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

• 批准号: 10381336
• 负责人: Gerardo Andres Cisneros
• 金额: $ 0.81万
• 依托单位: UNIVERSITY OF NORTH TEXAS
• 依托单位国家: 美国
• 财政年份: 2014
• 资助国家: 美国
• 起止时间: 2014-05-01 至 2023-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10381336
• 关键词: Advanced Development; Affect; Amber; Amination; Biochemical; Biological Markers; Communities; Complex; Computer Simulation; Computer software; Computing Methodologies; DNA; DNA Maintenance; DNA Modification Process; DNA Polymerase III; DNA Polymerase beta; DNA Repair; DNA Replication Proofreading; DNA Sequence Alteration; DNA biosynthesis; DNA-Directed DNA Polymerase; Deamination; Development; Diagnostic; Diagnostic Procedure; Disease; Endogenous Factors; Environment; Enzyme Inhibitor Drugs; Enzymes; Exogenous Factors; Exonuclease; Family; Free Energy; Future; Generations; Genome; Goals; Hybrids; Immune response; Investigation; Knowledge; Lead; Link; Maintenance; Malignant Neoplasms; Malignant neoplasm of lung; Mechanics; Methods; Molecular; Multiprotein Complexes; Mutation; Oncogenic; Organism; Polymerase; Procedures; Process; Proteins; Reaction; Research; Role; Route; Structural Models; Structure; Techniques; Therapeutic; Transact; Variant; Work; base; biological systems; cancer therapy; computerized tools; enzyme mechanism; epigenetic regulation; experimental study; human DNA; human disease; improved; insight; intermolecular interaction; member; molecular dynamics; mutant; programs; protein protein interaction; quantum; repaired; simulation; simulation software; tool

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.

通过计算模拟对DNA修饰酶的研究：开发和应用 项目摘要 DNA的准确合成，维护，修复和修饰对于有机生存至关重要，因为 DNA中的错误会导致不同疾病的发作。因此，与DNA交易有关的酶 需要准确有效地进行活动。由外源或内源性产生的突变 因素可能导致影响这些酶结构和/或功能的变化。有一个大 参与DNA的合成，修复和修饰的酶家族数量。其中两个家庭 涉及DNA聚合酶（DNA POLS）和AID/APOBEC酶。前家庭包括超过16人 DNA pol，负责DNA的准确合成和修复。 AID/APOBEC酶 包括A3G和A3H在内的几个成员都参与了DNA碱基的靶向脱氨 是免疫反应的关键参与者。了解天然的详细结构，功能和机制 这些酶的突变版可以从对基本生化问题的见解以多种方式帮助 例如与信息的各种分子之间的相互作用，这些信息可以帮助开发诊断和/或 治疗疗法。基于经典分子动力学（MD）和混合动力的计算模拟 量子机械（QM）/分子机械（MM）方法已证明提供了非常重要的 使用原子水平细节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方法来了解涉及酶的机制，结构和功能 在通过计算模拟的DNA修饰中。为此，本提案的目标是： i）使用MD和QM/MM模拟研究野生型和选定的结构/功能/反应性 两个DNA POL（DNA POL III和DNAPOLκ）和一种APOBEC酶的突变体，包括癌症变体 （A3H）。 ii）要继续开发我们的QM/MM软件Lichem，该软件将QM程序与 高级各向异性/极化力场（GEM和变形虫）准确地描述MM环境； 并扩展QM/mm-最小自由能路径（QM/mm-MFEP）方法 为QM/mm模拟实现有效的自由能计算的潜力。对 所选DNA POL和APOBEC3H的结构，功能和反应机理将提供见解 成为癌症突变体的作用，以及为这些酶开发抑制剂的可能途径。我们的 合作者，教授。 Penny Beuning，David Rueda和Rahul Kohli将进行基于实验研究的 关于我们的计算结果。拟议项目的成功完成将提供准确的 计算酶反应的计算工具以及结构和机械的产生 对两个重要酶家族的见解，这些酶可用于提高癌症治疗的效率。