Thermodynamic Properties of Water Molecules at a Protein–Protein Interaction Surface

Protein–protein interactions (PPIs) have been identified as a vital regulator of cellular pathways and networks. However, the determinants that control binding affinity and specificity at protein surfaces are incompletely characterized and thus unable to be exploited for the purpose of developing PPI inhibitors to control cellular pathways in disease states. One of the key factors in intermolecular interactions that remains poorly understood is the role of water molecules and in particular the importance of solvent entropy. This factor is expected to be particularly important at protein surfaces, and the release of water molecules from hydrophobic regions is one of the most important drivers of PPIs. In this work, we have studied the protein surface of a mutant of the protein RadA to quantify the thermodynamics of surface water molecules. RadA and its human homologue RAD51 function as recombinases in the process of homologous recombination. RadA binds to itself to form oligomeric structures and thus contains a well-characterized protein–protein binding surface. Similarly, RAD51 binds either to itself to form oligomers or to the protein BRCA2 to form filaments. X-ray crystallography has determined that the same interface functions in both interactions. Work in our group has generated a partially humanized mutant of RadA, termed MAYM, which has been crystallized in the apo form. We studied this apo form of MAYM using a combination of molecular dynamics (MD) simulations and inhomogeneous fluid solvation theory (IFST). The method locates a number of the hydration sites observed in the crystal structure and locates hydrophobic sites where hydrophobic species are known to bind experimentally. The simulations also highlight the importance of the restraints placed on the protein in determining the results. Finally, the results identify a correlation between the predicted entropy of water molecules at a given site and the solvent-accessible surface area and suggest that correlations between water molecules only need to be considered for water molecules separated by less than 3.2 Å. The combination of MD and IFST has been used previously to study PPIs and represents one of the few existing methods to quantify solvent thermodynamics. This is a vital aspect of molecular recognition and one which we believe must be developed.