The dynamics of protein hydration water: a quantitative comparison of molecular dynamics simulations and neutron-scattering experiments.
We present results from an extensive molecular dynamics simulation study of water hydrating the protein Ribonuclease A, at a series of temperatures in cluster, crystal, and powder environments. The dynamics of protein hydration water appear to be very similar in crystal and powder environments at moderate to high hydration levels. Thus, we contend that experiments performed on powder samples are appropriate for discussing hydration water dynamics in native protein environments. Our analysis reveals that simulations performed on cluster models consisting of proteins surrounded by a finite water shell with free boundaries are not appropriate for the study of the solvent dynamics. Detailed comparison to available x-ray diffraction and inelastic neutron-scattering data shows that current generation force fields are capable of accurately reproducing the structural and dynamical observables. On the time scale of tens of picoseconds, at room temperature and high hydration, significant water translational diffusion and rotational motion occur. At low hydration, the water molecules are translationally confined but display appreciable rotational motion. Below the protein dynamical transition temperature, both translational and rotational motions of the water molecules are essentially arrested. Taken together, these results suggest that water translational motion is necessary for the structural relaxation that permits anharmonic and diffusive motions in proteins. Furthermore, it appears that the exchange of protein-water hydrogen bonds by water rotational/librational motion is not sufficient to permit protein structural relaxation. Rather, the complete exchange of protein-bound water molecules by translational displacement seems to be required.
Tarek
M
M
National Institute of Standards and Technology, Center for Neutron Research, Gaithersburg, Maryland 20899-8562, USA.
Tobias
D J
DJ
D003198:Computer Simulation; D018360:Crystallography, X-Ray; D009502:Neutrons; D011487:Protein Conformation; D012259:Ribonuclease, Pancreatic / Q000737:chemistry*; D012542:Scattering, Radiation; D012984:Software; D014867:Water
D014867:Water; D012259:Ribonuclease, Pancreatic