Hydration-Dependent Protein Dynamics Revealed by Molecular Dynamics Simulation of Crystalline Staphylococcal Nuclease

Abstract

Molecular dynamics simulations of crystalline Staphylococcal nuclease in full and minimal hydration states were performed to study hydration effects on protein dynamics at temperatures ranging from 100 to 300 K. In a full hydration state (hydration ratio in weight, h=0.49), gaps are fully filled with water molecules, whereas only crystal waters are included in a minimal hydration state (h=0.09). The inflection of the atomic mean-square fluctuation of protein as a function of temperature, known as the glass-like transition, is observed at approximately 220 K in both cases, which is more significant in the full hydration state. By examining the temperature dependence of residual fluctuation, we found that the increase of fluctuations in the loop and terminal regions, which are exposed to water, is much greater than that in other regions in the full hydration state, but the mobilities of the corresponding regions are relatively restricted in the minimal hydration state by intermolecular contact. The atomic mean-square fluctuation of water molecules in the full hydration state at 300 K is 1 order of magnitude greater than that in the minimal hydration state. Above the transition temperature, most water molecules in the full hydration state behave like bulk water and act as a lubricant for protein dynamics. In contrast, water molecules in the minimal hydration state tend to form more hydrogen bonds with the protein, restricting the fluctuation of these water molecules to the level of the protein. Thus, intermolecular interaction and solvent mobility are important to understand the glass-like transition in proteins.