Computer Simulation Studies of the Origin of DNA Polymerase

DNA聚合酶起源的计算机模拟研究

• 批准号: 7464334
• 负责人: ARIEH WARSHEL
• 金额: $ 16.87万
• 依托单位: UNIVERSITY OF SOUTHERN CALIFORNIA
• 依托单位国家: 美国
• 财政年份: 2008
• 资助国家: 美国
• 起止时间: 2008-08-01 至 2013-07-13
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7464334
• 关键词: Active Sites; Address; Attention; Base Pairing; Binding; Binding Sites; Biochemistry; Chemistry; Chicago; Classification; Collaborations; Complement; Computer Simulation; Coupling; DNA-Directed DNA Polymerase; Depth; Educational process of instructing; Feedback; Free Energy; Hand; Human Resources; Kinetics; Mutation; Nature; Nucleotides; Object Attachment; Oxygen; Pharmaceutical Preparations; Polymerase; Property; Proteins; Range; Reaction; Site; Structure; Universities; analog; base; chemical reaction; insight; pol genes; research study; tool

Understanding the factors that control the fidelity of DNA polymerases is a problem of great fundamental and practical importance. Here we propose to exploit our recent advances and to continue the use of computer simulation approaches to gain a deeper insight that will complement the experimental progress in projects 1 and 3. It is proposed to use reliable theoretical tools for structure/fidelity correlation and to refine this correlation by a constant feedback from kinetic, binding, and structural experiments. The proposed projects include: (i) Establishing the cleavage mechanism of the PaO bond of dNTP substrates in the polymerase active site by a concerted use of different theoretical approaches, ranging from ab initio QM-MM free energy calculations to constraint DFT free energy calculations and to systematic empirical valence bond studies, (ii) Refining our calculations of substrate binding free energies as well as calculations of the effects of pol pi mutations on the these binding energies, (iii) Exploring factors that control the fidelity of polymerases while| paying special attention to the allosteric transfer of information between the base binding site and the! chemical reaction site. The allosteric information transfer will be studied by calculating the coupling between different residues and the transition state (TS) using the correlation matrix formalism. (iv)Exploring the nature of the TS for incorporating right (R) and wrong (W) nucleotides, including the study of the effect of the protein conformational landscape on the nature of the TS. These studies will be helped by structural studies of transition state analogues (TSAs) with correct and incorrect base pairs, (v) Determining the structure and binding energy of different TSAs that will be examined experimentally by our coworkers (Project 3) and explored theoretically. This study will teach us about the relationship between the TSAs and the actual TS and will help in verifying the calculated TS properties. All the above studies will involve constant feedback from the experimental counterparts of the project. This collaboration will help us develop a more general and coherent view about the nature of DNA polymerase fidelity.

了解控制 DNA 聚合酶保真度的因素是一个具有重大基础和意义的问题。 实际重要性。在这里，我们建议利用我们最新的进步并继续使用计算机 模拟方法以获得更深入的了解，这将补充项目 1 中的实验进展 3. 建议使用可靠的理论工具进行结构/保真度相关性并对其进行完善 通过动力学、结合和结构实验的持续反馈进行关联。拟议项目 包括： (i) 建立聚合酶中 dNTP 底物 PaO 键的裂解机制 通过协调使用不同的理论方法（从头开始 QM-MM 自由能）来确定活性位点 约束 DFT 自由能计算和系统经验价键研究的计算，(ii) 改进底物结合自由能的计算以及 pol pi 影响的计算 这些结合能上的突变，(iii) 探索控制聚合酶保真度的因素，同时| 特别注意碱基结合位点和!之间的信息变构传递！ 化学反应场所。将通过计算之间的耦合来研究变构信息传递 使用相关矩阵形式的不同残基和过渡态（TS）。 (iv)探索自然 TS 中掺入正确 (R) 和错误 (W) 核苷酸的研究，包括研究 蛋白质构象景观对 TS 性质的影响。这些研究将得到结构研究的帮助 具有正确和不正确碱基对的过渡态类似物 (TSA)，(v) 确定结构和 我们的同事将通过实验检查不同 TSA 的结合能（项目 3）以及 进行了理论上的探讨。这项研究将告诉我们 TSA 和实际 TS 之间的关系 并将有助于验证计算出的 TS 属性。 所有上述研究都将涉及项目实验对应方的持续反馈。这 合作将帮助我们对 DNA 聚合酶的性质形成更全面、更连贯的看法 保真度。