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目标，因为金属位置的可靠和计算高效的势函数并不容易获得。对于具有结构灵活的活性中心和/或动态的金属配位球的金属酶来说，挑战尤其严峻，例如具有开放的活性中心的金属酶，从而具有混杂的催化活性，以及其金属配位球经历重大氧化还原/pH耦合变化的蛋白质。在这里，我们建议发展新的QM/MM方法，基于密度泛函紧密结合(DFTB3)方法的最新公式，以达到金属酶计算效率和精度的适当平衡。其具体目的是：1.对闭壳体系(镁、锌、磷和S)的DFTB3进行参数化，以便于研究以镁和锌为辅助因子的柔性金属酶的反应活性。改进了一个新的DFTB3-MM相互作用哈密顿量和一个合理地结合了DFTB3/MM和高水平QM/MM势的多能级QM/MM自由能框架。这些方法将仔细地与小分子和金属酶系统进行基准比较。2.作为闭壳金属酶的应用，剖析了AP超家族酶在同源底物和非同源底物上的催化机理。验证这一假设，即AP超家族成员观察到的显著催化混杂是由于双金属活性中心具有显著的结构灵活性，能够识别不同底物不同性质的转位状态。通过将相关的观测数据(线性自由能关系、动力学同位素效应、突变和硫代效应)与实验进行比较来检验计算结果。3.在自旋极化DFTB方法中引入轨道角动量对Hubbard参数的依赖关系来描述开壳物种。我们将专注于铜的参数化，并将通过比较小分子和铜蛋白质的结构和能量(例如，还原电位和pKA)属性来系统地测试和改进该方法。应用该方法解决有关蓝铜蛋白氧化还原特性的pH依赖性的几个悬而未决的问题，为应用于更复杂的问题奠定基础，例如铜与涉及神经退行性疾病的蛋白质的结合。

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.