In this molecular dynamics simulation study, we analyze the local structural and dynamic properties of water hydrating the protein ubiquitin on a spatial grid with 1 Å resolution. This allows for insights into the spatial distribution of water number densities, molecular orientations, translations, and rotations as a function of distance from the protein surface. Water molecule orientations follow a heterogeneous distribution with preferred local orientations of water dipoles and O-H bond vectors up to 10-15 Å distances from the protein, while local variations of the water number density converge to homogeneous bulk-like values within less than 8 Å. Interestingly, we find that the long-ranged orientational structure of water does not impact either the translational or rotational dynamics of water. Instead, heterogeneous distributions of local dynamical parameters and averaged dynamical retardation factors are only found close to the protein surface and follow a distance dependence comparable to heterogeneities in the local water number density. This study shows that the formation of nanodomains of preferred water orientations far from the protein does not significantly impact dynamical processes probed as a non-local average in most experiments.
ASJC Scopus subject areas
- Physics and Astronomy(all)
- Physical and Theoretical Chemistry