Deducing dynamic protein 3D structural information from X-ray crystallography and NMR

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Dynamic 3D structural information of proteins is essential for elucidation of molecular mechanism of protein function. The purpose of this reseach project is firstly to develop new methods of analyzes of experimental X-ray crystallographic and NMR data and secondly to apply the developed methods for real systems to deduce such dynamic information. At first, we applied the new method of protein X-ray crystallographic refinement based on the normal mode concept to human lysozyme and its site-specific mutant, and demonstrated that information about anisotropic temperature factors of protein atoms and their concerted motions could be deduced. Furthermore interesting information was obtained about correlation of changes of 3D structure and fluctuation and also about molecular mechanism of enzymatic function by analyzing changes of 3D structure and fluctuation accompanied with site-derected mutation. At second, we developed a new method to deduce new information about collective motions in protein by analyzing X-ray diffuse scattering. At third, we derived a formula of expressing up to second order changes of protein atomic Cartesian coordinates for small changes of dihedral angles, and applied this formula for developing method of obtaining Lipari-Szabo order parameters from the normal mode analysis. This method will enable us to develop a new method by which dynamic as well as static protein 3D structural information can be deduced from experimental NMR data.