NEW METHODS OF BIOMOLECULAR STRUCTURE DETERMINATION

生物分子结构测定的新方法

• 批准号: 6578829
• 负责人: CHARLES M WEEKS
• 金额: $ 17.41万
• 依托单位: HAUPTMAN-WOODWARD MEDICAL RESEARCH INST
• 依托单位国家: 美国
• 财政年份: 2002
• 资助国家: 美国
• 起止时间: 2002-04-01 至 2003-03-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/6578829
• 关键词: X ray crystallography; bioimaging /biomedical imaging; biomedical automation; chemical models; chemical structure; computer data analysis; computer graphics /printing; computer program /software; cytochrome c; electron density; image processing; macromolecule; method development; phase change; protein structure; structural biology

X-ray diffraction or crystallography, with its unique ability to reveal the atomic or near-atomic structures of a wide range of biomedically important molecules, is the cornerstone of modern structural biology. As a resent of recent genome studies, there is now a need for efficient X-ray crystallographic analysis of hundreds of new proteins. This project addresses one of the critical steps in crystallography, the solution of the so-called 'phase problem.' Previous work within this project has resulted in the development of a powerful-direct methods algorithm, known as Shake-and-Bake, and a computer program, SnB, that can resolve the phase problem for structures with as many as 1300 unique non-hydrogen atoms. The selenium substructures of much larger proteins containing as many as 80 methionine residues can also be solved provided that these residues have been replaced by selenomethionine. The substructure can then be used as a bootstrap to locate the remainder of the protein molecule. The overall goal now is to extend the power and scope of the Shake-and- Bake algorithm. The ability of SnB to solve very large selenomethionine substructures (>100 Se sites) will be enhanced by the addition of a masking function to permit use of prior information concerning the molecular envelope or restrictions provided by non-crystallographic symmetry. Strategies will be devised for utilizing information from reference-beam diffraction to facilitate successful lower-resolution applications. Practical direct-methods algorithms will be developed for getting the most from diffraction data from one derivative (SIR) or for one wavelength with anomalous scattering (SAS). Concepts and routines from the PHASES program package will be used to integrate direct methods with other information and techniques commonly used in protein crystallography and to create pathway for the automated production of interpretable protein electron-density maps. Finally, the SnB website, http://www.hwi.buffalo.edu/SnB/, will be maintained for program dissemination and user education.

X射线衍射或晶体学，以其独特的能力，揭示原子或近原子结构的广泛的生物医学重要分子，是现代结构生物学的基石。随着近年来基因组研究的不断深入，人们迫切需要对数百种新的蛋白质进行有效的X射线晶体学分析。这个项目解决了晶体学中的一个关键步骤，即所谓的“相位问题”。该项目之前的工作已经开发出一种强大的直接方法算法，称为Shake-and-Bake，以及一种计算机程序SnB，可以解决多达1300个独特非氢原子的结构的相位问题。含有多达80个甲硫氨酸残基的大得多的蛋白质的硒亚结构也可以解决，只要这些残基已被硒代甲硫氨酸取代。然后，子结构可以被用作定位蛋白质分子的其余部分的引导。现在的总体目标是扩展Shake-and- Bake算法的功能和范围。SnB解决非常大的硒代甲硫氨酸亚结构（>100个Se位点）的能力将通过添加掩蔽功能来增强，以允许使用关于由非晶体对称性提供的分子包络或限制的先验信息。将制定战略，利用参考光束衍射的信息，以促进成功的低分辨率应用。将开发实用的直接方法算法，以从一个导数（SIR）或一个波长的异常散射（SAS）的衍射数据中获得最多。PHASES程序包中的概念和例程将用于将直接方法与蛋白质晶体学中常用的其他信息和技术相结合，并为自动化生产可解释的蛋白质电子密度图创建途径。最后，将维持SnB网站http：//www.hwi.buffalo.edu/SnB/，以便传播方案和进行用户教育。