Solvation Thermodynamic Costs of Cognate Binding Site Formation

Conformational flexibility complicates the identification of lead molecules that are shape and charge complementary to target proteins. Solvation thermodynamics has typically not been integrated into the exploration of alternate protein conformations. Here, we study the variation of solvation thermodynamic potentials as proteins adopt different conformations. Specifically, we analyze solvation thermodynamics of protein binding cavities with conformations obtained from molecular dynamics simulations with mobile side chains and side chains restrained about their cognate bound structure. We find that the reorganization of protein side chains has a significant effect on the structure and thermodynamics of binding site solvation and, in the vast majority of cases, that there is a significant solvation free energetic cost to forming cognate ligand bound structures when the ligand is absent. We discuss how understanding the interplay between solvation thermodynamics and protein structural fluctuations is crucial for discovering alternative binding pockets, estimating the contribution to binding affinity of displacing water upon ligand binding, and assessing revealed cryptic pocket bindability.