SIMULATION OF PROTON AND HYDRIDE TRANSFER IN ENZYMES

酶中质子和氢化物转移的模拟

• 批准号: 6340282
• 负责人: SHARON HAMMES-SCHIFFER
• 金额: $ 14.63万
• 依托单位: PENNSYLVANIA STATE UNIVERSITY, THE
• 依托单位国家: 美国
• 财政年份: 2000
• 资助国家: 美国
• 起止时间: 2000-09-01 至 2003-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/6340282
• 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 肝脏乙醇脱氢酶（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 反应是代谢的关键步骤，从它们产生的NADH 在氧化磷酸化中起重要作用。 而且 与酒精中毒相关的医学并发症（如酮症酸中毒和 低血糖）部分是由NADH/NAD+水平升高引起的 由于酒精代谢过量乙醇而产生 - 是的 第二个应用是葡萄糖氧化酶（GO）， 其催化葡萄糖被黄素氧化成葡内酯 腺嘌呤二核苷酸（FAD）和随后的氧气还原， 过氧化氢 GO是诊断试剂盒中的重要生物传感器，用于 糖尿病患者的血糖自我监测。 它还具有 抗肿瘤活性，并正在测试作为治疗某些类型的 癌 动力学同位素效应实验表明， 在许多质子和氢化物转移反应中起重要作用， 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，其中转移的氢原子被量子化 机械地，而其余的核被经典地处理。 的 将实施的具体方法是分子动力学， 量子跃迁方法，其中包括过渡之间的 绝热质子量子态 速率和动力学同位素效应 将计算用于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则， 质子和氢化物转移在酶中的意义，如 氢隧穿和作用的结构和动力学的 酵素 在LADH方面，氢隧穿的意义， 氢化物转移反应的详细机制（即直接H-或 顺序1 e-，H+，1 e-转移），和假设的机制 将研究质子中继系统。 在GO方面，详细 机制（即从葡萄糖到FAD或质子的氢化物转移 从糖苷中间体中提取），氢的作用 隧道效应，以及蛋白质动力学和氢之间的关系 隧道将被调查。 详细说明 LADH和GO的机制将加强对 优化其生物化学和生物医学特性。