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Biophys J, September 2001, p. 1666-1676, Vol. 81, No. 3
and
*Laboratoire Léon Brillouin, CEA-Centre National de
la Recherche Scientifique, CEA-Saclay, 91191 Gif-sur-Yvette,
France, Institute of Biochemistry, Splaiul
Independentei 296, 77700 Bucharest, Romania, and
Lehrstuhl für Biocomputing,
Interdisziplinäres Zentrum für Wissenschaftliches
Rechnen, Universität Heidelberg, D-69120
Heidelberg, Germany
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.
Biophys J, September 2001, p. 1666-1676, Vol. 81, No. 3
© 2001 by the Biophysical Society 0006-3495/01/09/1666/11 $2.00
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