Translational and rotational diffusion of proteins.
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 from 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, suggests 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.
Smith
P E
PE
Department of Physical Chemistry, Swiss Federal Institute of Technology, Zürich.
van Gunsteren
W F
WF
D000818:Animals; D007611:Aprotinin / Q000737:chemistry*; D002417:Cattle; D018360:Crystallography, X-Ray; D004058:Diffusion; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D009113:Muramidase / Q000737:chemistry*; D017510:Protein Folding; D017433:Protein Structure, Secondary; D014867:Water / Q000737:chemistry
D014867:Water; D007611:Aprotinin; D009113:Muramidase