Difference between revisions of "Structure based mutation analysis of GBA"
From Bioinformatikpedia
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| + | == Introduction == |
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| + | To carry out a structure-based analysis of the mutations chosen in [[Sequence_based_mutation_analysis_of_GBA#Introduction|Task 7]] a crystal structure had to be chosen. According to [http://www.uniprot.org/uniprot/P04062 Uniprot] 19 different crystal structures of glucocerebrosidase exist. The table below shows the six different structures with a resolution of or better than 2 Angstrom. 2NT0 is chosen as template for the analysis carried out in this section, as no residues are missing, the R-value is quite low, and it has the best resolution among the structures without missing residues. |
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{| border="1" style="text-align:center; border-spacing:0" align="left" cellpadding="3" cellspacing="3" |
{| border="1" style="text-align:center; border-spacing:0" align="left" cellpadding="3" cellspacing="3" |
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!PDB ID |
!PDB ID |
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| − | !Resolution |
+ | !Resolution [Å] |
!R-factor |
!R-factor |
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!Coverage |
!Coverage |
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!pH |
!pH |
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| − | !Missing |
+ | !Missing Residues (A/B) |
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|1OGS||2.00||0.195||||4.6||''0'' |
|1OGS||2.00||0.195||||4.6||''0'' |
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|2NT0||''1.79''||0.181||||4.5||''0'' |
|2NT0||''1.79''||0.181||||4.5||''0'' |
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| − | |2V3D||1.96||0.157||||6.5||9 |
+ | |2V3D||1.96||0.157||||6.5||9/8 |
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| − | |2V3E||2.00||0.163||||''7.5''||7 |
+ | |2V3E||2.00||0.163||||''7.5''||7/7 |
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| − | |2V3F||1.95||''0.154''||||6.5||8 |
+ | |2V3F||1.95||''0.154''||||6.5||8/14 |
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|3GXI||1.84||0.193||||NULL||''0'' |
|3GXI||1.84||0.193||||NULL||''0'' |
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| + | <br clear = "all"/> |
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| + | == Mutations == |
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| + | TODO: create image and so on ... |
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| + | |||
| + | === SCWRL === |
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| + | == Energy Calculation == |
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| + | |||
| + | === FoldX === |
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| + | === Minimise === |
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| + | === Gromacs === |
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| + | |||
| + | == Discussion == |
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Revision as of 14:20, 28 June 2011
Contents
Introduction
To carry out a structure-based analysis of the mutations chosen in Task 7 a crystal structure had to be chosen. According to Uniprot 19 different crystal structures of glucocerebrosidase exist. The table below shows the six different structures with a resolution of or better than 2 Angstrom. 2NT0 is chosen as template for the analysis carried out in this section, as no residues are missing, the R-value is quite low, and it has the best resolution among the structures without missing residues.
| PDB ID | Resolution [Å] | R-factor | Coverage | pH | Missing Residues (A/B) |
|---|---|---|---|---|---|
| 1OGS | 2.00 | 0.195 | 4.6 | 0 | |
| 2NT0 | 1.79 | 0.181 | 4.5 | 0 | |
| 2V3D | 1.96 | 0.157 | 6.5 | 9/8 | |
| 2V3E | 2.00 | 0.163 | 7.5 | 7/7 | |
| 2V3F | 1.95 | 0.154 | 6.5 | 8/14 | |
| 3GXI | 1.84 | 0.193 | NULL | 0 |
Mutations
TODO: create image and so on ...
