X-RAY DIFFUSE-SCATTERING AND RIGID-BODY MOTION IN CRYSTALLINE LYSOZYME PROBED BY MOLECULAR-DYNAMICS SIMULATION

Rigid-body motions are determined from a Ins molecular dynamics simula tion of the unit cell of orthorhombic hen egg-white lysozyme and their contribution to X-ray diffuse scattering intensities are examined. Us ing a dynamical cluster technique, groups of backbone atoms that move as al?proximately rigid bodies are derived from the intramolecular int eratomic fluctuation matrix. These groups tend to be local in the sequ ence or connected by disulphide bonds, and contain on average five res idues each. X-ray diffuse scattering patterns, which are sensitive to collective motions, are calculated from the full simulation trajectory (including all the protein degrees of freedom). The results reproduce the main features of the experimental scattering. Diffuse scattering is also calculated from fitted trajectories of the rigid bodies. The f ull simulation diffuse scattering and atomic displacements are found t o be well reproduced by a model in which the backbone atoms form the r igid groups determined using the dynamical cluster technique and the i ndividual side-chains behave as separate rigid bodies: the resulting X -factor with the full simulation scattering is 5%. Quantitatively poor er agreement is obtained from trajectories in which the secondary stru ctural elements of the protein are considered rigid. Rigid whole-molec ule and domain motions make only minor contributions to the protein at om displacements. Finally, correlations in the interatomic fluctuation s are examined directly using a canonical method. (C) 1998 Academic Pr ess Limited.