Structure-Energy Correlation in Proteins

蛋白质中的结构-能量相关性

• 批准号: 6486945
• 负责人: Bertrand Garcia-Moreno
• 金额: $ 8.5万
• 依托单位: JOHNS HOPKINS UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2001
• 资助国家: 美国
• 起止时间: 2001-03-01 至 2005-02-28
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/6486945
• 关键词: X ray crystallography; biochemistry; chemical hydration; computer simulation; dielectric property; green fluorescent proteins; ionic bond; nuclear magnetic resonance spectroscopy; nuclease; protein structure function; ribonuclease H; thermodynamics

DESCRIPTION (provided by applicant): Understanding the relationship between the structure, function, and energetics of proteins is one of the central problems in biochemistry today. Electrostatics govern many key biochemical processes, therefore one of the top priorities is to develop a solid understanding of electrostatic effects in proteins. Many computational methods for structure-based calculations of electrostatic energies and pKas have been developed towards this end, but their accuracy, reliability and utility is still limited. They fail most dramatically for groups secluded from bulk solvent in the protein interior or at interfaces between proteins and other molecules. Unfortunately, these are the cases of greatest biological interest. That is where processes that are governed by electrostatics, such as catalysis, redox, H+ and e- conduction, ion selectivity, and recognition and binding of drugs and other molecules, take place. Computational tools for relating structures to energy and function will play an increasingly important role in the post-genomic era. Therefore, experimental data are needed to test and challenge computational methods, as well as to provide the physical insight needed to improve them. Towards this end, Dr. Garcia-Moreno will perform unprecedented studies of the positional dependence of pKas of ionizable groups buried in the interior of 3 proteins: staphylococcal nuclease, RNaseH, and green fluorescent protein. This will entail burial of ionizable groups in the hydrophobic core by mutagenesis, measurement of pKas with equilibrium methods, and determination of structures by crystallography to characterize microenvironments of the buried group. A specific hypothesis that will be evaluated is that buried waters are more prevalent than is currently recognized, and that they hydrate ionizable groups in the interior of proteins very effectively. These experimental studies will answer longstanding questions about the origins, magnitude and meaning of dielectric effects in the protein interior, and Dr. Garcia-Moreno will guide all further refinement and improvement of existing methods for calculation of electrostatic effects in proteins. To the extent that these studies improve our ability to estimate stability and binding affinities from structure, Dr. Garcia-Moreno will have a significant impact on rational and structure-based design of drugs and proteins.

描述（由申请人提供）：了解以下内容之间的关系： 蛋白质的结构、功能和能量学是中心问题之一 今天的生物化学。静电控制许多关键的生化过程， 因此，首要任务之一是深入了解 蛋白质中的静电效应。多种计算方法 基于结构的静电能和 pKa 计算 为此目的而开发，但其准确性、可靠性和实用性是 仍然有限。对于与大众隔离的群体来说，他们的失败最为严重 蛋白质内部或蛋白质与其他物质之间界面的溶剂 分子。不幸的是，这些都是最具生物学意义的案例。 这就是由静电控制的过程，例如催化， 氧化还原、H+ 和电子传导、离子选择性以及识别和结合 药物和其他分子，发生。用于关联的计算工具 能源和功能结构将发挥越来越重要的作用 后基因组时代。因此需要实验数据来检验和 挑战计算方法，并提供物理洞察力 需要改进它们。为此，Garcia-Moreno 博士将表演 对可电离基团 pKa 位置依赖性的前所未有的研究 埋藏在 3 种蛋白质的内部：葡萄球菌核酸酶、RNaseH 和 绿色荧光蛋白。这将需要将可电离基团埋藏在 通过诱变形成疏水核心，通过平衡方法测量 pKa， 并通过晶体学测定结构来表征 埋藏群的微环境。一个具体的假设将是 据评估，埋藏水域比目前更为普遍 公认的，并且它们水合蛋白质内部的可电离基团 非常有效。这些实验研究将回答长期存在的问题 关于蛋白质介电效应的起源、大小和意义 内饰，加西亚-莫雷诺博士将指导所有进一步的改进和 改进现有静电效应计算方法 蛋白质。在某种程度上，这些研究提高了我们的估计能力 结构的稳定性和结合亲和力，加西亚-莫雷诺博士将有一个 对药物的合理和基于结构的设计产生重大影响 蛋白质。