Difference between revisions of "Task 9 (MSUD)"

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| 1OLX || X-ray || 2.25 || A || 46-445 || 0.161 || 5.5 || 301ARG-307ASN
 
| 1OLX || X-ray || 2.25 || A || 46-445 || 0.161 || 5.5 || 301ARG-307ASN
 
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| 1DTW || X-ray || 2.7 || A || 46-445 || 0.224 || 7.5 || 301ARG-314HIS
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| 1DTW || X-ray || 2.70 || A || 46-445 || 0.224 || 7.5 || 301ARG-314HIS
 
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Revision as of 17:10, 12 July 2013

Results

Lab journal

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:

DatabaseAccession_codeMutationPathogenic
dbSNPrs11549938M82LFalse
dbSNPrs141086188A222TFalse
HGMDCM045934C264WTrue
HGMDCM062448R346HTrue
dbSNPrs61736656I361V 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.

Mutant structures (SCWRL)

Energy comparisons

FoldX

Minimise

Gromacs