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

蛋白质的动态三维结构信息对于阐明蛋白质功能的分子机制至关重要。本研究项目的目的首先是开发新的分析实验x射线晶体学和核磁共振数据的方法，其次是将所开发的方法应用于实际系统来推断这些动态信息。首先，我们将基于正常模式概念的蛋白质x射线晶体细化新方法应用于人溶菌酶及其位点特异性突变体，并证明了蛋白质原子各向异性温度因子及其协同运动的信息可以推导出来。此外，通过分析三维结构变化和波动伴随位点定向突变的变化，获得了三维结构变化和波动的相关性以及酶功能的分子机制的有趣信息。其次，我们开发了一种新的方法，通过分析x射线漫射散射来推断蛋白质集体运动的新信息。第三，推导了二面角微小变化时蛋白质原子笛卡尔坐标最高二阶变化的表达式，并应用该公式建立了从正态分析中获得Lipari-Szabo阶参数的方法。该方法将使我们能够开发一种新的方法，通过该方法可以从实验核磁共振数据中推断出动态和静态蛋白质的三维结构信息。

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.