SIMULATION OF PROTON AND HYDRIDE TRANSFER IN ENZYMES

酶中质子和氢化物转移的模拟

• 批准号: 6519829
• 负责人: SHARON HAMMES-SCHIFFER
• 金额: $ 15.44万
• 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 2003-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/6519829
• 关键词: alcohol dehydrogenase; chemical transfer reaction; computer simulation; enzyme mechanism; glucose oxidase; hydrogen ions; oxidation reduction reaction; quantum chemistry

Novel computer simulation methods will be used to investigate proton and hydride transfer reactions in enzymes. The first application will be liver alcohol dehydrogenase (LADH), which catalyzes the reversible oxidation of alcohols to the corresponding aldehydes or ketones by the cofactor nicotinamide adenine dinucleotide (NAD+). These redox reactions are key steps in metabolism, and the NADH generated from them plays in important role in oxidative phosphorylation. Moreover, the medical complications associated with alcoholism (e.g. ketoacidosis and hypoglycemia) are caused in part by the elevation of the NADH/NAD+ level resulting from the metabolism of excess ethanol by alcohol dehydrogenases. The second application will be glucose oxidase (GO), which catalyzes the oxidation of glucose to gluconolactone by flavin adenine dinucleotide (FAD) and the subsequent reduction of oxgen to hydrogen peroxide. GO is a vital biosensor in diagnostic kits for the self-monitoring of blood glucose by diabetics. It also exhibits antitumor activity and is being tested as a treatment for some types of cancer. Kinetic isotope effect experiments indicate that hydrogen tunneling plays an important role in many proton and hydride transfer reactions, including those catalyzed by LADH and GO. The quantum dynamical behavior such as hydrogen tunneling will be incorporated into the simulations using a recently developed mixed quantum/classical molecular dynamics method, in which the transferring hydrogen atom(s) are treated quantum mechanically while the remaining nuclei are treated classically. The specific method that will be implemented is the molecular dynamics with quantum transitions method, which incorporates transitions among the adiabatic proton quantum states. The rates and kinetic isotope effects will be calculated for comparison to the available experimental data. These simulations will elucidate the fundamental general principles of proton and hydride transfer in enzymes, such as the significance of hydrogen tunneling and the role of the structure and dynamics of the enzyme. In terms of LADH, the significance of hydrogen tunneling, the detailed mechanism of the hydride transfer reaction (i.e. direct H- or sequential 1e-, H+, 1e-transfer), and the mechanism of the postulated proton relay system will be investigated. In terms of GO, the detailed mechanism (i.e. hydride transfer from glucose to FAD or proton abstraction from a glucosidic intermediate), the role of hydrogen tunneling, and the relation between protein dynamics and hydrogen tunneling will be investigated. The elucidation of the detailed mechanisms of LADH and GO will enhance the understanding of and guide the optimization of their biochemical and biomedical properties.

新的计算机模拟方法将用于研究质子和 酶中的氢化物转移反应。 第一个应用程序将是 肝醇脱氢酶（LADH），催化可逆的 醇氧化成相应的醛或酮 辅因子烟酰胺腺嘌呤二核苷酸 (NAD+)。 这些氧化还原 反应是新陈代谢的关键步骤，其中产生 NADH 在氧化磷酸化中起重要作用。 此外， 与酒精中毒相关的医疗并发症（例如酮症酸中毒和 低血糖）部分是由 NADH/NAD+ 水平升高引起的 由酒精代谢过量的乙醇而产生 脱氢酶。 第二个应用是葡萄糖氧化酶（GO）， 黄素催化葡萄糖氧化为葡萄糖酸内酯 腺嘌呤二核苷酸（FAD）和随后的氧气还原 过氧化氢。 GO 是诊断试剂盒中重要的生物传感器 糖尿病患者自我监测血糖。 还展出了 抗肿瘤活性，并正在作为某些类型的治疗方法进行测试 癌症。 动力学同位素效应实验表明氢隧道效应 在许多质子和氢化物转移反应中起着重要作用， 包括由 LADH 和 GO 催化的那些。量子动力学行为 例如氢隧道效应将被纳入模拟中 使用最近开发的混合量子/经典分子动力学 方法，其中转移氢原子被量子处理 机械处理，而剩余的核则进行经典处理。 这 将实施的具体方法是分子动力学 量子跃迁方法，其中结合了之间的跃迁 绝热质子量子态。 速率和动力学同位素效应 将进行计算以与可用的实验数据进行比较。 这些模拟将阐明基本的一般原理 酶中质子和氢化物转移的意义，例如 氢隧道效应以及结构和动力学的作用 酶。 就LADH而言，氢隧道效应的意义， 氢化物转移反应的详细机制（即直接H-或 顺序 1e-、H+、1e-转移），以及假设的机制 将研究质子中继系统。 就GO而言，详细 机制（即氢化物从葡萄糖转移到 FAD 或质子 从糖苷中间体中提取），氢的作用 隧道效应，以及蛋白质动力学与氢之间的关系 隧道建设将受到调查。 详细的说明 LADH和GO机制将增强理解和指导 其生化和生物医学特性的优化。