bold">Pymol -</span>  
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<span class="bold"> ExPASy</span>- Gasteiger E., Gattiker A., Hoogland C., Ivanyi I., Appel R.D., Bairoch A.
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The PyMOL Molecular Graphics System, Version 1.8 Schrödinger, LLC.
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ExPASy: the proteomics server for in-depth protein knowledge and analysis Nucleic Acids Res. 31:3784-3788 (2003).
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<span class="bold">Genbank - </span>
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Nucleic Acids Research, 28: 235-242. (www.rcsb.org)
 
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<span class="bold">PDB - </span>
 
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H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H. Weissig, I.N. Shindyalov, P.E. Bourne (2000) The Protein Data Bank
 
H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H. Weissig, I.N. Shindyalov, P.E. Bourne (2000) The Protein Data Bank
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The Phyre2 web portal for protein modelling, prediction and analysis. Kelley LA et al. Nature Protocols 10, 845-858 (2015)
 
The Phyre2 web portal for protein modelling, prediction and analysis. Kelley LA et al. Nature Protocols 10, 845-858 (2015)
 
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<span class="bold">Genbank - </span>
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<span class="bold">Pymol -</span>  
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Nucleic Acids Research, 28: 235-242. (www.rcsb.org)
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The PyMOL Molecular Graphics System, Version 1.8 Schrödinger, LLC.
 
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<span class="bold">ExPASy - </span>
 
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Gasteiger E., Gattiker A., Hoogland C., Ivanyi I., Appel R.D., Bairoch A.
 
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ExPASy: the proteomics server for in-depth protein knowledge and analysis <br />
 
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Nucleic Acids Res. 31:3784-3788(2003).
 
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Revision as of 01:46, 19 October 2016

NRP-UEA-NORWICH iGEM

PROTEIN MODELING

Aim

Apart from MtrC , the crystal structures of the hydrogenase and Mtr proteins are currently unknown. To help the general public to understand our project in a visual way using virtual reality, on posters and presentations, we decided to model the proteins.

Method

Genbank was used to find the sequence of the gene for each of the proteins. The DNA sequence was translated into an amino acid sequence using the web programme ExPASy. All modelling was carried out using the Phyre2 software, this works by aligning the amino acid sequence of the protein to be modelled against other proteins with solved structures in the Protein Data Bank. For the fumarate reductase FccA and small tetraheme cytochrome (STC), the existing PDB files were used for the figure.

Results

Although the sequence identity and coverage was low for many of the proteins (see table), the models are the most accurate possible approximations of these proteins available through homology modelling.

Table 1. Details of the structures Phyre2 used, the proteins used are the most accurate from the Phyre2 software.

Protein name Model Organism and protein model used PDB file PDB file % Sequence coverage
MtrA Wolinella succinogenes octaheme sulfite reductase MccA, form I 4RKM 14 76
MtrB Pseudomonas aeruginosa membrane bound ferripyoverdine receptor 2IAH 10 91
MtrC Shewanella oneidensis crystal structure of outer membrane decaheme cytochrome MtrC 4LM8 100 93
HyaA Escherichia coli hydrogenase-1 complexed with cytochrome b 4GD3 46 79
HyaB Salmonella enterica NiFe hydrogenase 4C3O 45 96
HyaC Escherichia coli formate dehydrogenase 1KQF 16 86
HydA Desulfovibrio desulfuricans Fe-only hydrogenase 1HFE 49 93
HydB Desulfovibrio desulfuricans small Fe-only subunit 1HFE 39 58
HydC Escerichia coli formate dehydrogenase 1KQF 22 91
References

ExPASy- Gasteiger E., Gattiker A., Hoogland C., Ivanyi I., Appel R.D., Bairoch A. ExPASy: the proteomics server for in-depth protein knowledge and analysis Nucleic Acids Res. 31:3784-3788 (2003).
Genbank - Nucleic Acids Research, 28: 235-242. (www.rcsb.org)
PDB - H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H. Weissig, I.N. Shindyalov, P.E. Bourne (2000) The Protein Data Bank
Phyre2 - The Phyre2 web portal for protein modelling, prediction and analysis. Kelley LA et al. Nature Protocols 10, 845-858 (2015)
Pymol - The PyMOL Molecular Graphics System, Version 1.8 Schrödinger, LLC.

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