Relationship between Dynamics of Structures and Dynamics of Hydrogen Bonds in Hras-GTP/GDP Complex

Hras protein is an intermediate for signals of cell proliferation and cell differentiation when Hras combines with guanosine triphosphate (GTP). In ordinary cells, GTP combined with Hras is hydrolyzed to guanosine diphosphate (GDP), and the structures of the protein-ligand complex strongly depend on hydrogen bonds. In such a system, hydrogen bonds exist between protein and ligand, between protein and water, and between ligand and water. In this study, we applied a relaxation mode analysis (RMA) to the trajectories of MD simulations for Hras-GTP/GDP to investigate the relationship between the dynamics of structures and those of hydrogen bonds. Different relaxation time of relaxation modes of Hras structures and Hras-solvent water hydrogen bonds were evident between Hras-GTP and Hras-GDP, and the results imply that the structure of Hras in Hras-GTP is stiffer than that in Hras-GDP. The method devised here and its interpretation can be applied to other systems focusing on objects with different stiffnesses.