Radially softening diffusive motions in a globular protein

Molecular dynamics simulation, quasielastic neutron scattering and analytic al theory are combined to characterize diffusive motions in a hydrated prot ein, C-phycocyanin. The simulation-derived scattering function is in approx imate agreement with experiment and is decomposed to determine the essentia l contributions. It is found that the geometry of the atomic motions can be modeled as diffusion in spheres with a distribution of radii. The time dep endence of the dynamics follows stretched exponential behavior, reflecting a distribution of relaxation times. The average side chain and backbone dyn amics are quantified and compared. The dynamical parameters are shown to pr esent a smooth variation with distance from the core of the protein. Moving outward from the center of the protein there is a progressive increase of the mean sphere size, accompanied by a narrowing and shifting to shorter ti mes of the relaxation time distribution. This smooth, "radially softening" dynamics may have important consequences for protein function. It also rais es the possibility that the dynamical or "glass" transition with temperatur e observed experimentally in proteins might be depth dependent, involving, as the temperature decreases, progressive freezing out of the anharmonic dy namics with increasing distance from the center of the protein.