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: 10475592
• 负责人: Gerardo Andres Cisneros
• 金额: $ 31.2万
• 依托单位: UNIVERSITY OF TEXAS DALLAS
• 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 2024-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10475592
• 关键词: Advanced Development; Affect; Amber; Amination; Binding; Biochemical; Biological Markers; Closure by clamp; Collaborations; Communities; Complex; Computer Simulation; Computer software; Computing Methodologies; DNA; DNA Maintenance; DNA Modification Process; DNA Polymerase III; DNA Repair; DNA Replication Proofreading; DNA biosynthesis; DNA-Directed DNA Polymerase; Deamination; Development; Diagnostic; Diagnostic Procedure; Disease; Distal; Electrostatics; Endogenous Factors; Environment; Enzyme Inhibitor Drugs; Enzymes; Exogenous Factors; Exonuclease; Family; Free Energy; Funding; Future; Generations; Genome; Goals; Homology Modeling; Hybrids; Immune; Immune response; Individual; Investigation; Knowledge; Lead; Maintenance; Malignant Neoplasms; Malignant neoplasm of prostate; Mechanics; Methods; Molecular; Mutation; Point Mutation; Polymerase; Procedures; Proteins; Reaction; Reporting; Role; Route; Structure; Techniques; Therapeutic; Transact; Variant; Work; base; biological systems; cancer therapy; computer studies; computerized tools; enzyme mechanism; experimental group; experimental study; human DNA; improved; insight; intermolecular interaction; member; molecular dynamics; mutant; programs; 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.

DNA修饰酶的计算机模拟研究进展及应用 项目摘要 DNA的精确合成、维护、修复和修饰对生物体的生存至关重要， DNA中的错误可能导致不同疾病的发生。因此，与DNA交易有关的酶 需要准确有效地执行其活动。外源性或内源性突变 这些因素可导致影响这些酶的结构和/或功能的变化。大量存在 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。前一个家庭包括超过16个人类 DNA pols，负责DNA的准确合成和修复。AID/APOBEC酶 包括A3 G和A3 H等几个成员，参与DNA碱基的靶向脱氨作用，并且 是免疫反应中的关键角色了解本机的详细结构、功能和机制 这些酶的突变体可以在许多方面提供帮助，从对基本生物化学问题的见解， 例如分子间相互作用，以获得有助于诊断和/或 治疗性治疗基于经典分子动力学（MD）和混合动力学的计算模拟 量子力学（QM）/分子力学（MM）方法已被证明提供了非常重要的 一种研究酶反应机理的原子级详细信息的工具。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 通过计算机模拟的方法来改变DNA。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择的野生型的结构/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）继续开发我们的QM/MM软件LICHEM，该软件将QM程序与 先进的各向异性/极化力场（GEM和AMOEBA），以准确描述MM环境; 并将QM/MM-最小自由能路径（QM/MM-MFEP）方法推广到各向异性/极化 潜力，使有效的自由能计算QM/MM模拟。详细了解 所选择的DNA pols和APOBEC 3 H的结构、功能和反应机制将为深入了解 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 合作者，教授。Penny Beuning，大卫Rueda和Rahul Kohli将进行基于 我们的计算结果。成功完成拟议项目将提供一个准确的 计算工具，用于计算酶反应，并生成结构和机理 对两个重要的酶家族的见解，可用于提高癌症治疗的疗效。

项目成果

DNArCdb: A database of cancer biomarkers in DNA repair genes that includes variants related to multiple cancer phenotypes.

• DOI: 10.1016/j.dnarep.2018.07.010
• 发表时间: 2018-10
• 期刊: DNA repair
• 影响因子: 3.8
• 作者: Silvestrov P;Maier SJ;Fang M;Cisneros GA
• 通讯作者: Cisneros GA

Molecular basis for the initiation of DNA primer synthesis.

• DOI: 10.1038/s41586-022-04695-0
• 发表时间: 2022-05
• 期刊: Nature
• 影响因子: 64.8

Modeling Molecular Interactions in Water: From Pairwise to Many-Body Potential Energy Functions.

• DOI: 10.1021/acs.chemrev.5b00644
• 发表时间: 2016-07-13
• 期刊: Chemical reviews
• 影响因子: 62.1
• 作者: Cisneros GA;Wikfeldt KT;Ojamäe L;Lu J;Xu Y;Torabifard H;Bartók AP;Csányi G;Molinero V;Paesani F
• 通讯作者: Paesani F

Insights into conformational changes in AlkD bound to DNA with a yatakemycin adduct from computational simulations

通过计算模拟深入了解 AlkD 与 yatakemycin 加合物结合到 DNA 时的构象变化

• DOI: 10.1007/s00214-018-2255-7
• 发表时间: 2018
• 期刊: Theoretical Chemistry Accounts
• 影响因子: 1.7
• 作者: P. Silvestrov;G. A. Cisneros
• 通讯作者: G. A. Cisneros

Electronic Structure Effects Related to the Origin of the Remarkable Near-Infrared Absorption of Blastochloris viridis' Light Harvesting 1-Reaction Center Complex.

• DOI: 10.1021/acs.jctc.2c00497
• 发表时间: 2022-07-12
• 期刊: JOURNAL OF CHEMICAL THEORY AND COMPUTATION
• 影响因子: 5.5
• 作者: Mondragon-Solorzano, Gustavo;Sandoval-Lira, Jacinto;Nochebuena, Jorge;Cisneros, G. Andres;Barroso-Flores, Joaquin
• 通讯作者: Barroso-Flores, Joaquin