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.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
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Molecular and Cellular Biophysics Study Section (BBCA)
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Flicker, Paula F
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Pennsylvania State University
Schools of Arts and Sciences
University Park
United States
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Li, Pengfei; Soudackov, Alexander V; Hammes-Schiffer, Sharon (2018) Fundamental Insights into Proton-Coupled Electron Transfer in Soybean Lipoxygenase from Quantum Mechanical/Molecular Mechanical Free Energy Simulations. J Am Chem Soc 140:3068-3076
Hammes-Schiffer, Sharon (2017) Catalysts by Design: The Power of Theory. Acc Chem Res 50:561-566
Bingaman, Jamie L; Zhang, Sixue; Stevens, David R et al. (2017) The GlcN6P cofactor plays multiple catalytic roles in the glmS ribozyme. Nat Chem Biol 13:439-445
Horitani, Masaki; Offenbacher, Adam R; Carr, Cody A Marcus et al. (2017) 13C ENDOR Spectroscopy of Lipoxygenase-Substrate Complexes Reveals the Structural Basis for C-H Activation by Tunneling. J Am Chem Soc 139:1984-1997
Hu, Shenshen; Soudackov, Alexander V; Hammes-Schiffer, Sharon et al. (2017) Enhanced Rigidification within a Double Mutant of Soybean Lipoxygenase Provides Experimental Support for Vibronically Nonadiabatic Proton-Coupled Electron Transfer Models. ACS Catal 7:3569-3574
Ucisik, Melek N; Hammes-Schiffer, Sharon (2017) Effects of Active Site Mutations on Specificity of Nucleobase Binding in Human DNA Polymerase ?. J Phys Chem B 121:3667-3675
Zhang, Sixue; Stevens, David R; Goyal, Puja et al. (2016) Assessing the Potential Effects of Active Site Mg2+ Ions in the glmS Ribozyme-Cofactor Complex. J Phys Chem Lett 7:3984-3988
Ucisik, Melek N; Bevilacqua, Philip C; Hammes-Schiffer, Sharon (2016) Molecular Dynamics Study of Twister Ribozyme: Role of Mg(2+) Ions and the Hydrogen-Bonding Network in the Active Site. Biochemistry 55:3834-46
Soudackov, Alexander V; Hammes-Schiffer, Sharon (2016) Proton-coupled electron transfer reactions: analytical rate constants and case study of kinetic isotope effects in lipoxygenase. Faraday Discuss 195:171-189
Yu, Tao; Soudackov, Alexander V; Hammes-Schiffer, Sharon (2016) Computational Insights into Five- versus Six-Coordinate Iron Center in Ferrous Soybean Lipoxygenase. J Phys Chem Lett 7:3429-33

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