Radially softening diffusive motions in a globular protein.
Molecular dynamics simulation, quasielastic neutron scattering and analytical theory are combined to characterize diffusive motions in a hydrated protein, C-phycocyanin. The simulation-derived scattering function is in approximate agreement with experiment and is decomposed to determine the essential 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 dependence of the dynamics follows stretched exponential behavior, reflecting a distribution of relaxation times. The average side chain and backbone dynamics are quantified and compared. The dynamical parameters are shown to present 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 times of the relaxation time distribution. This smooth, "radially softening" dynamics may have important consequences for protein function. It also raises the possibility that the dynamical or "glass" transition with temperature observed experimentally in proteins might be depth dependent, involving, as the temperature decreases, progressive freezing out of the anharmonic dynamics with increasing distance from the center of the protein.
Dellerue
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Laboratoire Léon Brillouin, CEA-Centre National de la Recherche Scientifique, CEA-Saclay, 91191 Gif-sur-Yvette, France.
Petrescu
A J
AJ
Smith
J C
JC
Bellissent-Funel
M C
MC
D003198:Computer Simulation; D004058:Diffusion; D008958:Models, Molecular; D009038:Motion; D009502:Neutrons; D010798:Phycocyanin / Q000737:chemistry* / Q000378:metabolism*; D017434:Protein Structure, Tertiary; D012542:Scattering, Radiation
D010798:Phycocyanin