Alexei Stuchebrukhov

Alexei Stuchebrukhov

Position Title

4471 Chemistry Annex

We are interested in two fundamental processes in chemistry and biology: electron transfer and proton transfer. In our research we develop theory and perform large-scale computer simulations of these processes in complex biological molecular systems.
Understanding of fundamental principles of electron and proton transport in proteins is crucial for characterization of many biological processes, such as photosynthesis and respiration. Results of such studies also find applications in the research on artificial photosynthetic systems and in the new field of molecular electronics (molecular wires, storage devices, picosecond switches, non- linear optics devices, etc.). The goal of our research is to develop a molecular understanding of biological electron and proton transport mechanisms at the most fundamental quantum mechanical level.

Most recently our research has been focused on the development of ab initio theory of electron tunneling in proteins and on the function of cytochrome c oxidase - the terminal redox mitochondrial enzyme that turns oxygen into water in our cells. The enzyme is a wonderful molecular machine that converts different forms of biological and chemical energy, and in which redox chemistry and electron transport are coupled to proton pumping across mitochondrial inner membrane. Another project is the function of DNA repair enzyme photolyase, which also uses redox chemistry in its biological function.
In our research we use methods of modern theoretical chemistry, quantum chemistry, and molecular dynamics for computer simulations of biomolecules.

Education, Awards and Professional Highlights

  • University Honors Program Outstanding Mentor, UC Davis (2017)
  • Arnold and Mabel Beckman Foundation Young Investigator (1997)
  • Alfred P. Sloan Foundation Fellow (1996)
  • Appointed to faculty, UC Davis (1994)
  • Invited Lecturer, Princeton University (1991)
  • Research Associate, California Institute of Technology (1990-1994)
  • Ph.D. Theoretical Physics and Chemistry, Moscow Physical and Technical Institute, P.N. Lebedev Physical Institute, Acad. Sci. USSR (1985)

Representative Publications

  • A. A. Stuchebrukhov, Long-distance electron tunneling in proteins: a new challenge for time-resolved spectroscopy, Laser Physics 19, 1-14 (2009)
  • A. A. Stuchebrukhov, Electron transfer reactions coupled to proton translocation in proteins. Computational studies or redox driven proton pumps, cytochrome c oxidase, and biological energy transduction, in: Energy, Heat and Signal Flows in Proteins, D. Leitner and J. Straub Eds., Taylor and Francis/CRC Press (2009).
  • J. Quenneville, D. Popovic, A. A. Stuchebrukhov, Combined DFT/Continuum Electrostatic studies of proton pumping mechanism in cytochrome c oxidase , in: Computational Inorganic and Bioinorganic Chemistry, Edward I. Solomon, R. Bruce King, Robert A. Scott Eds., Wiley (2009).
  • V. Couch, Emile S. Medvedev, A. A. Stuchebrukhov, Electrostatics of the FeS clusters in respiratory complex I, Biochim. Biophys. Acta 1787, 1266-71 (2009)
  • R. Sugitani, A. A. Stuchebrukhov, Molecular dynamics simulation of water in cytochrome c oxidase reveals two water exit pathways and the mechanism of its transport, Biochim. Biophys. Acta 1787 (9), 1140-50 (2009).
  • I. Leontyev, A. A. Stuchebrukhov, Dielectric relaxation of cytochrome c oxidase: Comparison of microscopic and continuum models, J. Chem. Phys. 130, 085103 (2009).
  • R. Sugitani, E. S. Medvedev, and A. A. Stuchebrukhov, Theoretical and computational analysis of the membrane potential generated by cytochrome c oxidase upon single electron injection into the enzyme, Biochim. Biophys. Acta 1777, 1129-1139 (2008).
  • X. Zheng, G. Garcia, and A.A. Stuchebrukhov, Theoretical study of excitation energy transfer in DNA photolyase, J. Phys. Chem. B 112, 8724-8729 (2008).
  • D.V. Makhov, A.A. Stuchebrukhov, An accurate and efficient procedure of fitting electric field potential by point charges for QM/MM calculations. Phys. Stat. Sol. (b), 243, 2030-2037, (2006).
  • J. Quenneville, D.M. Popovic, A.A. Stuchebrukhov Combined DFT and electrostatics study of the proton pumping mechanism in cytochrome c oxidase. Biochem. Biophys. Acta - Bioenerg., 1757, 1035-1046, (2006).
  • D. Popovic, A. A. Stuchebrukhov, Proton pumping mechanism in cytochrome oxidase: Coulomb pump with kinetic gating. FEBS Lett. 566, 126, 2004.
  • D. Popovic, A. A. Stuchebrukhov, Electrostatic study of proton pumping mechanism in cytochrome oxidase. JACS 126, 1858, 2004.