Importance of Buried Charges in Protein

本计画的目标是发展并使用计算方法来分析和比较蛋白质中带电基团的能量;分析三种光合作用蛋白质中的电子和质子转移;以及调查大量蛋白质活性位点中酸性、碱性和氧化还原活性基团的环境，以表征蛋白质设计中的静电因素。 该项目将通过计算添加到葡萄球菌核酸酶中的电荷的pKas来测试CCNY开发的MCCE（多构象连续静电）程序，并将开发评估蛋白质中质子通路的工具。将比较光系统I、光系统II和细菌RC。 它们是使用基本相同辅因子的类似蛋白质。 然而，辅因子电离的自由能在不同的蛋白质中是非常不同的，变化高达18千卡/摩尔。 MCCE计算将确定静电相互作用对观察到的化学的贡献。 短程相互作用的重要性，如氢键和带电残基的长程相互作用将被确定。 对于每个反应，将跟踪周围残基的质子化状态和旋转异构体偏好的变化。 此外，还将与耶鲁大学的巴蒂斯塔和布鲁德维格合作开展工作，研究质子与PSII的氧气释放复合物的Mn簇中发生的电子转移反应的耦合。 将研究数千种蛋白质，以确定不同蛋白质背景下带电基团的相互作用。分析将集中在蛋白质活性位点的配体和底物结合。 将在不同组蛋白质中计算活性位点残基的pKa。 辅因子的pKas和Ems（例如，黄素、铁硫簇）将在不同的蛋白质中被确定。 决定底物或辅因子上常见带电基团亲和力的因素（例如，磷酸盐基团）。 系统收敛进化带来了相同的活性位点氨基酸在非常不同的蛋白质在一起将被检查。 MCCE将确定活性位点残基的pKa，以了解蛋白质如何产生这些值。 MCCE将继续免费提供，一个新的完全重写的版本现在正在分发。 其他实验室也开始使用该程序的早期版本发布计算结果。 此外，还将在网上公布一份可供检索的pKas数据库分析表格。 将开发和维持一个可供公众搜索的网站，其中载有实验和计算的pKas和Ems。 CCNY是一所公立城市大学，拥有极其多样化、多民族的学生群体。 数据库项目已经并将继续由一系列有才华的本科生进行，并有一些高中生参与。

The objective of this project is to develop and use computational methods to analyze and compare the energies of charged groups in proteins; analyze electron and proton transfers in three photosynthetic proteins; and survey the environment of acidic, basic, and redox active groups in a large number protein active sites to characterize electrostatic factors in protein design. This project will test the MCCE (Multi Conformation Continuum Electrostatics) program, developed at CCNY, by calculating pKas for charges added into Staphylococcal nuclease and will develop tools to evaluate proton pathways in proteins. Photosystem I, photosystem II, and bacterial RCs will be compared. These are analogous proteins that use essentially the same cofactors. However, the free energy of cofactor ionization is very different in the different proteins, varying by as much as 18 Kcal/mol. MCCE calculations will determine the contribution of electrostatic interactions to the observed chemistry. The importance of short-range interactions such as hydrogen bonds and long-range interactions with charged residues will be determined. Changes in protonation states and rotamer preferences of surrounding residues will be followed for each reaction. In addition, work will be carried out in collaboration with Batista and Brudvig of Yale to look at the proton coupling to the electron transfer reactions that occur in the Mn cluster of the oxygen-evolving complex of PSII. Several thousand proteins will be studied to determine interactions of charged groups in different protein contexts. Analysis will focus on ligand and substrate binding in protein active sites. The pKas of active site residues will be calculated in a different group of proteins. The pKas and Ems of cofactors (eg. flavins, iron-sulfur clusters) will be determined in diverse proteins. The factors that determine the affinity of common charged groups on substrates or cofactors (eg. phosphate groups) will be determined. Systems where convergent evolution brings the same active site amino acids together in very different proteins will be examined. MCCE will determine the pKas of active site residues to see how the protein generates these values. MCCE will continue to be freely available and a new completely rewritten version is now being distributed. Other labs are beginning to publish results of calculations using the publicly accessible, early version of the program. In addition, a searchable form of the database analysis of pKas will be posted on the web. A public searchable web site with experimental and calculated pKas and Ems will be developed and maintained. CCNY, a public city university, has an extremely diverse, multi-ethnic student body. The database project has been and will continue to be carried out by a succession of talented undergraduates with some involvement of high school students.