Importance of Buried Charges in Protein

蛋白质中隐藏电荷的重要性

• 批准号: 0212696
• 负责人: Marilyn Gunner
• 金额: $ 42万
• 依托单位: CUNY City College
• 依托单位国家: 美国
• 项目类别: Continuing grant
• 财政年份: 2002
• 资助国家: 美国
• 起止时间: 2002-07-01 至 2006-06-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0212696&HistoricalAwards=false
• 关键词: Importance; Buried; Charges; Protein

A central problem in structural biology is to connect the structure of a protein to its function. To accomplish this, photosynthetic reaction centers of photosystem I and bacterial type II, the intramembrane F0 ATPase, and dihydrofolate reductase (DHFR) will be studied. These are electron, proton, or hydride transfer proteins where residues, cofactors and/or substrates change charge or position during reaction. The primary tool for analysis will be MCCE (Multi Conformation Continuum Electrostatics). This program, written with prior NSF support, combines continuum electrostatics and molecular mechanics for calculation of reaction free energy changes, residue pKa's and electrochemical midpoints (Em's). MCCE will provide the ionization state of residues and changes in protein conformation or ionization state that modify the reaction. This information will establish the structural determinates of function for each protein. The photosynthetic and ATPase proteins will be embedded in different membrane models to see how membrane structure and charge affect the proteins. The role of loop motions on catalysis will be studied in DHFR. Where possible, calculated pKa's and Em's for side chains and cofactors will be compared with experiment. Molecular dynamics will be used to generate modified structures and QM/MM simulations will be used to obtain new cofactor and substrate charge distributions. In addition, the protein structural data bank will be surveyed to identify motifs that stabilize buried charges. A data set of 5000 buried charges in 300 proteins will be used to characterize the distribution of buried ionizable residues. Ionization states at physiological pH will be calculated and the aspects of the protein structure that control ionization will be identified. Motifs identified in the detailed structure/function analysis of specific proteins will be placed in context by comparison with data-bank statistics. Lastly, MCCE will be made easier for non-expert users by enhancing error reporting and analysis of the output. The structural database is growing rapidly. The next challenge would be to fully analyze this information to connect structure to function. It will be necessary to calculate functional properties of proteins, with known structures, to identify most important aspects of the structure for a given property. The overall objective of this project is to accomplish this goal. The work will be carried out at City College of New York, a school with a significant population of underrepresented groups. Initial protein data bank analysis was carried out exclusively by undergraduates. The aim is to continue to integrate undergraduate training into these projects. Detailed information about buried acidic and basic residues and their predicted in situ pKa's will be distributed on the internet.

结构生物学的一个核心问题是将蛋白质的结构与其功能联系起来。 为了实现这一点，光合反应中心的光系统I和细菌II型，膜内F0 ATP酶，和二氢叶酸还原酶（DHFR）将进行研究。 这些是电子、质子或氢化物转移蛋白，其中残基、辅因子和/或底物在反应期间改变电荷或位置。 分析的主要工具将是MCCE（多构象连续静电）。该程序在NSF的支持下编写，结合了连续静电学和分子力学，用于计算反应自由能变化、残留物pKa和电化学中点（Em）。MCCE将提供残基的电离状态以及改变反应的蛋白质构象或电离状态的变化。这些信息将建立每种蛋白质功能的结构决定因素。将光合和ATP酶蛋白嵌入不同的膜模型中，以观察膜结构和电荷如何影响蛋白质。 环运动对催化作用的作用将在DHFR中进行研究。 在可能的情况下，将侧链和辅因子的计算pKa和Em与实验进行比较。分子动力学将被用来产生修改后的结构和QM/MM模拟将被用来获得新的辅因子和基板的电荷分布。 此外，还将对蛋白质结构数据库进行调查，以确定稳定掩埋电荷的基序。 将使用300种蛋白质中5000个掩埋电荷的数据集来表征掩埋的可电离残基的分布。 在生理pH值的电离状态将被计算和控制电离的蛋白质结构的方面将被确定。在特定蛋白质的详细结构/功能分析中确定的基序将通过与数据库统计数据进行比较而置于上下文中。最后，通过加强错误报告和输出分析，MCCE将使非专家用户更容易使用。结构化数据库正在迅速发展。 下一个挑战是充分分析这些信息，将结构与功能联系起来。 这将是必要的，以计算蛋白质的功能特性，与已知的结构，以确定最重要的方面的结构为一个给定的属性。本项目的总体目标是实现这一目标。 这项工作将在纽约城市学院进行，这所学校有大量代表性不足的群体。最初的蛋白质数据库分析完全由本科生进行。 目的是继续将本科生培训纳入这些项目。有关掩埋的酸性和碱性残基及其预测的原位pKa的详细信息将在互联网上发布。