Computer Simulation Studies of the Origin of DNA

DNA起源的计算机模拟研究

• 批准号: 6990383
• 负责人: ARIEH WARSHEL
• 金额: $ 24.54万
• 依托单位: UNIVERSITY OF SOUTHERN CALIFORNIA
• 依托单位国家: 美国
• 财政年份: 2004
• 资助国家: 美国
• 起止时间: 2004-08-16 至 2008-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/6990383
• 关键词: DNA directed DNA polymerase; DNA replication; X ray crystallography; binding sites; computer simulation; conformation; cooperative study; nucleotides; structural biology

Understanding the origin of the fidelity of DNA polymerases is a problem of enormous practical and fundamental importance. Despite great experimental progress we still do not have a detailed molecular picture of the factors that control the fidelity. Here we propose to use computer simulation approaches to gain a deeper insight that will complement the experimental advances in the field. The following projects are proposed: (i) The relative stabilities of right (R) and wrong (W) primer-template base pairs will be investigated both in the protein (polymerase) and in aqueous solution. These studies will help to determine the contribution of the binding step to the overall fidelity. (ii) X-ray structures of various polymerase/ DNA complexes will be used as a starting point for calculations of the mechanisms and activation energies of the chemical step for incorporating right (R) and wrong (W) nucleotides. (iii) The binding free energy of the transition state for R and W will be calculated. These calculations will be directly related to the corresponding overall fidelity. (iv) The reaction pathway and activation barriers in different conformational states of the pol b will be explored. This study will examine how the accommodation of W and R substrates in the nucleotide binding site are transmitted to the catalytic site. (v) The structures and energies of different TS-analogues (TSAs) will be used to refine the theoretical model of the TS. This study will also search for optimal TS-analogs and eventually for effective drugs. (vi) Computer simulation approaches will be used to study the consequences of key modifications in the substrate and the catalytic metal ions. (vii) The contributions of different protein residues to the overall fidelity will be analyzed in different polymerases. All the proposed studies will involve constant feedback from the experimental counterparts of the project. We hope that this collaboration will help us to develop a more general and coherent view about the nature of DNA polymerase fidelity.

了解 DNA 聚合酶保真度的起源是一个具有巨大实际意义和根本重要性的问题。尽管实验取得了巨大进展，但我们仍然没有控制保真度因素的详细分子图景。在这里，我们建议使用计算机模拟方法来获得更深入的见解，这将补充该领域的实验进展。提出了以下项目： (i) 将研究蛋白质（聚合酶）和水溶液中正确（R）和错误（W）引物-模板碱基对的相对稳定性。这些研究将有助于确定结合步骤对整体保真度的贡献。 (ii) 各种聚合酶/DNA复合物的X射线结构将用作计算掺入正确(R)和错误(W)核苷酸的化学步骤的机制和活化能的起点。 (iii) 的结合自由能 将计算 R 和 W 的过渡态。这些计算将直接关系到相应的整体保真度。 (iv)将探索pol b不同构象状态下的反应途径和激活势垒。本研究将研究核苷酸结合位点中 W 和 R 底物的调节如何传递到催化位点。 (v) 不同 TS 类似物 (TSA) 的结构和能量将用于完善 TS 的理论模型。这项研究还将寻找最佳的 TS 类似物 并最终找到有效的药物。 (vi) 计算机模拟方法将用于研究底物和催化金属离子的关键修饰的后果。 (vii) 将在不同聚合酶中分析不同蛋白质残基对整体保真度的贡献。所有拟议的研究都将涉及该项目实验对应方的持续反馈。我们希望这次合作将帮助我们对 DNA 聚合酶保真度的本质形成更普遍、更连贯的观点。