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.
In this project, using computer simulations and modeling and in collaboration with structural biology experts in the field, we will advance understanding of the molecular mechanism of NADH dehydrogenase (respiratory complex I) ? the entry point of the electron transport chain in aerobic cells. This work is part of our long-term goal to map the whole electron transport chain in mitochondria, to identify the mechanisms of 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.
| Stuchebrukhov, Alexei A (2018) Redox-Driven Proton Pumps of the Respiratory Chain. Biophys J 115:830-840 |
| Hagras, Muhammad A; Stuchebrukhov, Alexei A (2016) Internal switches modulating electron tunneling currents in respiratory complex III. Biochim Biophys Acta 1857:749-58 |
| Morozenko, A; Stuchebrukhov, A A (2016) Dowser++, a new method of hydrating protein structures. Proteins 84:1347-57 |
| Hagras, Muhammad A; Stuchebrukhov, Alexei A (2016) Novel Inhibitors for a Novel Binding Site in Respiratory Complex III. J Phys Chem B 120:2701-8 |
| Samudio, Benjamin M; Couch, Vernon; Stuchebrukhov, Alexei A (2016) Monte Carlo Simulations of Glu-242 in Cytochrome c Oxidase. J Phys Chem B 120:2095-105 |
| Stuchebrukhov, Alexei (2016) Tunneling Time and the Breakdown of Born-Oppenheimer Approximation. J Phys Chem B 120:1408-17 |
| Hagras, Muhammad A; Hayashi, Tomoyuki; Stuchebrukhov, Alexei A (2015) Quantum Calculations of Electron Tunneling in Respiratory Complex III. J Phys Chem B 119:14637-51 |
| Hagras, Muhammad A; Stuchebrukhov, Alexei A (2015) Transition Flux Formula for the Electronic Coupling Matrix Element. J Phys Chem B 119:7712-21 |
| Morozenko, A; Leontyev, I V; Stuchebrukhov, A A (2014) Dipole Moment and Binding Energy of Water in Proteins from Crystallographic Analysis. J Chem Theory Comput 10:4618-4623 |
| Leontyev, Igor V; Stuchebrukhov, Alexei A (2014) Polarizable molecular interactions in condensed phase and their equivalent nonpolarizable models. J Chem Phys 141:014103 |
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