Development and application of QM/MM methods for metalloenzymes

金属酶QM/MM方法的开发与应用

• 批准号: 8598325
• 负责人: Qiang Cui
• 金额: $ 25.39万
• 依托单位: UNIVERSITY OF WISCONSIN-MADISON
• 依托单位国家: 美国
• 财政年份: 2013
• 资助国家: 美国
• 起止时间: 2013-09-01 至 2017-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8598325
• 关键词: Active Sites; Address; Alkaline Phosphatase; Benchmarking; Binding; Biological Process; Chemistry; Complex; Computational Technique; Computing Methodologies; Copper; Coupled; Cyclic AMP-Dependent Protein Kinases; Data; Dependence; Development; Disease; Drug Formulations; Electron Transport; Elements; Employee Strikes; Enzymes; Equilibrium; Esters; Free Energy; Human; Hybrids; Inorganic Sulfates; Ions; Isotopes; Kinetics; Malignant Neoplasms; Metalloproteins; Metals; Methodology; Methods; Modeling; Mono-S; Mutation; Nature; Neurodegenerative Disorders; Oxidation-Reduction; Performance; Play; Property; Proteins; Reaction; Research; Role; Sampling; Set protein; Site; Site-Directed Mutagenesis; Solvents; Staging; System; Testing; Transition Elements; Unspecified or Sulfate Ion Sulfates; Zinc; base; blind; combat; computer studies; cytochrome c oxidase; density; design; experience; flexibility; improved; inorganic phosphate; insight; interest; member; metalloenzyme; nanosecond; next generation; novel; novel strategies; public health relevance; research study; simulation; small molecule; theories; tool

DESCRIPTION (provided by applicant): Metalloenzymes are important but challenging targets for computational studies because a reliable and computationally efficient potential function for the metal site is not straightforward to obtain. The challenges are particularly severe for metalloenzymes that feature structurally flexible active sites and/or dynamical metal coordination spheres, for which good examples include metalloenzymes with open active sites and thus promiscuous catalytic activities and proteins whose metal coordination sphere undergoes major redox/pH-coupled changes. Here we propose to develop novel QM/MM methods based on the latest formulation of density functional tight binding (DFTB3) approach to strike the proper balance of computational efficiency and accuracy for metalloenzymes. The specific aims are: 1. Parameterize DFTB3 for closed-shell systems (Mg, Zn, P and S) to facilitate the study of reactivity in flexible metalloenzymes that employ Mg and Zn as co-factors. Refine a novel DFTB3-MM interaction Hamiltonian and a multi-level QM/MM free energy framework that judiciously combines DFTB3/MM and high-level QM/MM potentials. The methods will be carefully benchmarked with both small molecule and metalloenzyme systems. 2. As an application to closed-shell metalloenzymes, dissect the catalytic mechanism of AP superfamily enzymes with both cognate and non-cognate substrates. Test the hypothesis that the remarkable catalytic promiscuity observed for the AP superfamily members is due to the significant structural flexibilities of the bi-metallic active site, which is able to recognize trasition states of distinct nature for different substrates. Test the computational results by comparing relevant observables (linear free energy relations, kinetic isotope effects, mutation and thio-effects) to experiments. 3. Introduce orbital angular momentum dependence of the Hubbard parameters into spin-polarized DFTB approach for the description of open-shell species. We will focus on the parameterization for copper and the method will be systematically tested and refined by comparing structural and energetic (e.g., reduction potential and pKa) properties of small molecules and copper proteins. Apply the approach to resolve several outstanding questions regarding the pH dependence of redox properties in blue copper proteins, setting the stage for applications to more complex problems, such as the binding of copper to proteins implicated in neurodegenerative diseases.

描述（由申请人提供）：金属酶是计算研究的重要但具有挑战性的目标，因为金属位点的可靠和计算效率的势函数不是直接获得的。对于具有结构灵活的活性位点和/或动态金属配位球的金属酶来说，挑战尤其严峻，其中很好的例子包括具有开放活性位点的金属酶，因此具有混杂的催化活性，以及金属配位球经历主要氧化还原/ ph偶联变化的蛋白质。在此，我们建议基于密度功能紧密结合（DFTB3）方法的最新配方开发新的QM/MM方法，以达到金属酶计算效率和准确性的适当平衡。具体目标是：1。参数化封闭壳体系（Mg、Zn、P和S）的DFTB3，便于研究以Mg和Zn为辅助因子的柔性金属酶的反应性。完善一个新的DFTB3-MM相互作用哈密顿量和一个明智地结合DFTB3/MM和高水平QM/MM势的多层次QM/MM自由能框架。这些方法将在小分子和金属酶系统中进行仔细的基准测试。2. 作为封闭壳金属酶的应用，分析AP超家族酶对同源和非同源底物的催化机制。验证这一假设，即观察到的AP超家族成员的显著催化乱交是由于双金属活性位点的显著结构灵活性，它能够识别不同底物的不同性质的过渡状态。通过将相关观测值（线性自由能关系、动力学同位素效应、突变和硫效应）与实验进行比较，验证计算结果。3. 将Hubbard参数的轨道角动量依赖引入到自旋极化DFTB方法中，用于描述开壳物质。我们将重点关注铜的参数化，并通过比较小分子和铜蛋白的结构和能量（例如，还原电位和pKa）特性，系统地测试和改进该方法。应用该方法解决了蓝铜蛋白中氧化还原特性的pH依赖性等几个悬而未决的问题，为应用于更复杂的问题奠定了基础，例如与神经退行性疾病有关的铜与蛋白质的结合。