Translational and Rotational Diffusion of Proteins

Abstract

We have investigated the translational and rotational diffusion of two proteins, bovine pancreatic trypsin inhibitor and hen egg white lysozyme, using molecular dynamics simulations in explicit solvent. The translational diffusion constants obtained form the simulations compare favourably with results from experiments. However, rotational diffusion constants indicate increased rotational diffusion compared to experiments. Further analysis, using simple hydration models, suggest that the observed rotational diffusion can be explained without invoking a fixed shell of hydration water associated with the protein. Within the assumptions of the hydration models, the results suggest that the strength of protein—water interactions in the current force field may be slightly underestimated.