Biophysical Model of Enzyme Catalysis: Conformational sub-states, solvent coupling and energy networks

酶催化的生物物理模型：构象亚态、溶剂耦合和能量网络

• 批准号: 10735359
• 负责人: Pratul K Agarwal
• 金额: $ 22.21万
• 依托单位: OKLAHOMA STATE UNIVERSITY STILLWATER
• 依托单位国家: 美国
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-08-01 至 2027-05-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10735359
• 关键词: Active Sites; Biliverdin reductase; Biological Response Modifier Therapy; Biophysical Process; Biophysics; Catalysis; Chemicals; Collaborations; Communities; Computing Methodologies; Coupled; Coupling; Cyclophilin A; Data; Deposition; Development; Dihydrofolate Reductase; Disease; Distal; Drug Industry; Elements; Enabling Factors; Energy-Generating Resources; Environment; Enzyme Kinetics; Enzymes; Family; Health; Hereditary Disease; Human; Investigation; Joints; Kinetics; Knowledge; Link; Malignant Neoplasms; Medical; Medicine; Metabolic; Methods; Modeling; Molecular; Molecular Conformation; Molecular Machines; Motion; Mutate; Mutation; Nature; Output; Pancreas; Paper; Pathogenicity; Pathway interactions; Pharmaceutical Preparations; Play; Poison; Positioning Attribute; Process; Proteins; Publications; Reaction; Relaxation; Research; Ribonucleases; Roentgen Rays; Role; Sampling; Solvents; Structure; Surface; System; Techniques; Testing; Thermodynamics; United States National Institutes of Health; Validation; Work; biochemical model; biophysical model; conformational conversion; design; enzyme model; enzyme structure; experimental study; human disease; improved; insight; interest; laboratory experiment; molecular dynamics; mutant; neuron loss; novel strategies; novel therapeutics; protein data bank; protein structure; reaction rate; side effect; simulation; small molecule; software development; success

ABSTRACT Enzymes have important implications for understanding many human diseases as well as for developing new medicines and therapies. Design of small molecule drugs without side-effects targeting enzymes and designer enzymes as biotherapeutics are widely pursued in the pharmaceutical industry. However, these endeavors are hindered, among other aspects, by the lack of fundamental understanding of enzyme function including the factors that enable enzymes to achieve high catalytic efficiencies. For more than a century, an immense wealth of information has been accumulated based on experimental and computational investigations. Collectively, the biochemical model of enzyme catalysis has revealed the vital roles of active-site residues and other secondary structure elements. However, clear understanding of the roles of: (1) the functionally important conformational sub-states (or rare intermediates); (2) the distal regions including the conserved residues and surface loops; and (3) the surrounding solvent, in enzyme catalysis still remain elusive. For close to two decades, Agarwal lab has been working on using joint computational-experimental approaches for obtaining answers to several important questions about enzymes. Investigations of >20 different enzyme systems have enabled us to contribute to building a biophysical model of enzyme catalysis, which is improving our knowledge of these highly efficient molecular machines. We have discovered conserved network of residues linking surface loop regions to the active-site in several medically important enzyme systems, and successfully developed and validated quasi-anharmonic analysis (QAA) method for identification of conformational sub- states. In this proposal, we describe computational investigations of several enzymes including human ribonucleases, dihydrofolate reductase and biliverdin reductase. Using previously developed and new approaches, the following key questions will be answered: (1) What roles do conformational sub-states play in enzyme catalysis? Specifically, functionally important higher energy sub-states and their linkage to kinetics of the rate-limiting step in enzyme cycle will be quantitatively characterized; (2) Energy flow within preferential pathways (or network channels) formed by conserved residues will be characterized as the biophysical mechanism for long-distance coupling; (3) Thermodynamical coupling between the surrounding environment (solvent) and the enzyme structure and catalyzed reaction will be characterized. A combination of molecular dynamics (MD) and new theoretical analysis methods will be used. We have and continue to work with a number of experimental laboratories to validate our models and their outputs. Experimental data from NMR, enzyme kinetics, X-ray and other techniques on wild type and mutant versions of enzyme systems will be used to iteratively refine our models. These investigations will provide new insights into mechanism of long-distance effects and insights into factors that contribute to the catalytic efficiency of enzymes. The developed software will continue to be made available to the community and we will support a wide variety of labs in their investigations of enzymes. Over long-term these efforts will lead to designing of better allosteric modulators and designer enzymes for biotherapies.

摘要 酶对于理解许多人类疾病以及开发新的 药物和疗法。酶靶向无副作用小分子药物的设计及设计者 酶作为生物治疗剂在制药工业中得到广泛应用。然而，这些努力是 阻碍，除其他方面外，由于缺乏对酶功能的基本了解， 使酶能够实现高催化效率的因素。世纪以来，巨大的财富 基于实验和计算研究积累了大量信息。总的来说， 酶催化的生物化学模型揭示了活性位点残基和其他 二级结构元素然而，清楚地认识到的作用：（1）功能重要 构象亚状态（或稀有中间体）;（2）包括保守残基的远端区域， 表面环;和（3）周围的溶剂，在酶催化仍然是难以捉摸的。了近两 几十年来，阿加瓦尔实验室一直致力于使用联合计算-实验方法来获得 关于酶的几个重要问题的答案。研究了超过20种不同的酶系统， 使我们能够为建立酶催化的生物物理模型做出贡献， 这些高效分子机器。我们发现了保守的残基连接网络， 表面环区域的活性位点在几个医学上重要的酶系统，并成功 开发并验证了准非调和分析（QAA）方法，用于识别构象亚基， states.在这个提议中，我们描述了几种酶的计算研究，包括人类 核糖核酸酶、二氢叶酸还原酶和胆绿素还原酶。使用以前开发的和新的 本文的主要工作如下：（1）构象亚态在分子结构中起着什么样的作用 酶催化？具体而言，功能上重要的高能亚态及其与聚合动力学的联系。 对酶循环中限速步骤进行定量表征;（2）优先循环中的能量流动 保守残基形成的途径（或网络通道）将被表征为生物物理途径 远距离耦合机制;（3）周围环境之间的热力学耦合 （溶剂）和酶的结构和催化的反应将被表征。分子的组合 动力学（MD）和新的理论分析方法将被使用。我们已经并将继续与 实验室的数量来验证我们的模型和他们的输出。来自NMR的实验数据， 将使用酶动力学、X射线和其他技术对酶系统的野生型和突变型进行分析 来反复完善我们的模型这些研究将为研究长距离的生物降解机制提供新的视角 影响和洞察因素，有助于酶的催化效率。所开发的软件 将继续向社区提供，我们将支持各种各样的实验室， 酶的研究。从长远来看，这些努力将导致设计出更好的变构调节剂 和生物疗法的设计酶。