SIMULATION OF PROTON AND HYDRIDE TRANSFER IN ENZYMES

酶中质子和氢化物转移的模拟

• 批准号: 2608983
• 负责人: SHARON HAMMES-SCHIFFER
• 金额: $ 14.7万
• 依托单位: UNIVERSITY OF NOTRE DAME
• 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/2608983
• 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.

新型的计算机仿真方法将用于研究质子和 氢化物转移反应在酶中。 第一个申请将是 肝醇脱氢酶（LADH），催化可逆的 将酒精氧化为相应的醛或酮的氧化 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，而nadh产生了 在氧化磷酸化中起着重要作用。 而且， 与酒精中毒相关的医学并发症（例如，酮症酸中毒和 低血糖）部分是由NADH/NAD+水平的升高引起的 由于酒精过量乙醇的代谢而产生 脱氢酶。 第二个应用将是葡萄糖氧化酶（GO）， 催化黄素催化葡萄糖氧化为葡萄糖酮 腺嘌呤二核苷酸（FAD）和随后的牛降低至 过氧化氢。 GO是诊断套件中至关重要的生物传感器 糖尿病患者对血糖的自我监测。 它也展出 抗肿瘤活性，正在对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穿 在许多质子和氢化物转移反应中起重要作用， 包括那些由Ladh和Go催化的。量子动态行为 例如氢隧穿将纳入模拟 使用最近开发的混合量子/经典分子动力学 方法，其中转移氢原子被处理量子 机械的同时对剩余的核进行经典处理。 这 将实现的特定方法是分子动力学 量子过渡方法，该方法结合了过渡 绝热质子量子状态。 速率和动力学同位素效应 将计算与可用的实验数据进行比较。 这些模拟将阐明 酶中的质子和氢化物转移，例如 氢隧穿以及结构和动力学的作用 酶。 就LADH而言，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1e-，h+，1e转移），以及假定的机制 质子继电器系统将进行研究。 在Go中，详细 机理（即氢化物从葡萄糖转移到FAD或质子 从葡萄糖中间体中抽象），氢的作用 隧道以及蛋白质动力学与氢之间的关系 将调查隧道。 详细说明 LADH和GO的机制将增强对的理解和指导 其生化和生物医学特性的优化。