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 q=0.28 angstrom(-1) originates from equal contributions from correlations in nearest-neighbor water molecule dynamics and from internal protein motions, the latter consisting of alpha-helix pitch and inter-beta-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.