Solvent-protein interactions diffusion constant

The dynamics of the solvent in the region near a protein can be characterized by a number of properties (e.g., solvent velocity correlation functions, mean-square displacement correlation functions, dipole orientation correlation functions, etc.). These properties provide information on a range of phenomena from local solute-solvent interactions (velocity correlation functions) to solvent mobility (mean-square displacement correlation functions) and dielectric behavior (dipole correlation functions). Here we focus on the diffusion constant, which provides a convenient measure of mobility for water molecules near protein atoms. The diffusion constant for solvent molecules may be computed directly from the slope of the mean-square displacement correlation function,... 

To treat more realistic models for the kinetics of biomolecular encounters, a simulation approach has been developed and applied to proteins.370,371,3718 This approach merges stochastic dynamics methodology (Chapt. IV.D) with the analytic result for the Debye rate constant for a pair of particles, moving diffusively through solvent with a centrosymmetric interaction potential.365 The analytical expression for the Debye rate constant, ko(,R), to first achieve a separation, R, is given by... 

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