Difference between revisions of "Task 9: Structure-based mutation analysis"
| Line 39: | Line 39: | ||
From the two available structures, we chose 1A6Z, because it has a slightly higher resolution and a nearly identical resolution compared to 1DE4. On the downside, 1A6Z was resolved at a pH value of 6.5, which is more distant to the physiological pH than the resolution pH of 1DE4. 1A6Z was chosen nevertheless, because it was used in all previous tasks, in order to keep consistency. |
From the two available structures, we chose 1A6Z, because it has a slightly higher resolution and a nearly identical resolution compared to 1DE4. On the downside, 1A6Z was resolved at a pH value of 6.5, which is more distant to the physiological pH than the resolution pH of 1DE4. 1A6Z was chosen nevertheless, because it was used in all previous tasks, in order to keep consistency. |
||
| − | == Mutations |
+ | == Mutations == |
| Line 58: | Line 58: | ||
== Structure Mutation using SCWRL == |
== Structure Mutation using SCWRL == |
||
| − | == Structure Mutation using foldX |
+ | == Structure Mutation using foldX == |
== Minimisation == |
== Minimisation == |
||
Revision as of 22:37, 25 August 2013
<css> table.colBasic2 { margin-left: auto; margin-right: auto; border: 1px solid black; border-collapse:collapse; width: 40%; }
.colBasic2 th,td { padding: 3px; border: 1px solid black; }
.colBasic2 td { text-align:left; }
/* for orange try #ff7f00 and #ffaa56 for blue try #005fbf and #aad4ff
maria's style blue: #adceff grey: #efefef
- /
.colBasic2 tr th { background-color:#efefef; color: black;} .colBasic2 tr:first-child th { background-color:#adceff; color:black;} </css>
| PDB ID | Res [A] | R-value (obs) | pH | missing residues | coverage |
|---|---|---|---|---|---|
| 1A6Z | 2.60 | 2.33 | 6.5 | 1-3 | 83.4% |
| 1DE4 | 2.80 | 2.31 | 8.0 | 1-3 | 83.4% |
Lab_Journal_Hemochromatosis_Task9
Contents
Structure Selection
From the two available structures, we chose 1A6Z, because it has a slightly higher resolution and a nearly identical resolution compared to 1DE4. On the downside, 1A6Z was resolved at a pH value of 6.5, which is more distant to the physiological pH than the resolution pH of 1DE4. 1A6Z was chosen nevertheless, because it was used in all previous tasks, in order to keep consistency.
Mutations
| Mutation | Disease causing ? |
| Val53Met | Yes |
| His63Asp | Yes |
| Met97Ile | No |
| Thr217Ile | No |
| Cys282Tyr | Yes |
Structure Mutation using SCWRL
Structure Mutation using foldX
Minimisation
| Method | Mutation | Iter. 1 | Iter. 2 | Iter. 3 | Iter. 4 | Iter. 5 |
|---|---|---|---|---|---|---|
| WT | - | -3724.15 | -5003.51 | -5118.38 | -5198.32 | -5301.44 |
| scwrl | V53M | -5022.73 | -5295.74 | -5154.72 | -5272.51 | -5260.4 |
| H63D | -4940.57 | -5212.88 | -5084.45 | -5190.74 | -5189.68 | |
| M97I | -5025.31 | -5291.5 | -5146.59 | -5247.72 | -5246.2 | |
| T217I | -5037.72 | -5307.97 | -5171.54 | -5277.0 | -5269.32 | |
| C282Y | -2596.78 | -5107.77 | -5037.12 | -5159.07 | -5191.73 | |
| foldx | 1a6z_a_1 | -5323.9 | -5544.42 | -5450.03 | -5377.19 | -5436.94 |
| 1a6z_a_2 | -5284.49 | -5493.82 | -5437.69 | -5364.69 | -5454.72 | |
| 1a6z_a_3 | -5264.67 | -5482.17 | -5405.78 | -5343.15 | -5255.85 | |
| 1a6z_a_4 | -5275.89 | -5492.39 | -5416.59 | -5343.98 | -5431.55 | |
| 1a6z_a_5 | -3376.95 | -5217.05 | -5194.04 | -5231.15 | -5290.49 |
