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: 9751312
• 负责人: Qiang Cui
• 金额: $ 33万
• 依托单位: BOSTON UNIVERSITY (CHARLES RIVER CAMPUS)
• 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 2021-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9751312
• 关键词: ATP Hydrolysis; Active Sites; Alkaline Phosphatase; Benchmarking; Biochemical; Biological; Biological Process; Biomedical Research; Biophysics; Charge; Chemicals; Chemistry; Computing Methodologies; Copper; Crystallography; DNA biosynthesis; DNA-Directed DNA Polymerase; Data Set; Dependence; Development; Drug Design; Elements; Enzymes; Equilibrium; Evolution; Free Energy; Funding; Hybrids; Ions; Isotopes; Kinetics; Ligands; Literature; Malignant Neoplasms; Mechanics; Metals; Methodology; Methods; Modeling; Molecular; Molecular Motors; Mutation; Myosin ATPase; Nature; Nobel Prize; Phosphoric Monoester Hydrolases; Play; Population; Property; Proteins; Protocols documentation; Proton Pump; Research; Role; Sampling; Site; Testing; Time; Transition Elements; Work; Yang; Zinc; base; combinatorial; cost; cytochrome c oxidase; density; design; experimental study; field theory; human disease; improved; insight; metallicity; metalloenzyme; mutant; novel; oxidation; quantum; theories

Project Summary: Metalloenzymes play various important biological roles and therefore are major targets for biomedical research. They also drive further development of computational methodologies that can strike the proper balance of accuracy and sampling efficiency. Encouraged by progress made in the last funding period, we continue to develop hybrid quantum mechanical/molecular mechanical (QM/MM) methods to un- derstand the catalytic mechanism of metalloenzymes that play major roles in key biological processes such as phosphoryl transfers and DNA replication. We will conduct extensive comparison of kinetic isotope effect (KIE) and combinatorial mutation effects with experiments to calibrate our methodologies. The specific aims are: 1. Further develop an approximate Density Functional method (DFTB3) for transition metal ions in biological applications. This involves: (i). improving the description of polarization and charge transfer of metal-ligand interactions for charged ligands, guided by the Natural Bonding Orbital analysis; (ii). establishing high quality benchmark dataset for metal-ligand interactions using highly correlated QM methods such as Density Matrix Renormalization Group with Canonical Transform theory; (iii). including explicit on-site d - d interactions at the orbital rather than population level in the framework of ligand-field theory. 2. Enhance mechanistic understand- ing in the roles of metal ions in phosphoryl transfer enzymes. Through a combination of QM/MM free energy and KIE calculations, we will: (i). explain why is the phosphoryl transfer transition state in phosphatase-1, but not in alkaline phosphatase, substantially modified relative to solution, despite their generally similar bimetallic active sites; establish whether the difference is dictated by the identity of the metal ions (Zn2+ vs. Mn2+), the distance between them or the distribution of charges/dipoles in the active site; (ii). quantify the catalytic con- tribution of the third “transient” Mg2+ to DNA polymerase ⌘ identified in recent time-resolved crystallography studies, and establish the impact of this ion on the mechanism of 3'OH activation. 3. Integrate DFTB3/MM and DFT/MM methodologies to provide a mechanistic understanding of co-operativity associated with various “catalytic modules” identified in alkaline phosphatase through combinatorial mutation of key motifs in the active site. The broad range of catalytic activities of these mutants, which span ten orders of magnitude in kcat/Km, provides an unprecedented opportunity to test and calibrate QM/MM methods. In the long run, our efforts will help establish “best-practice” QM/MM protocols that are able to aid rational design of metalloenzymes and understand their evolution.

项目摘要：金属酶发挥着各种重要的生物学作用，因此是主要目标 它们还推动了可打击的计算方法的进一步发展。 上次资助取得的进展鼓励了准确性和抽样效率的适当平衡。 在此期间，我们继续开发混合量子力学/分子力学（QM/MM）方法来解 了解金属酶的催化机制，这些酶在关键生物过程中发挥重要作用，例如 我们将对动力学同位素效应（KIE）进行广泛的比较。 和组合突变效应与实验来校准我们的方法具体目标是： 1. 进一步开发生物中过渡金属离子的近似密度泛函方法（DFTB3） 这涉及：（i）改进金属配体的极化和电荷转移的描述。 （二）建立高品质。 使用密度矩阵等高度相关的 QM 方法的金属-配体相互作用的基准数据集 具有规范变换理论的重整化群；(iii) 包括显式的现场 d - d 交互作用。 配体场理论框架中的轨道而不是布居水平 2. 增强机制理解。 通过 QM/MM 自由能的组合参与金属离子在磷酰基转移酶中的作用。 和 KIE 计算，我们将： (i) 解释为什么磷酸酶-1 中存在磷酰基转移过渡态，但是。 不在碱性磷酸酶中，相对于溶液进行了大幅修改，尽管它们通常是相似的双金属 建立活性位点；差异是否由金属离子的特性决定（Zn2+ 与 Mn2+）， 它们之间的距离或活性位点中电荷/偶极子的分布；(ii)。 最近时间分辨晶体学鉴定出第三个“瞬态”Mg2+ 对 DNA 聚合酶 ⌘ 的贡献 研究，确定该离子对 3'OH 活化机制的影响 3. 整合 DFTB3/MM。 和 DFT/MM 方法，提供对与各种相关的协作性的机械理解 通过活性中关键基序的组合突变在碱性磷酸酶中鉴定出“催化模块” 这些突变体的催化活性范围广泛，以 kcat/Km 为单位跨越十个数量级， 为测试和校准 QM/MM 方法提供了前所未有的机会。从长远来看，我们的努力将会。 帮助建立“最佳实践”QM/MM 协议，能够帮助合理设计金属酶和 了解它们的演变。