Search Results - "Stuchebrukhov, A. A"

Dowser++, a new method of hydrating protein structures by Morozenko, A., Stuchebrukhov, A. A.

“…ABSTRACT A new method of hydrating protein structures, which we call Dowser++, is presented. The method is based on a semi‐empirical modification of a popular…”
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Theory of Coupled Electron and Proton Transfer Reactions by Hammes-Schiffer, Sharon, Stuchebrukhov, Alexei A

“…Hammes-Schiffer and Stuchebrukhov examine the theory of coupled electron and proton transfer reactions. In addition, they assess electron transfer reaction…”
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Mutation at the entrance of the quinone cavity severely disrupts quinone binding in respiratory complex I by Yi, Jason Tae, Wang, Panyue, Stuchebrukhov, Alexei A.

“…In all resolved structures of complex I, there exists a tunnel-like Q-chamber for ubiquinone binding and reduction. The entrance to the Q-chamber in ND1…”
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Electronic Continuum Model for Molecular Dynamics Simulations of Biological Molecules by Leontyev, I. V, Stuchebrukhov, A. A

“…Electronic polarizability is an important factor in molecular interactions. In the conventional force fields such as AMBER or CHARMM, however, there is…”
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Electron tunneling in respiratory complex I by Hayashi, Tomoyuki, Stuchebrukhov, Alexei A., Gray, Harry B.

“…NADH:ubiquinone oxidoreductase (complex I) plays a central role in the respiratory electron transport chain by coupling the transfer of electrons from NADH to…”
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Electronic Polarizability and the Effective Pair Potentials of Water by Leontyev, I. V, Stuchebrukhov, A. A

“…Employing the continuum dielectric model for electronic polarizability, we have developed a new consistent procedure for parametrization of the effective…”
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Similarity of cytochrome c oxidases in different organisms by Popovic, D. M., Leontyev, I. V., Beech, D. G., Stuchebrukhov, A. A.

“…Most of biological oxygen reduction is catalyzed by the heme‐copper oxygen reductases. These enzymes are redox‐driven proton pumps that take part in generating…”
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Mutations in NDUFS1 Cause Metabolic Reprogramming and Disruption of the Electron Transfer by Ni, Yang, Hagras, Muhammad A, Konstantopoulou, Vassiliki, Mayr, Johannes A, Stuchebrukhov, Alexei A, Meierhofer, David

“…Complex I (CI) is the first enzyme of the mitochondrial respiratory chain and couples the electron transfer with proton pumping. Mutations in genes encoding CI…”
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Proton diffusion along biological membranes by Medvedev, E S, Stuchebrukhov, A A

“…Biological surfaces are known to be capable of retaining protons and facilitating their lateral diffusion. Since the surface dynamically exchanges protons with…”
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Coupled electron and proton transfer reactions during the O→E transition in bovine cytochrome c oxidase by Popović, Dragan M., Stuchebrukhov, Alexei A.

“…A combined DFT/electrostatic approach is employed to study the coupling of proton and electron transfer reactions in cytochrome c oxidase (CcO) and its proton…”
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Long-distance electron tunneling in proteins by Stuchebrukhov, Alexei A.

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Proton pumping mechanism and catalytic cycle of cytochrome c oxidase: Coulomb pump model with kinetic gating by Popović, Dragan M., Stuchebrukhov, Alexei A.

“…Using electrostatic calculations, we have examined the dependence of the protonation state of cytochrome c oxidase from bovine heart on its redox state. Based…”
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Dipole Moment and Binding Energy of Water in Proteins from Crystallographic Analysis by Morozenko, A, Leontyev, I. V, Stuchebrukhov, A. A

“…The energetics of water molecules in proteins is studied using the water placement software Dowser. We compared the water position predictions for 14…”
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Electrostatic Study of the Proton Pumping Mechanism in Bovine Heart Cytochrome c Oxidase by Popović, Dragan M., Stuchebrukhov, Alexei A.

“…Cytochrome c oxidase (CcO) is the terminal enzyme of the cell respiratory chain in mitochondria and aerobic bacteria. It catalyzes the reduction of oxygen to…”
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Mechanisms of generation of local ΔpH in mitochondria and bacteria by Medvedev, E. S., Stuchebrukhov, A. A.

“…The concepts of global and local coupling between proton generators, the enzymes of the respiratory chain, and the consumer, the ATP synthase, coexist in the…”
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Proton Exit Channels in Bovine Cytochrome c Oxidase by Popović, Dragan M, Stuchebrukhov, Alexei A

“…Cytochrome c oxidase (CcO) is the terminal transmembrane enzyme of the respiratory electron transport chain in aerobic cells. It catalyzes the reduction of…”
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Combined DFT and electrostatics study of the proton pumping mechanism in cytochrome c oxidase by Quenneville, Jason, Popović, Dragan M., Stuchebrukhov, Alexei A.

“…Cytochrome c oxidase is a redox-driven proton pump which converts atmospheric oxygen to water and couples the oxygen reduction reaction to the creation of a…”
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Single protonation of the reduced quinone in respiratory complex I drives four‐proton pumping by Stuchebrukhov, Alexei A., Hayashi, Tomoyuki

“…Complex I is a key proton‐pumping enzyme in bacterial and mitochondrial respiratory electron transport chains. Using quantum chemistry and electrostatic…”
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Thermodynamic Properties of Internal Water Molecules in the Hydrophobic Cavity around the Catalytic Center of Cytochrome c Oxidase by Tashiro, Motomichi, Stuchebrukhov, Alexei A

“…Cytochrome c oxidase is a redox-driven proton pump that creates a membrane proton gradient responsible for driving ATP synthesis in aerobic cells. The crystal…”
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Redox-Driven Proton Pumps of the Respiratory Chain by Stuchebrukhov, Alexei A.

“…In aerobic cells, the proton gradient that drives ATP synthesis is created by three different proton pumps—membrane enzymes of the respiratory electron…”
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