Residue-Specific Structural and Dynamical Coupling of Protein and Hydration Water Revealed by Molecular Dynamics Simulations
Shuai Wang, Jun Gao, Xiakun Chu
Abstract
Proteins and their surrounding hydration water engage in a dynamic interplay that is critical for maintaining structural stability and functional integrity. However, the intricate coupling between protein dynamics and the structural order of hydration water remains poorly understood. Here, we employ all-atom molecular dynamics simulations to investigate this relationship across four representative proteins. Our results reveal that protein residues with greater flexibility or solvent exposure are surrounded by more disordered hydration water, akin to bulk water, whereas rigid and buried non-polar residues are associated with structurally ordered hydration shells. Due to their strong hydrogen bonding and electrostatic interactions, charged residues exhibit the most disordered hydration water, while non-polar residues are associated with the structurally most ordered hydration water. We further uncovered a positive correlation between the relaxation dynamics of protein residues and their hydration water: slower (faster) protein relaxation is coupled with slower (faster) relaxation of the structural order of hydration water. Notably, this coupling weakens with increasing residue flexibility or solvent exposure, with non-polar residues displaying the strongest coupling, and charged residues the weakest. To further uncover their coupling mechanism, we elucidate residue-specific coupled fluctuations between protein residues and hydration water by generating scatter plots. These findings provide a comprehensive understanding of the mechanisms underlying protein-water interactions, offering valuable insights into the role of hydration water in protein stability, dynamics, and function.