Heterogeneous Hydration of p53/MDM2 Complex: Molecular Dynamics Simulations vs. Variational Implicit Solvent Model

Dr. Zuojun Guo
Genomics Institute of Novartis Research Foundation


It is well know that water-mediated interactions play critical roles in biomolecular recognition processes. Decades of theoretical and experimental studies showed us a very complicated picture. No single reliable model can provide simple and consistent descriptions to its role in kinetics, thermodynamic, and structural characterizations yet.

However, a joint explicit solvent molecular dynamics (MD) simulations and the variational implicit-solvent model (VISM) may still provide semi-quantitative insight into these complicated heterogeneous hydration, the solute-solvent interface, and individual interesting water molecules around proteins.

In this study, we used this combination approach to study the hydration properties of the biologically important p53/MDM2 complex. Unlike simple model solutes, in such a realistic and heterogeneous solute-solvent system with both geometrical and chemical complexity, it occurs that the local water distribution sensitively depends on nearby amino acid properties and the geometric shape of the protein. We show that the VISM can accurately describe the locations of high and low density solvation shells identified by the MD simulations, and can explain them by a local coupling balance of solvent-solute interaction potentials and curvature. In particular, capillary transitions between local dry and wet hydration states in the binding pocket are captured for inter-domain distance between 4 to 6 Å right at the onset of binding. The underlying physical connection between geometry and polarity are illustrated and quantified. Our study offers a microscopic and physical insight into the heterogeneous hydration behavior of the biologically highly relevant p53/MDM2 system and demonstrates the fundamental importance of hydrophobic effects for biological binding processes. We hope this study may help to establish new design rules for drugs and medical substances.