Structure-based mutation analysis (Phenylketonuria)
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Summary
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Preparation
Structure selection
In some Tasks before, we used the protein structure of 2PAH as reference, but now we have to check some more constraints for the protein structure selection:
- Structure with the highest resolution (small Å value)
- Smallest R-factor
- Highest coverage
- pH-value ideally near physiological pH of 7.4
- No gaps (missing residues) included in the structure, so a consecutive numbering of residues should be given
To check which protein structure to use for further analysis, we compared the constraint data for all sequences given in the PAH (P00439) Uniprot entry. <figtable id="pro-struc">
| Protein | Resolution(Å) | R-factor | pH | Gaps | Chain | Positions in P00439 | Coverage % |
|---|---|---|---|---|---|---|---|
| 1DMW | 2.00 | 0.20 | 6.80 | x | A | 118-424 | x |
| 1J8T | 1.70 | 0.20 | 6.80 | x | A | 103-427 | x |
| 1J8U | 1.50 | 0.16 | 6.80 | 0 | A | 103-427 | 71.68 |
| 1KW0 | 2.50 | 0.22 | 6.80 | x | A | 103-427 | x |
| 1LRM | 2.10 | 0.21 | 6.80 | x | A | 103-427 | x |
| 1MMK | 2.00 | 0.20 | 6.80 | x | A | 103-427 | x |
| 1MMT | 2.00 | 0.21 | 6.80 | x | A | 103-427 | x |
| 1PAH | 2.00 | 0.18 | 6.80 | x | A | 117-424 | x |
| 1TDW | 2.10 | 0.21 | 6.80 | x | A | 117-424 | x |
| 1TG2 | 2.20 | 0.21 | 6.80 | x | A | 117-424 | x |
| 2PAH | 3.10 | 0.25 | 7.00 | x | A/B | 118-452 | 73.89 |
| 3PAH | 2.00 | 0.18 | 6.80 | x | A | 117-424 | x |
| 4ANP | 2.11 | 0.20 | 6.80 | x | A | 104-427 | x |
| 4PAH | 2.00 | 0.17 | 6.80 | x | A | 117-424 | x |
| 5PAH | 2.10 | 0.16 | 6.80 | x | A | 117-424 | x |
| 6PAH | 2.15 | 0.17 | 6.80 | x | A | 117-424 | x |
</figtable> In <xr id="pro-struc"/> we can see, that the protein 1J8U has a better resolution value as well as R-factor than the other proteins...
Visualisation of used mutations
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Mutated structure creation
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Energy comparisons
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FoldX
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Minimise
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References
<references/>
