Difference between revisions of "Team:NRP-UEA-Norwich/Results/ProteinModeling"
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<tr> | <tr> | ||
<th>Protein name</th> | <th>Protein name</th> | ||
| − | |||
<th>Organism and protein model used</th> | <th>Organism and protein model used</th> | ||
<th>PDB file</th> | <th>PDB file</th> | ||
| Line 44: | Line 43: | ||
<tr> | <tr> | ||
<td>MtrA</td> | <td>MtrA</td> | ||
| − | |||
<td><i>Wolinella succinogenes</i> octaheme sulfite reductase MccA, form I</td> | <td><i>Wolinella succinogenes</i> octaheme sulfite reductase MccA, form I</td> | ||
<td> | <td> | ||
| Line 54: | Line 52: | ||
<tr> | <tr> | ||
<td>MtrB</td> | <td>MtrB</td> | ||
| − | |||
<td><i>Pseudomonas aeruginosa</i> membrane bound ferripyoverdine receptor</td> | <td><i>Pseudomonas aeruginosa</i> membrane bound ferripyoverdine receptor</td> | ||
<td> | <td> | ||
| Line 64: | Line 61: | ||
<tr> | <tr> | ||
<td>MtrC</td> | <td>MtrC</td> | ||
| − | |||
<td><i>Shewanella oneidensis</i> MR-1 crystal structure of outer membrane decaheme cytochrome MtrC</td> | <td><i>Shewanella oneidensis</i> MR-1 crystal structure of outer membrane decaheme cytochrome MtrC</td> | ||
<td> | <td> | ||
| Line 74: | Line 70: | ||
<tr> | <tr> | ||
<td>HyaA</td> | <td>HyaA</td> | ||
| − | |||
<td><i>Escherichia coli</i> hydrogenase-1 complexed with cytochrome b</td> | <td><i>Escherichia coli</i> hydrogenase-1 complexed with cytochrome b</td> | ||
<td> | <td> | ||
| Line 84: | Line 79: | ||
<tr> | <tr> | ||
<td>HyaB</td> | <td>HyaB</td> | ||
| − | |||
<td><i>Salmonella enterica</i> NiFe hydrogenase</td> | <td><i>Salmonella enterica</i> NiFe hydrogenase</td> | ||
<td> | <td> | ||
| Line 94: | Line 88: | ||
<tr> | <tr> | ||
<td>HyaC</td> | <td>HyaC</td> | ||
| − | |||
<td><i>Escherichia coli</i> formate dehydrogenase</td> | <td><i>Escherichia coli</i> formate dehydrogenase</td> | ||
<td> | <td> | ||
| Line 104: | Line 97: | ||
<tr> | <tr> | ||
<td>HydA</td> | <td>HydA</td> | ||
| − | |||
<td>Desulfovibrio desulfuricans Fe-only hydrogenase</td> | <td>Desulfovibrio desulfuricans Fe-only hydrogenase</td> | ||
<td> | <td> | ||
| Line 114: | Line 106: | ||
<tr> | <tr> | ||
<td>HydB</td> | <td>HydB</td> | ||
| − | |||
<td><i>Desulfovibrio desulfuricans</i> small Fe-only subunit</td> | <td><i>Desulfovibrio desulfuricans</i> small Fe-only subunit</td> | ||
<td> | <td> | ||
| Line 124: | Line 115: | ||
<tr> | <tr> | ||
<td>HydC</td> | <td>HydC</td> | ||
| − | |||
<td><i>Escerichia coli</i> formate dehydrogenase</td> | <td><i>Escerichia coli</i> formate dehydrogenase</td> | ||
<td> | <td> | ||
Latest revision as of 18:39, 19 October 2016
PROTEIN MODELING
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.
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.
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 | Organism and protein model used | PDB file | % Sequence identity | % 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 MR-1 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 |
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