X-ray diffuse scattering and rigid-body motion in crystalline lysozyme probed by molecular dynamics simulation.

摘要: Rigid-body motions are determined from a 1 ns molecular dynamics simulation of the unit cell orthorhombic hen egg-white lysozyme and their contribution to X-ray diffuse scattering intensities examined. Using dynamical cluster technique, groups backbone atoms that move as approximately rigid bodies derived intramolecular interatomic fluctuation matrix. These tend be local in sequence or connected by disulphide bonds, contain on average five residues each, patterns, which sensitive collective motions, calculated full trajectory (including all protein degrees freedom). The results reproduce main features experimental scattering. Diffuse is also fitted trajectories bodies. atomic displacements found well reproduced model form using technique individual side-chains behave separate bodies: resulting R-factor with 5%. Quantitatively poorer agreement obtained secondary structural elements considered rigid. Rigid whole-molecule domain make only minor contributions atom displacements. Finally, correlations fluctuations examined directly canonical method.