Investigation of DNA Modifying Enzymes by Computational Simulations: Development and Applications

通过计算模拟研究 DNA 修饰酶：开发和应用 项目概要 DNA 的准确合成、维护、修复和修饰对于生物体的生存至关重要，因为 DNA错误可能导致不同疾病的发生。因此，与DNA交易相关的酶 需要准确有效地执行他们的活动。外源或内源引起的突变 因素可能导致影响这些酶的结构和/或功能的变化。有一个大 参与 DNA 合成、修复和修饰的酶家族的数量。其中两个家庭 涉及 DNA 聚合酶 (DNA pol) 和 AID/APOBEC 酶。前家庭成员包括超过16人 DNA聚合体，负责DNA的精确合成和修复。 AID/APOBEC 酶 由几个成员组成，包括 A3G 和 A3H，参与 DNA 碱基的靶向脱氨基，并且 是免疫反应的关键参与者。了解native的详细结构、功能和机制 这些酶的突变版本可以通过对基本生化问题的见解以多种方式提供帮助 例如分子间相互作用的信息，可以帮助诊断和/或 治疗。基于经典分子动力学（MD）和混合的计算模拟 量子力学（QM）/分子力学（MM）方法已被证明提供了非常重要的 以原子级细节研究酶反应机制的工具。我们的长期目标是 开发准确的 QM/MM 方法来了解相关酶的机制、结构和功能 通过计算模拟进行 DNA 修饰。为此，本提案的目标是： i) 使用MD和QM/MM模拟来研究野生型和选定的结构/功能/反应性 两种 DNA Pol（DNA Pol III 和 DNA Pol κ）和一种 APOBEC 酶的突变体，包括癌症变体 （A3H）。 ii) 继续开发 LICHEM，我们的 QM/MM 软件，它将 QM 程序与 先进的各向异性/极化力场（GEM 和 AMOEBA）可准确描述 MM 环境； 并扩展了各向异性/极化的QM/MM-最小自由能路径（QM/MM--MFEP）方法 为 QM/MM 模拟实现高效自由能计算的潜力。详细了解 所选 DNA pol 和 APOBEC3H 的结构、功能和反应机制将提供见解 研究癌症突变体的影响，以及开发这些酶抑制剂的可能途径。我们的 合作者，教授。 Penny Beuning、David Rueda 和 Rahul Kohli 将基于 关于我们的计算结果。拟议项目的成功完成将提供准确的 用于计算酶反应以及生成结构和机理的计算工具 对两个重要酶家族的见解，可用于增强癌症治疗的功效。

Investigation of DNA Modifying Enzymes by Computational Simulations: Development and Applications Project Summary The accurate synthesis, maintenance, repair, and modification of DNA is crucial for organismal survival since errors in DNA can lead to the onset of different diseases. Therefore, enzymes related to DNA transactions need to perform their activities accurately and efficiently. Mutations arising from exogenous or endogenous factors can result in changes that affect the structure and/or function of these enzymes. There are a large number of enzyme families involved in the synthesis, repair and modification of DNA. Two of these families involve DNA polymerases (DNA pols) and AID/APOBEC enzymes. The former family includes over 16 human DNA pols, which are responsible for the accurate synthesis and repair of DNA. The AID/APOBEC enzymes comprise several members, including A3G and A3H, are involved in targeted deamination of DNA bases, and are key players in immune response. Understanding the detailed structure, function and mechanism of native and mutant versions of these enzymes can help in myriad ways, from insights on basic biochemical issues such as inter-molecular interactions to information that can aid in the development of diagnostic and/or therapeutic treatments. Computational simulations based on classical molecular dynamics (MD) and hybrid quantum mechanical (QM)/molecular mechanical (MM) methods have been shown to provide a very important tool to investigate the reaction mechanism of enzymes with atomic level detail. Our long-term goal is to develop accurate QM/MM methods to understand the mechanism, structure and function of enzymes involved in DNA modification by means of computational simulations. To this end, the goals of the present proposal are: i) To use MD and QM/MM simulations to study the structure/function/reactivity of wild type and selected mutants, including cancer variants, of two DNA Pols (DNA Pol III, and DNA Pol κ), and one APOBEC enzyme (A3H). ii) To continue the development of LICHEM, our QM/MM software, which interfaces QM programs with advanced anisotropic/polarizable force fields (GEM and AMOEBA) to accurately describe the MM environment; and to extend the QM/MM--minimum free energy path (QM/MM--MFEP) method for anisotropic/polarizable potentials to enable efficient free energy calculations for QM/MM simulations. The detailed understanding of the structure, function and reaction mechanism of the selected DNA pols and APOBEC3H will provide insights into effects of cancer mutants, as well as possible routes to develop inhibitors for these enzymes. Our collaborators, Profs. Penny Beuning, David Rueda and Rahul Kohli, will perform experimental studies based on our computational results. The successful completion of the proposed project will provide an accurate computational tool for the calculation of enzyme reactions, and the generation of structural and mechanistic insights on two important families of enzymes, that may be used to enhance the efficacy of cancer treatments.