Enzyme-inhibitor association thermodynamics: Explicit and continuum solvent studies

Studying the thermodynamics of biochemical association reactions at the microscopic level requires efficient sampling of the configurations of the reactants and solvent as a function of the reaction pathways. In most cases, the associating ligand and receptor have complementary interlocking shapes. Upon association, loosely connected or disconnected solvent cavities at and around the binding site are formed. Disconnected solvent regions lead to severe statistical sampling problems when simulations are performed with explicit solvent. it was recently proposed that, when such limitations are encountered, they might be overcome by the use of the grand canonical ensemble. Here we investigate one such case and report the association free energy profile (potential of mean force) between trypsin and benzamidine along a chosen reaction coordinate as calculated using the grand canonical Monte Carlo method. The free energy profile is also calculated for a continuum solvent model using the Poisson equation, and the results are compared to the explicit water simulations. The comparison shows that the continuum solvent approach is surprisingly successful in reproducing the explicit solvent simulation results. The Monte Carlo results are analyzed in detail with respect to solvation structure. In the binding site channel there are waters bridging the carbonyl oxygen groups of Asp-189 with the NH2 groups of benzamidine, which are displaced upon inhibitor binding. A similar solvent-bridging configuration has been seen in the crystal structure of trypsin complexed with bovine pancreatic trypsin inhibitor. The predicted locations of other internal waters are in very good agreement with the positions found in the crystal structures, which supports the accuracy of the simulations.