Protein Dynamics at the Picosecond-Nanosecond Time Scale: a Complementary Study by Dielectric Spectroscopy, Neutron Spectroscopy and MD Simulation

Abstract

We have studied dynamics of hydrated protein (h ∼ 0.4 grams of water per gram of protein) in picoseconds-nanosecond time scale using dielectric spectroscopy, neutron spectroscopy and molecular dynamics (MD) simulations. We have observed two relaxation processes in dielectric spectra of hydrated protein: “main” (tens of picoseconds) and “slow” (nanoseconds). Traditionally these processes have been attributed to the relaxation of bound hydration water and not to the protein. Using Neutron scattering data, the “main” process has been assigned to the protein-water coupled motion. MD simulations focused on protein relaxation processes in picoseconds-nanosecond time range also revealed protein motions at the same time-scale as the processes observed in dielectric spectra of hydrated protein. Detailed analysis of the MD simulations and comparison to dielectric data indicate that the observed relaxation process in the nanosecond time range is mainly due to the protein. The relaxation processes involve the entire structure of the protein, including atoms in the protein backbone, side chains and turns. Both surface and buried protein atoms contribute to this motion, however surface atoms demonstrate slightly faster dynamics. Analysis of the water atom residence times reveals that 90% of hydration water exchange with the bulk on time scale shorter than 100 ps, and indicates that there are not enough stationary water molecules at the protein surface to support the bound water-only interpretation of the observed dielectric process in nanosecond time range.