Structure-based mutation analysis GLA
by Benjamin Drexler and Fabian Grandke
Contents
Introduction
In this task we analyse the structure of our protein to find out what effects the point mutations have. Therefor we created mutated structures and compared them to the wild-type protein. Several tools based on different methods have been used to achieve that aim. We used the mutations that we have chosen in the previous task.
Structure Selection
There are several structure files available for our protein:
| PDB ID | Resolution [Å] | ph-Value | R-Factor | Coverage [%] | Missing Residues |
|---|---|---|---|---|---|
| 1R46 | 3.25 | 8.0 | 0.262 | 99.7 | 422-429 |
| 1R47 | 3.45 | 8.0 | 0.285 | 99.5 | 422-429 |
| 3GXN | 3.01 | NULL | 0.239 | 88.08 | 422-429 |
| 3GXP | 2.20 | NULL | 0.204 | 81.9 | 422-429 |
| 3GXT | 2.70 | NULL | 0.245 | 97.29 | 422-429 |
| 3HG2 | 2.30 | 4.6 | 0.178 | 97.32 | 422-429 |
| 3HG3 | 1.90 | 6.5 | 0.167 | 98.64 | 427-435 |
| 3HG4 | 2.30 | 4.6 | 0.166 | 99.86 | 422-429 |
| 3HG5 | 2.30 | 4.6 | 0.192 | 100 | 422-429 |
| 3LX9 | 2.04 | 6.5 | 0.178 | 98.92 | 423-435 |
| 3LXA | 3.04 | 6.5 | 0.216 | 99.52 | 427-435 |
| 3LXB | 2.85 | 6.5 | 0.227 | 99.3 | 427-435 |
| 3LXC | 2.35 | 6.5 | 0.186 | 98.31 | 423-435 |
We set two cutoffs to decide which structures are excluded:
- ph-value: < 6.5
- resolution: > 2.7
After we applied the cutoffs to our set of structures three were left (exclusion factors are colored red in the table). One of them was slightly better than the other ones so we decided to use 3HG3 (worse values are colored gray in the table). Additionally 3GH3 has the best overall resolution and R-factor (colored green). As the missing residues are very similar for all structures they are not further taken into account.
Mutation Mapping
Energy Comparison
| Number | AA-Position | Codon change | Amino acid change | SCWRL4 | FoldX | FoldX - Diff | Minimise | Minimise - Diff |
|---|---|---|---|---|---|---|---|---|
| WT | - | -20.93 | - | -20481.23 | - | |||
| 1 | 42 | ATG-ACG | Met -> Thr | 343.25 | 157.29 | -178.22 | -20324.41 | -156.82 |
| 2 | 65 | AGT-ACG | Ser -> Thr | 327.798 | 152.87 | -173.8 | -20339.34 | -141.89 |
| 3 | 117 | ATT-AGT | Ile -> Ser | 333.027 | 157.97 | -178.9 | -20353.47 | -127.76 |
| 4 | 143 | cGCA-ACA | Ala -> Thr | 333.944 | 154.40 | -175.33 | -20339.32 | -141.91 |
| 5 | 186 | CAC-CGC | His -> Arg | 323.717 | 154.57 | -175.5 | -20321.32 | -159.91 |
| 6 | 205 | gCCT-ACT | Pro -> Thr | 340.619 | 155.96 | -176.89 | -20345.87 | -135.36 |
| 7 | 244 | gGAC-CAC | Asp -> His | 333.594 | 152.08 | -173.01 | -20393.12 | -88.11 |
| 8 | 283 | CAG-CCG | Gln -> Pro | 332.631 | 159.91 | -180.84 | -8027.71 | -12453.52 |
| 8.2 | - | - | - | - | - | - | -19134.48 | -1346,95 |
| 9 | 321 | tCAG-TAG | Gln -> Glu | 332.853 | 160.95 | -181.88 | -20246.98 | -234.25 |
| 10 | 363 | TATa-TAA | Arg -> Cys | 330.56 | 150.50 | -171.43 | -20295.77 | -185.46 |
Wildtype
| Force Field | Average | Error Estimat | RMSD | Tot-Drift (kJ/mol) |
|---|---|---|---|---|
| Bond | ||||
| AMBERGS | 1826.99 | 420 | 4409.39 | -2499.37 |
| AMBER03 | 1639.74 | 410 | 4358.68 | -2424.42 |
| CHARMM27 | 2908.14 | 350 | 4779.8 | -2033.44 |
| Angle | ||||
| AMBERGS | 5496.47 | 74 | 476.18 | 408.548 |
| AMBER03 | 5324.13 | 72 | 469.75 | 369.24 |
| CHARMM27 | 7975.2 | 86 | 798.12 | 432.901 |
| Potential | ||||
| AMBERGS | -114713 | 1200 | 5648.79 | -7915.46 |
| AMBER03 | -91307.7 | 1200 | 5559.82 | -7839.05 |
| CHARMM27 | 136.699 | 32 | 64.3892 | 227.896 |
Gromacs
References
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