Correlated dynamics determining x-ray diffuse scattering from a crystalline protein revealed by molecular dynamics simulation.
The dynamical origin of the x-ray diffuse scattering by crystals of a protein, Staphylococcal nuclease, is determined using molecular dynamics simulation. A smooth, nearly isotropic scattering shell at originates from equal contributions from correlations in nearest-neighbor water molecule dynamics and from internal protein motions, the latter consisting of -helix pitch and inter--strand fluctuations. Superposed on the shell are intense, three-dimensional scattering features that originate from a very small number of slowly varying (>10 ns) collective motions. The individual three-dimensional features are assigned to specific collective motions in the protein, and some of these explicitly involve potentially functional active-site deformations.
Meinhold
Lars
L
Computational Molecular Biophysics, Interdisciplinary Center for Scientific Computing (IWR), University of Heidelberg, Im Neuenheimer Feld 368, D-69120 Heidelberg, Germany.
Smith
Jeremy C
JC
D003198:Computer Simulation; D008836:Micrococcal Nuclease / Q000737:chemistry*; D008956:Models, Chemical; D008958:Models, Molecular; D011487:Protein Conformation; D013816:Thermodynamics; D014961:X-Ray Diffraction
D008836:Micrococcal Nuclease