Difference between revisions of "Task 9 (MSUD)"
m (→Visualization of mutant structures) |
|||
Line 13: | Line 13: | ||
<tr><td>dbSNP</td><td>rs61736656</td><td>I361V </td><td>False</td></tr> |
<tr><td>dbSNP</td><td>rs61736656</td><td>I361V </td><td>False</td></tr> |
||
</table> |
</table> |
||
+ | |||
+ | |||
+ | ===Selection of structure model=== |
||
+ | |||
+ | The following table shows an overview of all structures that are available for our protein: |
||
+ | |||
+ | |||
+ | {| class='wikitable' border='1' style='width:800px' |
||
+ | ! 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 |
||
+ | |- style="background-color: #FFBBBB;" |
||
+ | | 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 || 1.8 || A || 46-445 || 0.158 || 5.5 || 222ASN-231SER,286TYR-314HIS |
||
+ | |- |
||
+ | | 2BEV || X-ray || 1.8 || 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 || 1.9 || A || 46-445 || 0.161 || 5.5 || 26ASN-30GLY,287ARG-313ASP |
||
+ | |- |
||
+ | | 1V16 || X-ray || 1.9 || 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 || A || 46-445 || 0.13 || 5.5 || 289GLY-313ASP |
||
+ | |- |
||
+ | | 1X80 || X-ray || 2 || A || 46-445 || 0.161 || 5.8 || 287ARG-313ASP |
||
+ | |- |
||
+ | | 1X7X || X-ray || 2.1 || 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 || 2.7 || 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=== |
===Visualization of mutant structures=== |
Revision as of 17:47, 12 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 | 1.8 | A | 46-445 | 0.158 | 5.5 | 222ASN-231SER,286TYR-314HIS |
2BEV | X-ray | 1.8 | 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 | 1.9 | A | 46-445 | 0.161 | 5.5 | 26ASN-30GLY,287ARG-313ASP |
1V16 | X-ray | 1.9 | 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 | A | 46-445 | 0.13 | 5.5 | 289GLY-313ASP |
1X80 | X-ray | 2 | A | 46-445 | 0.161 | 5.8 | 287ARG-313ASP |
1X7X | X-ray | 2.1 | 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 | 2.7 | 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.
- Visualization of mutations in BCKDHA (PDB: 2BFF, all residue positions refer to the reference sequence of BCKDHA)