Difference between revisions of "Structure-based mutation analysis (Phenylketonuria)"
From Bioinformatikpedia
(→Preparation) |
(→Preparation) |
||
| Line 6: | Line 6: | ||
[[Lab Journal - Task 9 (PAH) |Lab journal]] <br> |
[[Lab Journal - Task 9 (PAH) |Lab journal]] <br> |
||
| + | '''Structure selection'''<br> |
||
In some Tasks before, we used the protein structure of [http://www.rcsb.org/pdb/explore/explore.do?structureId=2PAH 2PAH] as reference, but now we have to check some more constraints for the protein structure selection: |
In some Tasks before, we used the protein structure of [http://www.rcsb.org/pdb/explore/explore.do?structureId=2PAH 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) |
* Structure with the highest resolution (small Å value) |
||
| Line 58: | Line 59: | ||
|} |
|} |
||
In Table x we can see, that the protein [http://www.rcsb.org/pdb/explore/explore.do?structureId=1J8U 1J8U] has a better resolution value as well as R-factor than the other proteins... |
In Table x we can see, that the protein [http://www.rcsb.org/pdb/explore/explore.do?structureId=1J8U 1J8U] has a better resolution value as well as R-factor than the other proteins... |
||
| + | |||
| + | |||
| + | '''Visualisation of used mutations'''<br> |
||
| + | ... |
||
| + | |||
| + | |||
| + | '''Mutated structure creation'''<br> |
||
| + | ... |
||
== Energy comparisons == |
== Energy comparisons == |
||
Revision as of 17:57, 2 July 2013
Page still under construction!!!
Summary
...
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 terms of the constraints for all sequences given in the PAH (P00439) Uniprot entry in Table x below:
| 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 |
In Table x 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
...
Mutated structure creation
...
Energy comparisons
...
FoldX
...
Minimise
...
References
<references/>
