Table 3.
Prediction of VRK1 pathogenic variant protein stability.
| Pathogenic variant | Structure used and difference in total energy from wild type and VRK1 pathogenic variant proteins | Stability prediction | ||
|---|---|---|---|---|
| 2RSV_diff (2018) | diff_2RSV | diff_2LAV | ||
| G135R | 2,4208 | 2,9714 | 0,6761 | destabilizing |
| H119R | −0,8401 | −0,7466 | −1,5024 | stabilizing |
| L195V | 0,1785 | 0,0108 | 1,5525 | destabilizing |
| R133C | −0,7308 | −0,783 | −0,6514 | Light stabilizing |
| R321C | 1,7191 | 1,7558 | 0,725 | Light destabilizing |
| R89Q | −0,1242 | −0,065 | −0,72 | stabilizing |
| V236M | 0,3835 | 0,3926 | −0,3905 | neutral |
| R358X | Not applicable: truncated protein | |||
Differences in total energy between wild type and each VRK1 pathogenic variant proteins, and prediction of the effect on their stability. The reported accuracy of FoldX is 0.46 kcal/mol (i.e., the SD of the difference between ΔΔGs calculated by FoldX and the experimental values. The ΔΔG values are classified into seven categories regarding their impact on protein stability (Supplementary Table S1).