The general goal of this project is to advance understanding of the principles and molecular mechanism of proton pumping in Cytochrome c oxidase (CcO) - the terminal enzyme of the respiratory electron transport chain - by using computer simulations. The crystal structure of the enzyme has been solved a decade ago;however, the molecular mechanism of its proton pumping remains unknown. In the proposed work, electron and proton transfer reactions occurring in this enzyme will be investigated;the computational and theoretical methods for electron and proton transfer developed in the previous grant period will be applied and further advanced. Significant part of the work is devoted to analysis of experimental data and collaboration with experimental groups, producing rigorous theories with predictive power that can guide experiment.
Specific aims i nclude: 1. Study of electron tunneling between redox centers in CcO;The mechanism of Pr state formation. 2. Theory of membrane potential generated by cytochrome c oxidase. 3. Calculation of the protonation states of CcO for various redox states along its catalytic cycle. The search for proton pump element and the proton exit sites. 4. Calculation of energy barriers for coupled electron and proton transfer reactions in cytochrome c oxidase;Study of kinetic gating mechanism for chemical and pumped protons. PUBLICE

Public Health Relevance

This work is part of our long-term goal to map the whole electron transport chain in mitochondria, to study 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.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
Project #
Application #
Study Section
Macromolecular Structure and Function D Study Section (MSFD)
Program Officer
Anderson, Vernon
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
University of California Davis
Schools of Arts and Sciences
United States
Zip Code
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
Morozenko, A; Stuchebrukhov, A A (2016) Dowser++, a new method of hydrating protein structures. Proteins 84:1347-57
Stuchebrukhov, Alexei (2016) Tunneling Time and the Breakdown of Born-Oppenheimer Approximation. J Phys Chem B 120:1408-17
Hagras, Muhammad A; Stuchebrukhov, Alexei A (2016) Internal switches modulating electron tunneling currents in respiratory complex III. Biochim Biophys Acta 1857:749-58
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
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
Leontyev, Igor V; Stuchebrukhov, Alexei A (2014) Polarizable molecular interactions in condensed phase and their equivalent nonpolarizable models. J Chem Phys 141:014103
Medvedev, E S; Stuchebrukhov, A A (2014) Mechanisms of generation of local ?pH in mitochondria and bacteria. Biochemistry (Mosc) 79:425-34
Medvedev, Emile S; Stuchebrukhov, Alexei A (2013) Mechanism of long-range proton translocation along biological membranes. FEBS Lett 587:345-9

Showing the most recent 10 out of 36 publications