Table IV.
Average Association Free Energies of the Human and Rat C3c:Compstatin Complexes, Computed From the MD Simulations (All Values in kcal mol−1)
| Runs | Total ΔGa | Intermolecular contributions to ΔGb |
|||
|---|---|---|---|---|---|
| Total | Nonpolar components | Polar components | Polar interactionsc | ||
| H1 | −43 (6) | −55 (1) | −62 (1) | 7 (2) | −48 (5) |
| H2 | −53 (6) | −54 (2) | −59 (1) | 5 (0) | −47 (1) |
| Average | −48 (6) | −55 (1) | −61 (1) | 6 (2) | −47 (4) |
| R1 | −25 (5) | −47 (1) | −51 (2) | 4 (2) | −38 (4) |
| R2 | −36 (5) | −45 (1) | −55 (1) | 10 (1) | −35 (2) |
| R3 | −24 (5) | −45 (7) | −49 (9) | 4 (2) | −36 (4) |
| Average | −29 (5) | −46 (4) | −52 (5) | 6 (1) | −36 (4) |
| ΔΔG | −19 (8) | −9 (4) | −9 (5) | 0 (2) | −11 (5) |
| X1 | −54 | −64 | 10 | −42 | |
| X2 | −57 | −59 | 2 | −46 | |
The association-free energies were computed by application of Eqs. (1) and (2) for the complex, free protein, and free ligand (Methods). Values were averaged over 700 snapshots, spanning the 7-ns runs. Errors (in parentheses) correspond to the standard deviation of mean values, evaluated over four successive trajectory segments of equal length (1.75 ns). X1 and X2 are the two independent complexes of the asymmetric crystallographic unit.3
Intermolecular components were computed by application of Eqs. (1) and (2), assuming that the free protein and free ligand had the same conformation as in the complex. Polar and nonpolar components are defined in Eq. (2).
The polar interaction components measure the strength of intermolecular polar interactions (Coulomb + GB) in the complex. They are evaluated by Eq. (3) (Methods).