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，如淀粉样变性。蛋白质的动态结构提供了一个重要的不同的观点，他们的生物学功能，并提供专业知识，在药物开发。应用X射线晶体学方法测定了A型流感病毒血凝素（HA）和牛α-乳白蛋白的蛋白质多态性结构，并进行了分子动力学计算。在感染后第三天，收集培养液中的病毒粒子。通过30-50%蔗糖梯度沉降纯化病毒。HA的可溶形式通过蛋白酶菠萝蛋白酶从其膜锚上剪切下来，并通过几种色谱法纯化。通过改变沉淀剂的pH值、离子强度和聚合度，优化了结晶条件。提供了一些晶体样品用于收集X射线衍射数据。用三氟乙醇诱导牛α-乳清蛋白形成Meta稳的熔融球状结构。该溶液样品为结晶条件的探索提供了条件。尝试了几种新的结晶度概念，例如使用动态光散射（DLS），这对聚集和大杂质非常敏感。用MacroModel程序对具有柔性环结构的有机化合物进行分子动力学模拟计算，并将其坐标轨迹与X射线结构进行了分类和比较。所开发的可视化程序可用于多种构象的分析和比较。

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.