Inspection of three-dimensional structures of proteins with dynamical information from the normal mode analysis

In this paper it is demonstrated that, to analyze structural data of proteins obtained from X-ray crystallography, the normal mode analysis in dihedral angle space can serve to supplement X-ray data as a useful system for gaining information on their dynamical as well as static structures. Especially, the following two subjects are discussed; first, the breakdown of the motions of a limited region in a polypeptide chain (e.g., an alpha-helix, a beta-strand or a loop) into internal and external motions reveals whether the region is flexible, or it is rigid but mobile when it has large fluctuations. Second, the correlation map between atomic motions serves to provide information for dividing the chain into segments, such as domains or modules, from a dynamical rather than from a geometrical point of view. It is shown that the modules proposed by M. Go appear distinctly in the correlation map as the regions in which clusters of atoms with positive correlation coefficients of their movements to each other exist. Furthermore, the modules are characterized by the negative correlation coefficients of the movements of the atoms in the clusters in a particular module to such movements in a different module.