Simulation of Proton and Hydride Transfer in Enzymes

酶中质子和氢化物转移的模拟

• 批准号: 8247720
• 负责人: SHARON HAMMES-SCHIFFER
• 金额: $ 7.25万
• 依托单位: PENNSYLVANIA STATE UNIVERSITY, THE
• 依托单位国家: 美国
• 财政年份: 1998
• 资助国家: 美国
• 起止时间: 1998-05-01 至 2012-08-16
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8247720
• 关键词: Acids; Active Sites; Address; Binding; Biochemical; Catalysis; Catalytic RNA; Chemicals; Cleaved cell; Collaborations; Computing Methodologies; Coupling; Cytosine; Cytosine Nucleotides; DNA Sequence Rearrangement; Data; Development; Disease; Distal; Electronics; Electrostatics; Enzyme Inhibitor Drugs; Enzyme Inhibitors; Enzymes; Hepatitis B Virus; Hepatitis Delta Virus; Hybrids; Hydrogen; Hydrogen Bonding; Ions; Isomerase; Ketosteroids; Kinetics; Lead; Liver diseases; Measurement; Mechanics; Molecular; Motion; Mutate; Mutation; Naphthols; Pharmaceutical Preparations; Phenols; Proteins; Protons; Public Health; RNA; Reaction; Research; Role; Sampling; Series; Severities; Solutions; Steroid Isomerases; Steroids; Structure; System; Testing; Theoretical Studies; Therapeutic Agents; Time; Time Study; Tyrosine; Virus Replication; Water; absorption; analog; base; chemical reaction; design; inhibitor/antagonist; insight; magnesium ion; molecular dynamics; mutant; phosphodiester; public health relevance; quantum; research study; simulation; theories; viral RNA

DESCRIPTION (provided by applicant): The broad, long-term objectives of this research are to elucidate the fundamental principles and mechanisms of hydrogen transfer in both protein and RNA enzyme catalysis. These objectives will be accomplished with a broad range of theoretical and computational methods, including quantum mechanical/molecular mechanical calculations, classical molecular dynamics simulations, and hybrid quantum/classical molecular dynamics simulations that provide atomic-level information about structural rearrangements and conformational motions during the catalyzed chemical reaction. These calculations will probe the roles of hydrogen bonding, electrostatics, active site reorganization, and conformational sampling in both protein and RNA enzyme catalysis. These theoretical studies will be performed in close collaboration with experimental groups, assisting in the interpretation of experimental data and providing experimentally testable predictions. The first two specific aims center on the enzyme ketosteroid isomerase (KSI), which catalyzes the isomerization of steroids. The first specific aim is to probe the role of hydrogen bonding in KSI, focusing on inductive effects along the hydrogen-bonding network, coupling among the hydrogen bonds, and the role of water molecules in the active site. The second specific aim is to examine the significance of enzyme motion in KSI, focusing on active site reorganization, conformational sampling, and the impact of distal mutations. These two specific aims will provide predictions related to several different types of experimental data, including NMR chemical shifts and electronic absorption spectra of inhibitors, time-dependent Stokes shifts of bound photoacids, and kinetics of mutants. This strong connection between theory and experiment provides an opportunity to dissect fundamental issues pertaining to hydrogen transfer reactions in enzymes. The last two specific aims center on the hepatitis delta virus (HDV) RNA enzyme (ribozyme), which catalyzes the cleavage of an internal phosphodiester bond. These two specific aims are motivated by the recent solution of a catalytically competent pre-cleaved crystal structure of this ribozyme. The third specific aim is to elucidate the proton transfer mechanism in the HDV ribozyme, focusing on the catalytic roles of a cytosine nucleotide and a magnesium ion in the active site. The fourth specific aim is to understand the role of motion in the HDV ribozyme, focusing on the correlated motions and the conformational changes occurring during the catalyzed chemical reaction. The biomedical relevance of this ribozyme is that HDV increases the severity of liver diseases caused by hepatitis B virus, and replication of HDV depends on self-cleavage of the HDV ribozyme. All of these studies are relevant to public health because the elucidation of the underlying fundamental principles of enzyme catalysis will facilitate the design of more efficient enzymes and inhibitors, thereby potentially assisting in the development of more effective drugs for a wide range of diseases. Furthermore, insights into RNA catalysis may assist in the development of ribozymes for use as therapeutic agents to cleave pathogenic RNAs. PUBLIC HEALTH RELEVANCE: These studies are relevant to public health because the elucidation of the underlying fundamental principles of enzyme catalysis will facilitate the design of more efficient enzymes and inhibitors, thereby potentially assisting in the development of more effective drugs for a broad range of diseases. Furthermore, insights into RNA catalysis may assist in the development of RNA enzymes for use as therapeutic agents to cleave pathogenic RNAs.

描述（由申请人提供）：这项研究的广泛长期目标是阐明蛋白质和RNA酶催化中氢转移的基本原理和机制。这些目标将通过广泛的理论和计算方法来实现，包括量子机械/分子机械计算，经典的分子动力学模拟以及混合量子/经典分子动力学模拟，这些模拟提供了有关在催化化学反应过程中有关结构重排和构象运动的原子级信息。这些计算将探测蛋白质和RNA酶催化中氢键，静电位点重组和构象采样的作用。这些理论研究将与实验组密切合作，有助于解释实验数据并提供实验测试的预测。前两个特定目的中心在酮酮异构酶（KSI）上，催化类固醇的异构化。第一个具体目的是探测氢键在KSI中的作用，重点沿氢键网络沿氢键，氢键之间的耦合以及水分子在活性位点中的作用。第二个具体目的是检查酶运动在KSI中的重要性，重点是主动部位重组，构象采样以及远端突变的影响。这两个特定的目标将提供与几种不同类型的实验数据有关的预测，包括抑制剂的NMR化学移位和电子吸收光谱，依赖时间依赖的绑定光酸的Stokes Shift和突变体的动力学。理论与实验之间的这种牢固联系为剖析与酶中氢转移反应有关的基本问题提供了机会。最后两个特定目的中心在肝炎三角病病毒（HDV）RNA酶（核酶）上，该酶催化内部磷酸二酯键的裂解。这两个特定的目标是由最近催化能力的预切晶体结构的溶液进行的。第三个具体目的是阐明HDV核酶中的质子转移机制，重点是活性位点中细胞质核苷酸和镁离子的催化作用。第四个具体目的是了解运动在HDV核酶中的作用，重点是相关运动和催化化学反应过程中发生的构象变化。该核酶的生物医学相关性是HDV增加了由乙型肝炎病毒引起的肝病的严重程度，而HDV的复制取决于HDV核酶的自我切断。所有这些研究都与公共卫生有关，因为阐明了基本的酶催化基本原理将有助于设计更有效的酶和抑制剂，从而有助于开发更有效的药物来为广泛的疾病开发。此外，对RNA催化的洞察力可能有助于开发核酶作为治疗剂裂解致病性RNA。 公共卫生相关性：这些研究与公共卫生有关，因为阐明酶催化的基本基本原理将有助于设计更有效的酶和抑制剂，从而有助于开发更有效的药物来开发广泛的疾病。此外，对RNA催化的见解可能有助于开发RNA酶，以用作裂解致病性RNA的治疗剂。