Electronic Structure and Reactions of Fe-oxo Enzymes

描述（申请人提供）：与生物学相关的铁-氧二聚体配合物的电子结构的理论计算现在对生物无机化学做出了重要贡献。采用高精度密度泛函理论（DFT）方法描述过渡金属二聚体配合物活性位点。然后使用基于静电和介电的表征来评估能量相互作用，将活性位点复合物嵌入到较长距离的蛋白质和溶剂环境中。长期目标是详细了解铁氧二聚体酶的关键中间体、酶机制、反应途径和能量学。这些特征将与活性位点的潜在电子和几何结构有关，作为氧化态、配体环境和蛋白质环境的函数。研究的铁氧化酶是甲烷单加氧酶（MMO）和核糖核苷酸还原酶（RNR），它们分别将烷烃羟基化和将核糖核苷酸还原为脱氧核糖核苷酸（dNDP）。该项目的主要目标包括：(1)利用DFT方法计算MMO和RNR中关键中间体的一些可行结构的最佳活性位点几何形状和相关能量，然后将其与光谱或x射线结构的实验结构结果进行比较；(2)评价不同酶和突变体的反应途径和比较能量学；(3)通过比较DFT电子结构计算的光谱性质与光学、MCD、穆斯堡尔和ENDOR光谱以及磁化率测量的相应实验结果，建立与实验数据的重要联系。这些比较对于那些无法获得X射线结构的催化循环的关键中间体，特别是MMO的中间Q和RNR的中间X是非常重要的；(4)将现有的量子力学/静电学方法扩展和改进为量子团簇、蛋白质和溶剂的多介电区全量子力学/分子力学（QM/MM）。

DESCRIPTION (provided by applicant): Theoretical calculations of the electronic structure of iron-oxo dimer complexes relevant to biology are now making important contributions to bioinorganic chemistry. High-accuracy density functional theory (DFT) methods are used to describe the transition metal dimer complex active site. The active site complex is then embedded in the longer range protein and solvent environment using an electrostatics and dielectric based representation for the evaluation of energetic interactions. The long-term goal is to develop a detailed understanding of critical intermediates, enzymatic mechanisms, reaction pathways, and energetics in iron-oxo dimer enzymes. These features will be related to the underlying electronic and geometric structure of the active site as a function of oxidation state, ligand environment and the protein surroundings. The iron-oxo enzymes to be studied are methane monooxygenase (MMO) and ribonucleotide reductase (RNR), which hydroxylate alkanes and reduce ribonucleotides (NDP) to deoxyribonucleotides (dNDP), respectively. The major goals of the project include: (1) Using DFT methods to calculate optimal active site geometries with associated energies for a number of feasible structures of key intermediates in MMO and RNR, which will then be compared with experimental structural results from spectroscopies or X-ray structures; (2) To evaluate reaction pathways and comparative energetics of different enzymes and mutants; (3) To make important connections with experimental data by comparing calculated spectroscopic properties from DFT electronic structures with corresponding experimental results from optical, MCD, Mossbauer and ENDOR spectroscopies, and from magnetic susceptibility measurements. These comparisons are very important for those critical intermediates of the catalytic cycles where X-ray structures are not available, particularly intermediate Q of MMO and intermediate X of RNR; (4) To extend and improve the current quantum mechanics/electrostatics methodology to full quantum mechanics/molecular mechanics (QM/MM) with multiple dielectric regions for the quantum cluster, protein and solvent.