Development and application of QM/MM methods for metalloenzymes

金属酶QM/MM方法的开发与应用

基本信息

批准号：
9980920
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
项目类别：
财政年份：
2013
资助国家：
美国
起止时间：
2013-09-01 至 2022-07-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/9980920
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

项目摘要

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：金属酶扮演着各种重要的生物学角色，因此是主要靶标用于生物医学研究。它们还推动了可以罢工的计算方法的进一步发展准确性和抽样效率的适当平衡。在上次资金中取得的进步鼓励时期，我们继续开发杂交量子机械/分子机械（QM/mm）的方法在关键生物学过程中起着重要作用（例如磷酸化转移和DNA复制。我们将进行动力学同位素效应（KIE）的广泛比较并与实验结合突变效应，以校准我们的方法。特定目的是： 1。进一步开发生物学中过渡金属离子的近似密度函数方法（DFTB3）申请。这涉及：（i）。改善金属配体极化和电荷传递的描述在自然粘结分析的指导下，带电配体的相互作用；（ii）。建立高质量使用高度相关的QM方法（例如密度矩阵）的基准数据集用于金属配体相互作用具有规范变换理论的重新归一化组；（iii）。包括明确的现场D -D相互作用在配体领域理论框架中，轨道而不是种群水平。 2。增强机械理解 - 金属离子在磷酸转移酶中的作用。通过QM/mm自由能的组合和Kie计算，我们将：（i）。解释为什么磷酸化酶-1中的磷酸转移过渡态，而是不在酒精磷酸酶中，基本相对于溶液进行了基本修饰，而是它们通常相似的双金属金属活动地点；确定差异是否取决于金属离子的身份（Zn2+ vs. Mn2+），它们之间的距离或活动位点中电荷/偶极子的分布；（ii）。量化催化结合第三个“瞬态” Mg2+对DNA聚合酶的贡献是在最近的时间分辨晶体学中确定的研究，并确定该离子对3'OH激活机制的影响。 3。集成DFTB3/mm 和DFT/MM方法，以提供与各种相关的合作社的机械理解通过活性基序的联合突变在葡萄酒磷酸酶中鉴定的“催化模块” 地点。这些突变体的广泛催化活性跨越了KCAT/KM的十个数量级，提供了前所未有的机会来测试和校准QM/mm方法。从长远来看，我们的努力将帮助建立能够帮助金属酶和合理设计的“最佳实践” QM/MM协议了解他们的进化。