MONTE-CARLO SIMULATIONS FOR PROTEINS - BINDING AFFINITIES FOR TRYPSIN-BENZAMIDINE COMPLEXES VIA FREE-ENERGY PERTURBATIONS

Monte Carlo computer simulations have been performed in conjunction wi th free-energy perturbation calculations to determine the relative bin ding constants of four benzamidine inhibitors with trypsin. The protei n backbone was constrained in the simulations, but sampling of the sid e chains was allowed. The calculated free energies are very precise an d are shown to yield closed thermodynamic cycles. The calculations cor rectly predict p-aminobenzamidine to be the strongest inhibitor and gi ve relative free energies of binding for p-methyl-and p-chlorobenzamid ine in excellent agreement with experiment. The predicted overly weak binding of the parent benzamidine is most likely due to a deficiency i n the partial charges. The relative binding affinities are justified i n terms of bulk-solvation arguments whereby the more polar inhibitors are preferentially stabilized in water. The calculations demonstrate t hat Monte Carlo computer simulations can be used to determine accurate and precise relative binding constants for protein systems.