Development and application of QM/MM methods for metalloenzymes

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靶标，因为金属位点的可靠且计算有效的势能函数并不容易获得。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，挑战特别严峻，其中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和金属配位球经历主要氧化还原/pH偶联变化的蛋白质。在这里，我们建议开发新的QM/MM方法的基础上，最新制定的密度泛函紧密结合（DFTB 3）的方法，以达到适当的平衡的计算效率和准确性的金属酶。具体目标是：1.参数化DFTB 3的闭壳系统（镁，锌，磷和硫），以促进灵活的金属酶，采用镁和锌作为辅因子的反应性的研究。完善一个新的DFTB 3-MM相互作用哈密顿量和一个多层次的QM/MM自由能框架，明智地结合DFTB 3/MM和高层次的QM/MM潜力。该方法将仔细基准与小分子和金属酶系统。2.作为对闭壳金属酶的应用，剖析了AP超家族酶在同源和非同源底物下的催化机理。检验AP超家族成员观察到的显着催化混杂性是由于双金属活性位点的显着结构灵活性的假设，该双金属活性位点能够识别不同底物的不同性质的过渡态。通过比较相关的观测值（线性自由能关系，动力学同位素效应，突变和硫代效应）与实验来测试计算结果。3.将Hubbard参数对轨道角动量的依赖性引入到自旋极化的DFTB方法中来描述开壳层物种。我们将专注于铜的参数化，并通过比较结构和能量（例如，还原电位和pKa）性质。应用该方法来解决几个悬而未决的问题，关于蓝铜蛋白质中氧化还原特性的pH依赖性，为应用于更复杂的问题奠定了基础，例如铜与神经退行性疾病中涉及的蛋白质的结合。

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.