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.

理解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的进展，我们仍然没有一个详细的分子图片的因素，控制保真度。在这里，我们建议使用计算机模拟方法来获得更深入的了解，这将补充该领域的实验进展。（1）研究正确（R）和错误（W）引物-模板碱基对在蛋白质（聚合酶）和水溶液中的相对稳定性。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)分子的束缚自由能 将计算R和W的过渡态。这些计算将与相应的整体保真度直接相关。(iv)探讨了聚合物B在不同构象状态下的反应途径和活化能垒。本研究将探讨W和R底物在核苷酸结合位点的调节如何传递到催化位点。(v)不同的TS-类似物（TSA）的结构和能量将被用来完善TS的理论模型。本研究还将寻找最佳的TS-类似物 并最终用于有效的药物。(vi)计算机模拟方法将被用来研究在基板和催化金属离子的关键修改的后果。(vii)将在不同的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不断反馈。我们希望这项合作将有助于我们对DNA聚合酶保真度的性质形成更普遍和一致的观点。