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

蛋白质错误折叠与许多疾病有关，例如淀粉样变性。蛋白质动态结构提供了对其生物功能的重要不同观点，并为药物开发提供了专业知识。对甲型流感病毒血凝素(HA)和牛α-乳清蛋白进行了X射线结晶学分析和分子动力学计算。开发了几种可视化工具来监测和分析分子动态结构。感染后三天，收集到培养基中的病毒粒子。用30-50%蔗糖梯度沉淀法提纯病毒。用菠萝酶从其膜锚上切下一种可溶性形式的透明质酸，并通过几次层析进行纯化。通过改变沉淀剂的pH值、离子强度和聚合度来优化结晶条件。提供了一些晶体样品，用于收集X射线衍射数据。用三氟乙醇在牛α-乳清蛋白溶液中诱导形成亚稳定的熔融球状结构。该溶液样品为寻找结晶条件提供了依据。尝试了几个新的结晶性概念，如利用对聚集和大杂质非常敏感的动态光散射(DLS)。采用分子动力学模拟计算程序MacroModel，以柔性环状有机化合物为模型化合物，对其配位轨迹进行了分类，并与X-射线结构进行了比较。开发的可视化程序对分析和比较多种构象是有用的。

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.