Superspace Refinement of Protein Crystals

蛋白质晶体的超空间精炼

• 批准号: 1518145
• 负责人: Gloria Borgstahl
• 金额: $ 60.09万
• 依托单位: University of Nebraska Medical Center
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2015
• 资助国家: 美国
• 起止时间: 2015-08-15 至 2020-07-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1518145&HistoricalAwards=false
• 关键词: Superspace; Refinement; Protein; Crystals

Macromolecular crystallographers visualize in extraordinary detail the large molecules needed for life, using X-ray diffraction analysis of crystals of these molecules to determine the locations of each atom in three dimensions, thereby describing the entire structure of the macromolecule. However, sometimes the crystals do not form in a way that permits accurate X-ray diffraction and analysis. The analytical tools to deal with this problem, when it happens, have not yet been developed, and the goal of this research project is to provide the methods and computer software needed to study the atomic structure of protein crystals of this nature. This method will computationally add another (4th) dimension to the structural analysis permitting "superstructures" of the molecule to be defined. This highly innovative project will open the field, permitting others to complete difficult but important multidimensional crystallography projects. This research will provide training for graduate and undergraduate students including members of groups underrepresented in science.This project includes activities that will be beneficial to many areas of the biological sciences including macromolecular crystallography, cell biology and DNA repair. The project is focused on the structure determination of incommensurately modulated protein crystals. The unique diffraction patterns from modulated crystals contain "off-lattice" satellite reflections next to the main reflections. The intellectual merits of the proposed activity are multifold. The first incommensurately modulated protein crystal structures will be solved and advances will be made to the methodology of macromolecular crystallography. The main objective of this research is to develop new macromolecular X-ray crystallographic software for the refinement of incommensurately modulated crystals in superspace and to apply them to solve several crystal structures that currently cannot be solved. The methods employed include protein crystal growth, X-ray diffraction data collection and structure determination. Innovative approaches to protein crystallography and software development will be used. Activities will include extensive modification of crystallography software for the determination of macromolecular structures in superspace using modulation functions. Simulated data will be used as a test case. Then the algorithms will be applied to well characterized incommensurately modulated crystals of profilin:actin, UvsY recombination mediator crystals and then to many other unsolved modulated crystals. The resulting continuum of structures within each crystal will be analyzed within the framework of the current biological/biochemical literature.This project is supported jointly by the Division of Molecular and Cellular Biosciences and the Division of Biological Infrastructure in the Directorate for Biological Sciences.

大分子晶体学家利用这些分子晶体的 X 射线衍射分析来确定每个原子在三个维度上的位置，从而以极其详细的方式可视化生命所需的大分子，从而描述大分子的整个结构。然而，有时晶体的形成方式无法进行精确的 X 射线衍射和分析。当这个问题发生时，处理这个问题的分析工具还没有开发出来，这个研究项目的目标是提供研究这种性质的蛋白质晶体的原子结构所需的方法和计算机软件。该方法将通过计算在结构分析中添加另一个（第四）维度，从而允许定义分子的“上层结构”。这个高度创新的项目将打开这个领域，允许其他人完成困难但重要的多维晶体学项目。这项研究将为研究生和本科生提供培训，包括科学界代表性不足的群体成员。该项目包括有益于生物科学许多领域的活动，包括大分子晶体学、细胞生物学和 DNA 修复。该项目的重点是非通约调制蛋白质晶体的结构测定。调制晶体的独特衍射图案包含主反射旁边的“晶格外”卫星反射。拟议活动的智力价值是多方面的。第一个非通约调节的蛋白质晶体结构将得到解决，并且大分子晶体学方法将取得进展。本研究的主要目标是开发新的高分子X射线晶体学软件，用于超空间中不通约调制晶体的细化，并应用它们来解决目前无法解决的几种晶体结构。所采用的方法包括蛋白质晶体生长、X 射线衍射数据收集和结构测定。将使用蛋白质晶体学和软件开发的创新方法。活动将包括对晶体学软件进行广泛修改，以使用调制函数确定超空间中的大分子结构。模拟数据将用作测试用例。然后，这些算法将应用于已充分表征的 profilin：肌动蛋白、UvsY 重组介体晶体的非通约调制晶体，然后应用于许多其他未解决的调制晶体。每个晶体内所产生的结构连续体将在当前生物/生化文献的框架内进行分析。该项目由生物科学局分子和细胞生物科学部和生物基础设施部共同支持。