Dynamic structure of biological related molecules : X-ray determination and Molecular dynamic simulation

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Protein misfolding has been implicated in a large number of diseases, such as amyloidoses. Protein dynamic structures afford an important different view of their biological function and provide expertise in a drug development. X-ray crystallography method to determine the polymorphic structure of the protein and molecular dynamic calculation are applied to influenza A virus hemagglutinin (HA) and bovine α-lactalbumin. Several visualization tools to monitor and analyze the molecular dynamic structures are developed.Three days after infection, virions in the culture medium are collected. The virus was purified by sedimentation through 30-50% sucrose gradients. A soluble form of the HA is clipped from its membrane anchor by the proteinase, bromelain and purified by several chromatographies. Crystallization condition was optimized by changing the pH, ionic strength and polymer degree of precipitant reagent. Some crystalline samples are provided for collection of X-ray diffraction data. By using trifluoroethanol, meta stable moltenglobular structure is induced in bovine α-lactalbumin solution. This solution sample affords to seek of crystallization condition. Several new concepts of crystallizabity are tried such as by using dynamic light scattering (DLS), which is very sensitive to aggregation and large impurities. The organic compound with the flexible ring moiety is used as model compound in molecular dynamic simulation calculations by the program MacroModel and the coordinate trajectories are classified and compared to x-ray structures. The developed visualization programs are useful to analyze and compare the multiple conformers.