Difference between revisions of "Task 9 (MSUD)"
m (→FoldX) |
m (→FoldX) |
||
Line 119: | Line 119: | ||
<gallery perrow=3 widths="330" heights="200" caption="Mutation residues with different side-chain conformations (FoldX in red, SCWRL in blue)"> |
<gallery perrow=3 widths="330" heights="200" caption="Mutation residues with different side-chain conformations (FoldX in red, SCWRL in blue)"> |
||
File:M82L-foldx-scwrl.png|Slightly difference between side-chain conformations of LEU82 in mutant '''M82L'''(FoldX in <span style="color:red">red</span>, SCWRL in <span style="color:blue">blue</span>) |
File:M82L-foldx-scwrl.png|Slightly difference between side-chain conformations of LEU82 in mutant '''M82L'''(FoldX in <span style="color:red">red</span>, SCWRL in <span style="color:blue">blue</span>) |
||
− | File:C264W-foldx-scwrl.png|Difference between side-chain conformations of |
+ | File:C264W-foldx-scwrl.png|Difference between side-chain conformations of TRP264 in mutant '''C264W'''(FoldX in <span style="color:red">red</span>, SCWRL in <span style="color:blue">blue</span>). They show completely different orientation of the heterocyclic ring in histidine. |
File:R346H-foldx-scwrl.png|Slightly difference between side-chain conformations of HIS346 in mutant '''R346H'''(FoldX in <span style="color:red">red</span>, SCWRL in <span style="color:blue">blue</span>) |
File:R346H-foldx-scwrl.png|Slightly difference between side-chain conformations of HIS346 in mutant '''R346H'''(FoldX in <span style="color:red">red</span>, SCWRL in <span style="color:blue">blue</span>) |
||
</gallery> |
</gallery> |
Revision as of 12:20, 14 July 2013
Contents
Results
For this task we have chosen 5 mutations from HGMD and dbSNP. 2 of them are neutral mutations which do not have functional changes over the protein structure. Following are the 5 mutations:
Database | Accession_code | Mutation | Pathogenic |
dbSNP | rs11549938 | M82L | False |
dbSNP | rs141086188 | A222T | False |
HGMD | CM045934 | C264W | True |
HGMD | CM062448 | R346H | True |
dbSNP | rs61736656 | I361V | False |
Selection of structure model
The following table shows an overview of all structures that are available for our protein:
Entry | Method | Resolution [Å] | Chain | Positions | R-value | pH | gaps |
---|---|---|---|---|---|---|---|
2BFD | X-ray | 1.39 | A | 46-445 | 0.15 | 5.5 | 289GLY-292SER,293THR-313ASP |
2BFF | X-ray | 1.46 | A | 46-445 | 0.15 | 5.5 | 301ARG-305GLU |
1X7Y | X-ray | 1.57 | A | 46-445 | 0.15 | 5.8 | 287ARG-313ASP |
2BFC | X-ray | 1.64 | A | 46-445 | 0.144 | 5.5 | 288ILE-313ASP |
2BFE | X-ray | 1.69 | A | 46-445 | 0.15 | 5.5 | 289GLY-291HIS,293THR-313ASP |
1X7Z | X-ray | 1.72 | A | 46-445 | 0.154 | 5.8 | 301ARG-306VAL |
1X7W | X-ray | 1.73 | A | 46-445 | 0.148 | 5.8 | 287ARG-313ASP |
2BFB | X-ray | 1.77 | A | 46-445 | 0.145 | 5.5 | 287ARG-313ASP |
2BEW | X-ray | 1.79 | A | 46-445 | 0.147 | 5.5 | 301ARG-307ASN |
1V1R | X-ray | 1.80 | A | 46-445 | 0.158 | 5.5 | 222ASN-231SER,286TYR-314HIS |
2BEV | X-ray | 1.80 | A | 46-445 | 0.139 | 5.5 | 301ARG-307ASN |
1U5B | X-ray | 1.83 | A | 46-445 | 0.156 | 5.8 | 301ARG-306VAL |
1WCI | X-ray | 1.84 | A | 46-445 | 0.149 | 5.5 | 301ARG-309TRP |
1OLS | X-ray | 1.85 | A | 46-445 | 0.172 | 5.5 | 292SER-295ASP,298SER-300TYR,301ARG-308TYR |
2J9F | X-ray | 1.88 | A/C | 46-445 | 0.171 | 5.5 | 300TYR-313ASP |
2BEU | X-ray | 1.89 | A | 46-445 | 0.171 | 5.5 | 301ARG-307ASN |
1OLU | X-ray | 1.90 | A | 46-445 | 0.161 | 5.5 | 26ASN-30GLY,287ARG-313ASP |
1V16 | X-ray | 1.90 | A | 46-445 | 0.132 | 5.5 | 288ILE-313ASP |
1V11 | X-ray | 1.95 | A | 46-445 | 0.139 | 5.5 | 288ILE-313ASP |
1V1M | X-ray | 2.00 | A | 46-445 | 0.13 | 5.5 | 289GLY-313ASP |
1X80 | X-ray | 2.00 | A | 46-445 | 0.161 | 5.8 | 287ARG-313ASP |
1X7X | X-ray | 2.10 | A | 46-445 | 0.149 | 5.8 | 287ARG-313ASP |
1OLX | X-ray | 2.25 | A | 46-445 | 0.161 | 5.5 | 301ARG-307ASN |
1DTW | X-ray | 2.70 | A | 46-445 | 0.224 | 7.5 | 301ARG-314HIS |
Unfortunately all structures contain gaps that span positions 302-304 (corresponding to 347-349 in the reference sequence), so we cannot create a composite structure, that does not contain this gap. We chose 2BFF because it has the smallest gap, a good resolution and a low R-value. It is not resolved at physiological pH, but the only structure with pH 7.5 (1DTW) has a bad resolution. The RMSD between 2BFF and 1DTW is about 0.3, so the different pH does not lead to a different structure and therefore the low pH at that 2BFF was resolved should not be a problem.
Visualization of mutant structures
The mutagen tool of PyMOL was used to introduce mutations to the protein structure. Mutations and their neighboring residues are visualized and shown in following figures.
Energy comparisons
FoldX
Mutation | PDB | SD | total | energy | Backbone | Hbond | Sidechain | Hbond | Van der Waals |
M82L | pdb2bff_1 | 0 | 0.08 | 0.01 | -0.05 | 0.46 | -0.1 | 0 | 0.44 |
A222T | pdb2bff_2 | 0 | 1.22 | 0.17 | -1.17 | -0.7 | 0.02 | 1.48 | -0.51 |
C264W | pdb2bff_3 | 0 | 34.77 | -0.16 | -0.15 | -1.99 | -0.09 | 2.88 | -2.95 |
R346H | pdb2bff_4 | 0 | 1.55 | 1.28 | 1.9 | 1.36 | -0.57 | -3.03 | 0.73 |
I361V | pdb2bff_5 | 0 | 0.78 | -0.02 | 0.01 | 0.54 | -0.02 | -0.29 | 1.06 |
Resulted structural models were compared to the structures calculated by SCWRL. By using alignment tool of PyMOL, we did not find any global deviation between the structures. Sequentially, structures produced by SCWRL have some residues missing. Following table shows the sequential difference.
Mutation | RMSD(Å) | Missing residues in SCWRL |
M82L | 0.0 | SER76,HIS96,MET146,LEU325,SER326 |
A222T | 0.0 | SER76,HIS96,MET146,LEU325,SER326 |
C264W | 0.0 | SER76,HIS96,MET146,LEU325,SER326 |
R346H | 0.0 | SER76,HIS96,MET146,LEU325,SER326 |
I361V | 0.0 | SER76,HIS96,MET146,LEU325,SER326 |
In 3 mutant structures the mutation residues have different side-chain conformation between results of FoldX and SCWRL. The other 2 mutant structures do not show such difference.
Minimise
The enegies of each Minimise run for the wild type and mutant structures are given in the following table. For the mutant structures there was only an output for structres calculated with FoldX. For input structures from SCWRL, Minimise gave no output (probably there was a problem with gaps).
run | 1 | 2 | 3 | 4 | 5 |
---|---|---|---|---|---|
WT | -17591 | -17424 | -16955 | -16792 | -16578 |
M82L FoldX | -17981 | -17722 | -17298 | -17001 | -16809 |
A222T FoldX | -17940 | -17708 | -17297 | -17001 | -16800 |
C264W FoldX | -15606 | -17724 | -17319 | -17164 | -16897 |
R346H FoldX | -18014 | -17769 | -17339 | -17049 | -16853 |
I361V FoldX | -18010 | -17684 | -17313 | -17012 | -16799 |
A reduction in the energy can only be observed for C264W, and only for the second recursive run. All other energies increase slightly with every run, but are overall similar to each other.