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Proton Coupled Electron Transfer Mechanism of NADH dehydrogenase, respiratory complex I

NADH 脱氢酶、呼吸复合物 I 的质子耦合电子传递机制

基本信息

批准号：
10237217
负责人：
ALEXEI A STUCHEBRUKHOV
金额：
$ 26.46万
依托单位：
UNIVERSITY OF CALIFORNIA AT DAVIS
依托单位国家：
美国
项目类别：
财政年份：
1996
资助国家：
美国
起止时间：
1996-05-01 至 2024-08-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/10237217
关键词：
Address Aerobic Affect Amino Acids Apoptosis Binding Brain Diseases Cell Aging Cells Coenzymes Collaborations Complex Computer Simulation Computing Methodologies Coupled Coupling Cryoelectron Microscopy Cytochrome c Reductase Data Defect Degenerative Disorder Electron Transport Electron Transport Complex III Electrons Electrostatics Enzymes Free Radicals Freezing Functional disorder Generations Goals Health Heart Diseases Human Institutes Ischemia Kinetics Light Lipids Longevity Maps Mechanics Membrane Mitochondria Mitochondrial Diseases Modeling Molecular Molecular Conformation Mutation NADH NADH dehydrogenase (ubiquinone)Oxidation-Reduction Oxygen Pathway interactions Peripheral Phase Process Production Property Proteomics Proton Pump Protons Pump Reaction Reactive Oxygen Species Respiratory Chain Respiratory System Structure Testing Time Ubiquinone Work base cell injury complex IV enzyme structure in silico in vivo metabolomics mitochondrial dysfunction models and simulation molecular dynamics mutant operation oxidation protonation quantum semiquinone simulation structural biology targeted treatment therapy development

项目摘要

A. A. Stuchebrukhov, Electron Transfer in NADH Dehydrogenase Proton Coupled Electron Transfer in NADH dehydrogenase: Project Summary The goal of this computational project is to investigate fundamental principles and atomistic details of electron tunneling along the chain of eight FeS clusters, its coupling to proton translocation, and ultimately to uncover molecular mechanism of redox-driven proton pumping in NADH dehydrogenase – an enzyme which is the entry point of the electron transport chain in the respiratory system of aerobic cells (respiratory Complex I). The work includes collaboration with leading experimental experts in the field, who recently solved the structure of the enzyme. We will test the hypothesis that the electron tunneling along the chain of eight FeS clusters to the terminal FeS cluster in the peripheral part of the enzyme is coupled to a long-range conformational change that in turn is coupled to proton translocation by the membrane part of the enzyme; electron tunneling along the chain of FeS clusters provides a kinetic gate necessary for operation of the conformation-driven proton pumping machine. Mutations along the FeS chain can disrupt electron flow and render complex I dysfunctional. The approach is based on atomistic and quantum mechanical simulations of electron and proton transport, using state-of-the art quantum tunneling calculations and molecular dynamics simulations, and will involve: A1) A study of various aspects of electron tunneling along the chain of eight FeS clusters of the enzyme, redox properties of enzymes cofactors, and their redox reactions, prediction of the key amino acids participating in the tunneling process; theoretical analysis of freeze-quench kinetic EPR data; A2) A study of conformations, electrostatics, and redox-coupled protonation states of the enzyme, finding proton transfer channels and the key groups involved in proton pumping; A3) Modeling of the pumping mechanism. This work is part of our long-term goal to map the whole electron transport chain in mitochondria, to indentify molecular mechanisms of redox-driven proton pumping, oxygen reduction, and generation of Reactive Oxygen Species (ROS). The importance of such studies is underscored by the growing evidence that the dysfunction of the electron transport chain in mitochondria and free radical production are contributing to cell aging, apoptosis, and to a number of degenerative diseases of the heart and brain in humans.

A. A. Stuchebrukhov，NADH脱氢酶中的电子转移 NADH脱氢酶中的质子耦合电子转移：项目总结这个计算项目的目标是研究基本原理，原子细节的电子隧穿沿着链的八个FeS集群，其耦合到质子移位，并最终揭示氧化还原驱动的分子机制质子泵在NADH脱氢酶-一种酶，这是进入点的需氧细胞呼吸系统中的电子传递链（呼吸复合物I）。这项工作包括与该领域领先的实验专家合作，最近解决了酶的结构。我们将检验电子沿着沿着八个FeS团簇的链隧穿的假设在酶的外周部分的末端FeS簇与长距离的构象变化，进而通过膜与质子移位偶联酶的一部分;电子隧道沿着链的FeS簇提供了一个动力学构象驱动质子泵机运行所需的门。沿着FeS链的突变可以破坏电子流并使复合物I 功能失调该方法是基于电子的原子和量子力学模拟，质子传输，使用最先进的量子隧道计算和分子动力学模拟，并将涉及：A1）电子隧穿的各个方面的研究沿着该酶的八个FeS簇的链，酶辅因子的氧化还原性质，以及它们的氧化还原反应，预测参与隧穿的关键氨基酸 A2）研究过程中的冷冻淬火动力学EPR数据的理论分析; 构象，静电学和氧化还原偶联质子化状态的酶，发现质子转移通道和参与质子泵送的关键基团; A3）泵送机制。这项工作是我们长期目标的一部分，即绘制整个电子传递链，线粒体，以确定氧化还原驱动质子泵的分子机制，氧还原和产生活性氧（ROS）。这样的重要性越来越多的证据表明，电子的功能障碍线粒体中的运输链和自由基产生有助于细胞老化，细胞凋亡，以及人类心脏和大脑的许多退行性疾病。