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

DNA修饰酶的计算机模拟研究：发展与应用 项目摘要 DNA的准确合成、维护、修复和修饰对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 需要准确和高效地执行他们的活动。由外源性或内源性引起的突变 这些因素可以导致影响这些酶的结构和/或功能的变化。有一个很大的 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 Pols)和AID/APOBEC酶。前一个家庭包括16个以上的人类 DNA极体，负责DNA的准确合成和修复。艾滋病/APOBEC酶 包括A3G和A3H在内的几个成员参与了DNA碱基的靶向脱氨基，以及 在免疫反应中起着关键作用。了解Native的详细结构、功能和机制 这些酶的突变版本可以在许多方面提供帮助，从对基本生化问题的洞察 例如分子间相互作用到可帮助开发诊断和/或 治疗性治疗。基于经典分子动力学(MD)和杂化的计算模拟 量子力学(QM)/分子力学(MM)方法已被证明提供了非常重要的 以原子水平详细研究酶的反应机理的工具。我们的长期目标是 开发准确的QM/MM方法以了解所涉及的酶的机制、结构和功能 通过计算模拟的方式进行DNA修饰。为此，本提案的目标是： I)用MD和QM/MM模拟研究野生型和选育的 两个DNAPOL(DNAPOL III和DNAPOLκ)和一个APOBEC酶的突变体，包括癌症变异体 (A3H)。二)继续开发我们的QM/MM软件LICHEM，该软件将QM程序与 先进的各向异性/可极化力场(宝石和变形虫)，以准确描述MM环境； 推广了各向异性/极化的QM/MM--最小自由能路径(QM/MM-MFEP)方法 使QM/MM模拟的有效自由能计算成为可能。详细了解 选定的DNA Pols和APOBEC3H的结构、功能和反应机理将为我们提供见解 癌症突变的影响，以及开发这些酶的抑制剂的可能途径。我们的 合作者，教授。Penny Beuning，David Rueda和Rahul Kohli将进行基于 基于我们的计算结果。拟议项目的成功完成将提供一个准确的 用于计算酶反应和产生结构和机理的计算工具 对两个重要的酶家族的洞察，这两个家族可能被用来提高癌症治疗的疗效。

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.