Table 2:
Folding free energy differences of RTT-causing single point mutations. First number reported for each mutation is for 1QK9 structure and the second value is for 3C2I structure. Also, since Pro does not have a standard backbone, FEP simulations cannot be applied to Pro-involving mutations. Note that negative value of the predicted folding free energy change means stabilizing effect of the mutation.
| MBD Mutants | ΔΔG (kcal/mol) | |||||||
|---|---|---|---|---|---|---|---|---|
| NeEMO | IMutant3 | FoldX | DUET | mCSM | PoPMuSiC | FEP | Exp | |
| T158M | −0.25 −0.24 |
0.83 0.75 |
−0.24 −0.32 |
−0.07 −0.03 |
−0.06 −0.01 |
0.93 0.90 |
1.81 1.23 |
0.25 |
| R133C | 0.63 0.49 |
0.91 1.06 |
0.79 0.97 |
1.45 0.59 |
1.27 0.62 |
0.62 0.59 |
6.03 8.01 |
0.37 |
| R106W | 1.80 2.01 |
0.61 0.67 |
1.95 2.58 |
0.98 0.34 |
1.00 0.44 |
−0.38 −0.27 |
1.66 4.71 |
0.04 |
| P152R | 0.03 0.09 |
0.96 0.96 |
1.82 2.21 |
0.57 1.23 |
0.87 1.20 |
0.43 1.40 |
- - |
1.46 |
| A140V | 0.49 0.73 |
0.07 0.07 |
1.18 0.33 |
0.16 −0.02 |
0.34 0.24 |
0.88 0.67 |
1.08 0.28 |
−0.67 |
| S134C | 0.90 1.34 |
0.47 0.44 |
1.03 0.08 |
0.34 0.31 |
0.34 0.32 |
0.57 0.68 |
0.40 0.69 |
1.05 |
| R106Q | 1.73 1.94 |
1.14 1.19 |
2.04 2.08 |
1.42 0.94 |
0.25 0.42 |
0.86 1.55 |
1.05 2.81 |
0.12 |
| D156E | 0.89 0.62 |
0.86 0.56 |
0.55 2.65 |
0.05 0.35 |
0.25 0.42 |
0.86 1.55 |
1.05 2.81 |
0.88 |
| R133H | 1.35 1.22 |
1.19 1.38 |
1.77 0.74 |
1.86 1.19 |
1.58 1.24 |
0.24 0.22 |
7.40 7.33 |
0.24 |
| L100V | 1.97 2.69 |
1.08 0.93 |
2.23 2.46 |
1.45 1.23 |
1.43 1.00 |
1.24 1.41 |
0.63 0.28 |
1.11 |
| F155S | 1.23 1.11 |
1.73 2.07 |
6.48 2.15 |
2.90 3.31 |
2.70 3.05 |
3.46 3.43 |
1.90 −0.36 |
0.43 |
| T158A | 0.19 0.25 |
1.59 1.31 |
−0.06 −0.10 |
0.26 −0.58 |
0.43 0.65 |
0.77 1.24 |
0.40 −1.28 |
0.47 |
| R111G | 1.81 1.96 |
1.28 1.10 |
1.30 2.20 |
0.70 1.85 |
0.74 1.59 |
0.59 1.11 |
5.30 4.47 |
−0.43 |