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: 8725702
• 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/8725702
• 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; Geometry; 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目标但具有挑战性的目标，因为金属位点的可靠且在计算上有效的潜在功能并不直接获得。对于具有结构柔性的活性位点和/或动态金属配位球体的金属酶而言，挑战尤其严重，其中一个很好的例子包括具有开放式活性位点的金属酶，以及滥交的催化活性和蛋白质的金属坐标球体，其金属坐标球体会经历重大的REDOX/pH耦合耦合式变化。在这里，我们建议根据最新的密度功能紧密结合方法（DFTB3）方法开发新的QM/MM方法，以实现冶金酶的计算效率和准确性的适当平衡。具体目的是：1。用于封闭系统（MG，Zn，P和S）的参数化DFTB3，以促进采用MG和Zn作为辅助因素的柔性金属酶的反应性研究。优化一种新型的DFTB3-MM相互作用哈密顿量和一个多级QM/mm自由能框架，该框架明智地结合了DFTB3/mm和高级QM/mm电位。这些方法将通过小分子和金属酶系统仔细测定。 2。作为封闭壳金属酶的应用，将AP超家族酶的催化机理与同源和非同名底物相关。检验以下假设：AP超家族成员观察到的显着催化滥交是由于双金属活性位点的显着结构灵活性，该位点能够识别不同底物的不同性质的态度。通过比较相关可观察到的结果（线性自由能关系，动能同位素效应，突变和硫代效应）来测试计算结果。 3。将哈伯德参数的轨道角动量依赖性引入自旋偏置DFTB方法中，以描述开放壳物种。我们将专注于铜的参数化，该方法将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）特性来系统地测试和完善。应用该方法解决有关蓝色铜蛋白中氧化还原性能的pH依赖性的几个未出现的问题，为应用程序的应用奠定了阶段，例如铜的结合与与神经退行性疾病有关的蛋白质的结合。