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much larger proteins containing as many as 80 methionine residues can also be solved provided that these residues have been replaced by selenomethionine.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 射线衍射或晶体学具有揭示各种生物医学重要分子的原子或近原子结构的独特能力，是现代结构生物学的基石。作为最近基因组研究的最新成果，现在需要对数百种新蛋白质进行有效的 X 射线晶体学分析。该项目解决了晶体学的关键步骤之一，即所谓“相问题”的解决方案。该项目之前的工作开发了一种强大的直接方法算法（称为“Shake-and-Bake”）和计算机程序 SnB，可以解决具有多达 1300 个独特非氢的结构的相位问题原子。含有多达 80 个蛋氨酸残基的较大蛋白质的硒亚结构也可以被解析，前提是这些残基已被硒代蛋氨酸取代。然后可以将该子结构用作引导程序来定位蛋白质分子的其余部分。现在的总体目标是扩展 Shake-and-Bake 算法的功能和范围。 SnB 解决非常大的硒代蛋氨酸子结构（> 100 个 Se 位点）的能力将通过添加掩蔽功能来增强，以允许使用有关分子包膜的先验信息或非晶体对称性提供的限制。将设计利用参考光束衍射信息来促进成功的低分辨率应用的策略。我们将开发实用的直接法算法，以充分利用一导数 (SIR) 或反常散射波长 (SAS) 的衍射数据。 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集成，并为自动生成可解释的蛋白质电子密度图创建途径。最后，SnB 网站 http://www.hwi.buffalo.edu/SnB/ 将继续维护，用于程序传播和用户教育。