Table 1. MM/PBSA binding free energies (kJ/mol) of wild-type and mutant AIRE-PHD1/H3K4me0 complexes.
| mutants | Experiment | Computation | Polar contributions | Non-polar contributions | ||||||
| 1ΔGexp | 2ΔΔGexp | 3ΔGcomp | 4ΔΔGcomp | 5ΔGcoul | 6ΔGps | 7ΔGpolar | 8ΔGvdW | 9ΔGnps | 10ΔGnonpolar | |
| wild-type | −29.73 | 0 | −170.7(4.0) | 0 | −4337.7(16.3) | 4416.4(15.6) | 78.7 | −217.6(2.7) | −31.8(0.2) | −249.4 |
| Glu307Ala | −24.70 | 5.0 | −164.5(3.6) | 6.1 | −3779.3(16.4) | 3860.0(16.5) | 80.6 | −214.2(2.8) | −30.9(0.2) | −245.1 |
| Glu298Ala | −24.70 | 5.0 | −147.7(3.8) | 22.9 | −3632.3(16.4) | 3742.5(15.1) | 110.2 | −226.6(2.6) | −31.3(0.2) | −257.9 |
| R8A | −24.28 | 5.5 | −136.1(3.4) | 34.5 | −3384.0(13.4) | 3486.6(12.7) | 102.6 | −209.3(2.5) | −29.5(0.1) | −238.7 |
| Asp304Ala | −21.77 | 8.0 | −117.2(3.1) | 53.4 | −3681.2(16.8) | 3817.2(16.0) | 136 | −222.1(2.6) | −31.2(0.2) | −253.2 |
| Asp297Ala | −21.72 | 8.0 | −132.7(4.1) | 38 | −3507.5(16.0) | 3634.3(15.2) | 126.8 | −228.0(2.5) | −31.5(0.2) | −259.5 |
2
difference between wild-type and mutant experimental binding free energies.
3
computational binding free energies.
4
difference between computational binding free energies of wild-type and mutant complex.
5
coulombic term.
6
polar solvation term.
7
polar term (sum of coulombic and polar solvation terms).
8
van der Waals term.
9
non-polar solvation term.
10
non-polar term (sum of van der Waals and non polar solvation terms).
Standard errors are given in parentheses.