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.

将使用新的计算机模拟方法来研究质子和 酶中的氢化物转移反应。第一个申请将是 肝醇脱氢酶(LADH)，催化可逆的 将醇氧化成相应的醛或酮 辅因子烟酰胺腺二核苷酸(NAD+)。这些氧化还原 反应是新陈代谢的关键步骤，由此产生的nadh。 在氧化磷酸化过程中起着重要作用。此外， 与酒精中毒有关的医疗并发症(例如酮症酸中毒和 低血糖)部分是由NADH/NAD+水平升高引起的 因酒精代谢过量的乙醇而产生的 脱氢酶。第二种应用是葡萄糖氧化酶(GO)， 它催化黄素将葡萄糖氧化成葡萄糖内酯 腺嘌呤二核苷酸(FAD)和随后的氧还原为 过氧化氢。GO是诊断试剂盒中至关重要的生物传感器 糖尿病患者的血糖自我监测。它还展示了 具有抗肿瘤活性，目前正被测试为治疗某些类型的 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 利用最近发展起来的量子/经典混合分子动力学 方法，其中转移氢原子(S)被量子处理 而其余的原子核则用经典的方法来处理。这个 将实施的具体方法是分子动力学 量子跃迁方法，它结合了 绝热质子量子态。速率和动力学同位素效应 将与现有的实验数据进行比较。 这些模拟将阐明基本的一般原则 质子和氢化物在酶中的转移，如 氢隧道效应及其结构和动力学的作用 酵素。就LADH而言，氢隧道的意义， 氢化物转移反应的详细机理(即直接氢或 顺序的1e-，H+，1e-转移)，以及假设的 将对质子接力系统进行研究。在围棋方面，详细的 机理(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 将对隧道行为进行调查。对细节的阐释 LADH和GO的机制将提高对LADH和GO的理解和指导 它们的生化和生物医学性质的优化。