Computer Simulation Studies of the Origin of DNA Polymerase Fidelity

DNA 聚合酶保真度起源的计算机模拟研究

• 批准号: 8591706
• 负责人: ARIEH WARSHEL
• 金额: $ 22.77万
• 依托单位: UNIVERSITY OF SOUTHERN CALIFORNIA
• 依托单位国家: 美国
• 财政年份: 2013
• 资助国家: 美国
• 起止时间: 2013-09-03 至 2018-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8591706
• 关键词: Active Sites; Address; Attention; Base Excision Repairs; Base Pairing; Benchmarking; Binding; Biochemical; Catalysis; Cereals; Chemicals; Comparative Study; Complement; Complex; Computer Simulation; Coupling; DNA; DNA-Directed DNA Polymerase; Distant; Enzymatic Biochemistry; Enzymes; Excision; Feedback; Free Energy; Future; Goals; Human; Incidence; Instruction; Kinetics; Laboratories; Lyase; Malignant Neoplasms; Mechanics; Methods; Modeling; Modification; Molecular; Mutation; Nature; Nucleotides; Oxygen; Pathway interactions; Pharmaceutical Preparations; Polymerase; Reaction; Sampling; Simulate; Solutions; Structure; Surface; System; Testing; Time; analog; aqueous; computer studies; design; experience; inhibitor/antagonist; innovation; inorganic phosphate; insight; interest; molecular mechanics; mutant; quantum; research study; simulation; theories; tool

Elucidating the factors that control the replication fidelity of DNA polymerases is a goal of great fundamental and practical importance. In order to advance in this direction we will generate realistic atomic-level simulations of the catalysis and replication fidelity of wild-type and mutant DNA polymerases, focusing on DNA polymerase B(pol B), which is a key player In human base excision repair and has been Implicated in the incidence of cancer. The main strength of our laboratories has been our combined expertise in state-of- the art simulations of enzyme catalysis and catalytic landscapes, with a deep understanding of the available experimental information on the structural and mechanistic underpinnings of the fidelity of DNA polymerases. Our theoretical toolbox includes the empirical valence bond (EVB), the paradynamics that provides effective way of obtaining ab initio quantum mechanical /molecular mechanics (QM/MM) free energy profiles using the EVB as a reference potential, as well as coarse grained (CG) renormalizatlon approaches for exploring long time coupling between the conformational and chemical coordinates. We have also develop and refined effective sampling methods that should allow us to increase the accuracy of the calculated free energies. These computational studies will be applied in concert with the biochemical studies of Project 3 of kinetic effects of mutations of pol B and of changes in its substrates. Our simulations will reproduce and/or predict the functional effects of these changes and analyze their origin. At the same time, we will rely on the important structural information from Project 1. The atomic level understanding Of the structure of the transition state for the insertion of a new nucleotide by pol B and the malleability of this structure by modifications of the active site will greatly increase the possibilities of effective design of a potent and selective inhibitor of pol B.

阐明控制 DNA 聚合酶复制保真度的因素是一个具有重要基础和实际意义的目标。为了朝这个方向前进，我们将对野生型和突变型 DNA 聚合酶的催化和复制保真度进行真实的原子级模拟，重点关注 DNA 聚合酶 B(pol B)，它是人类碱基切除修复中的关键角色并与癌症的发生有关。我们实验室的主要优势在于我们综合了最先进的酶催化和催化景观模拟方面的专业知识，并对 DNA 聚合酶保真度的结构和机械基础的现有实验信息有深入的了解。我们的理论工具箱包括经验价键 (EVB)、副动力学，它提供了使用 EVB 作为参考势获得从头算量子力学/分子力学 (QM/MM) 自由能分布的有效方法，以及粗粒度 (CG) ）重整化方法用于探索构象和化学坐标之间的长时间耦合。我们还开发和完善了有效的采样方法，这将使我们能够提高计算自由能的准确性。这些计算研究将与项目 3 的生化研究相结合，研究 pol B 突变及其底物变化的动力学效应。我们的模拟将重现和/或预测这些变化的功能影响并分析其起源。同时，我们将依赖项目 1 中的重要结构信息。 对 pol B 插入新核苷酸的过渡态结构的原子水平理解以及通过活性位点修饰对该结构的可塑性将大大增加有效设计有效的选择性 pol B 抑制剂的可能性。