Table 1. MM-PBSA free energy (kcal·mol−1) components for the Smadn+DNA+Smadn models.
Smad4+DNA+Smad4 | Smad1+DNA+Smad1 | Smad4+DNA+Smad1 | Smad3+DNA+Smad3 | Smad4+DNA+Smad3 | |
Receptor | Smad4+DNA | Smad1+DNA | Smad4+DNA | Smad3+DNA | Smad4+DNA |
Ligand | Smad4 | Smad1 | Smad1 | Smad3 | Smad3 |
ΔEele | −3453.95 | −3728.48 | −3855.88 | −4582.86 | −4724.77 |
ΔEvdw | −58.86 | −58.27 | −53.80 | −87.87 | −83.84 |
ΔE int | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
ΔGnp/solv | −10.18 | −10.49 | −10.33 | −16.21 | −15.61 |
ΔGpb/solv | 3445.83 | 3710.30 | 3843.88 | 4577.85 | 4710.65 |
ΔGnp | −69.04 | −68.76 | −64.13 | −104.08 | −99.45 |
ΔGpb | −8.12 | −18.18 | −12.00 | −8.01 | −14.12 |
ΔTS | −59.82 | −68.52 | −46.62 | −85.41 | −78.01 |
ΔHbinding | −77.16 | −86.94 | −76.13 | −109.09 | −113.57 |
ΔGbinding | −17.34(0.18)a | −18.42(0.17) | −29.51(0.18) | −23.68(0.20) | −35.56(0.22) |
The values in parentheses are the calculated standard errors.
ΔG np = ΔE vdw+ΔG np/solv.
ΔG pb = ΔE ele+ΔG pb/solv.
ΔGbinding = ΔGnp +ΔGpb –ΔTS.
= ΔHbinding –ΔTS.