Solvation Thermodynamic Costs of forming Cognate Binding Site Formation

Proteins are inherently flexible which complicates the identification of lead molecules that are shape and charge complementary to target proteins. While significant effort has been dedicated to exploring alternate protein conformations, solvation thermodynamics has typically not been integrated into these studies. Here, we study how solvation thermodynamics fluctuate as proteins adopt different conformations. We analyze solvation thermodynamics within the binding cavities of conformations for which side chains are mobile in molecular dynamics simulations and compare these to conformations for which they remain restrained about the cognate bound structure. We identify structural motifs that present significant costs to the sampling of cognate ligand bound structures. We find that the reorganization of protein side chains has a significant effect on the structure and thermodynamics of binding site solvation. We discuss how understanding the interplay between solvation thermodynamics and protein structural fluctuations is crucial for both discovering alternative binding pockets, estimating the contribution to binding affinity of displacing water upon ligand binding, and assessing revealed cryptic pocket bindability.