Справочник "Биофизики России"

Найдено: 69.

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• Kovalenko I. B., Diakonova A. N., Abaturova A. M., Riznichenko G. Yu., Rubin A. B. Direct computer simulation of ferredoxin and FNR complex formation in solution // Phys. Biol. 7 (2010) 026001 (8pp)
• Riznichenko G. Yu., Kovalenko I. B., Abaturova A. M., Diakonova A. N., Ustinin D. M., Grachev E. A., Rubin A. B. New direct dynamic models of protein interactions coupled to photosynthetic electron transport reactions // Biophys. Rev. 2010
• Riznichenko G. Yu., Belyaeva N. E., Kovalenko I. B., Rubin A. B. Mathematical and Computer Modeling of Primary Photosynthetic Processes // Biophysics, 2009, Vol. 54, No. 1, pp. 10–22
  We review the recent research on kinetic and direct multiparticle modeling of the processes in the photosynthetic membrane conducted at the Chair of Biophysics of the Biological Faculty, Moscow State University. The models take into account the modern experimental data on the heterogeneous structure and the kinetic characteristics of the system. The generalized kinetic model describes the processes in multisubunit complexes (photosystems I and II, the cytochrome complex), the coupled transmembrane ion fluxes and generation of the electrical and electrochemical potentials. Identification of the model parameters allows estimation of the rate constants for reactions that cannot be examined experimentally. Multiparticle models provide a vivid picture of the interaction between the electron transport chain components in the thylakoid lumen and stroma, and explicitly represent Brownian diffusion and electrostatic interactions between electron carriers. Combination of different description methods (differential equations and the Brownian dynamics formalism) makes it possible to model, in the complicated 3D environment of the plant cell, the processes that in the aggregate ensure the high efficacy of energy transduction in photosynthesis.
• Kovalenko I. B., Abaturova A. M., Riznichenko G. Yu., Rubin A. B. A Novel Approach to Computer Simulation of Protein–Protein Complex Formation // Doklady Biochemistry and Biophysics, 2009, Vol. 427, pp. 215–217
• Antal T. K., Volgusheva A. A., Kukarskih G. P., Krendeleva T. E., Rubin A. B. Relationships between H₂ photoproduction and different electron transport pathways in sulfur-deprived Chlamydomonas reinhardtii // International Journal of Hydrogen Energy. 2009. V. 34. P. 9087-9094
• Krasilnikov P. M., Knox P. P., Rubin A. B. Relaxation mechanism of molecular system containing hydrogen bonds and free energy temperature dependence of reaction of charges recombination within Rhodobacter sphaeroides RC // Photochem. Photobiol. Sci. 2009. V. 8. P. 181-195.
• Kovalenko I. B., Abaturova A. M., Gromov P. A., Ustinin D. M., Riznichenko G. Yu., Grachev E. A., Rubin A. B. Computer Simulation of Plastocyanin–Cytochrome f Complex Formation in the Thylakoid Lumen // Biophysics, 2008, Vol. 53, No. 2, pp. 140–146
  Plastocyanin diffusion in the thylakoid lumen and its binding to cytochrome f (a subunit of the membrane b₆f complex) were studied with a direct multiparticle simulation model that could also take account of their electrostatic interaction. Experimental data were used to estimate the model parameters for plastocyanin–cytochrome f complexing in solution. The model was then employed to assess the dependence of the association rate constant on the dimensions of the lumen. Highest rates were obtained at a lumen span of 8–10 nm; narrowing of the lumen below 7 nm resulted in drastic deceleration of complexing. This corresponded to the experimentally observed effect of hyperosmotic stress on the interaction between plastocyanin and cytochrome f in thylakoids.
• Belyaeva N. E., Schmitt F.-J., Steffen R., Paschenko V. Z., Riznichenko G. Yu., Chemeris Yu. K., Renger G., Rubin A. B. PS II model-based simulations of single turnover flash-induced transients of fluorescence yield monitored within the time domain of 100ns–10s on dark-adapted Chlorella pyrenoidosa cells // Photosynth. Res., 2008, 98 105–119.
• Kovalenko I. B., Abaturova A. M., Ustinin D. M., Riznichenko G. Yu., Grachev E. A., Rubin A. B. Miltiparticle Computer Simulation of Photosynthetic Electron Transport in the Thylakoid Membrane // Biophysics, 2007, Vol. 52, No. 5, pp. 481–488
  Further developing the method for direct multiparticle modeling of electron transport in the thylakoid membrane, here we examine the influence of the shape of the reaction volume on the kinetics of the interaction of the mobile carrier with the membrane complex. Applied to cyclic electron transport around photosystem I, with account of the distribution of complexes in the membrane and restricted diffusion of the reactants, the model demonstrates that the biphasic character of the dark reduction of P700⁺ is quite naturally explained by the spatial heterogeneity of the system.
• Krasilnikov P. M., Mamonov P. A., Knox P. P., Paschenko V. Z., Rubin A. B. The influence of hydrogen bonds on electron transfer rate in photosynthetic RCs // BBA/Bioenergetics 2007, vol.1767, num.6, pp.541-549
• Chamorovsky S. K., Chamorovsky C. S., Knox P. P., Chizhov I. V., Zubov B. V. Dynamics of Electron Transfer from High-Potential Cytochrome c to Bacteriochlorophyll Dimer in Photosynthetic Reaction Centers as Probed using Laser-Induced Temperature Jump // Eur. Biophys. J., 2007, V. 36, P. 601-608.
• Kovalenko I. B., Abaturova A. M., Gromov P. A., Ustinin D. M., Grachev E. A., Riznichenko G. Yu., Rubin A. B. Direct simulation of plastocyanin and cytochrome f interactions in solution // Phys. Biol., 2006, vol. 3, pp. 121–129
  Most biological functions, including photosynthetic activity, are mediated by protein interactions. The proteins plastocyanin and cytochrome f are reaction partners in a photosynthetic electron transport chain. We designed a 3D computer simulation model of diffusion and interaction of spinach plastocyanin and turnip cytochrome f in solution. It is the first step in simulating the electron transfer from cytochrome f to photosystem 1 in the lumen of thylakoid. The model is multiparticle and it can describe the interaction of several hundreds of proteins. In our model the interacting proteins are represented as rigid bodies with spatial fixed charges. Translational and rotational motion of proteins is the result of the effect of stochastic Brownian force and electrostatic force. The Poisson–Boltzmann formalism is used to determine the electrostatic potential field generated around the proteins. Using this model we studied the kinetic characteristics of plastocyanin–cytochrome f complex formation for plastocyanin mutants at pH 7 and a variety of ionic strength values.
• Kudryashov Yu. B., Goncharenko E. N. Modern problems of antiradiation chemical defense of organisms / In book: "The Effects of Low Dose Radiation: New Aspects of Radiobiological Research Prompted by The Chernobyl Nuclear Disaster". Edited by E.B.Burlakova and V.I.Naidich. VSPBV, NE/Brill Academic Pubs, 2004, p. 396-419.
• Kudryashov Yu. B. The main principles of radiation biology / In book: "The Effects of Low Dose Radiation: New Aspects of Radiobiological Research Prompted by The Chernobyl Nuclear Disaster". Edited by E.B.Burlakova and V.I.Naidich. VSPBV, NE/Brill Academic Pubs, 2004, p. 362-395.
• Kovalenko I. B., Ustinin D. M., Grachev N. E., Krendeleva T. E., Kukharskikh G. P., Timofeev K. N., Riznichenko G. Yu., Grachev E. A., Rubin A. B. Cyclic Electron Transport around Photosystem I: An Experimental and Theoretical Study // Biophysics, 2003, Vol. 48, No.4, pp. 614-623
  Electron spin resonance spectroscopy was used to monitor photoinduced changes in the redox state of P700, a photoactive pigment of phctosystemL in isolated Pisum sativum chloroplasts. The kinetics of the ESR signal from P700 (ESR signal I) was recorded at different concentrations of exogenous ferredoxin. A kinetic model was developed for ferredoxin-dependent cyclic electron transport around photosystem I. A multiparticle model was built to directly describe electron transfer in multienzyme complexes and restricted diffusion of mobile carriers in individual compartments (stroma, lumen, intramembrane space) of the system. The two models were compared, and a conclusion was made that the spatial organization of the system plays a significant role in shaping the kinetics of redox transitions of P700.
• Krasilnikov P. M., Paschenko V. Z., Gorohov V. V., Knox P. P., Redlin H., Renger G., Rubin A. B. Energetics and mechanisms of high efficiency of charge separations and electron transfer processes in Rb. sphaeroides reaction centers Bioelectrochemistry, 2003, V. 61, No. 1, p. 73-84.
• Graevskaya E. E., Yasutake A., Aramaki R., Rubin A. B. Effect of methylmercury on histamine release from rat mast cells" // Arch. Toxicol (2003) 77: 17-21
• Medvinsky A. B., Tikhonova I. A., Petrovskii S. V., Malchow H., Venturino E. Chaos and order in plankton dynamics. Complex behavior of a simple model // Журн. общ. биологии, 2002, т. 63, №2, с. 149 - 158.
• Strakhovskaya M. G., Shumarina A. O., Fraikin G. Ya., Rubin A. B. Fluorescence photobleaching of endogenous protoporphyrin IX in Saccharomyces cerevisiae cells // Biophysics. 2002. V.47. P.791-796
• Plyusnina T. Yu., Lobanov A. I., Lavrova A. I., Starozhilova T. K., Riznichenko G. Yu., Rubin A. B. New Spatiotemporal Modes in the Reaction-Electrodiffusion System // Biophysics, 2002, Vol. 47, No.2, pp. 277-282.
  A study was made of the properties of a reacuon-elcctrodiffusion system. A two-component model was developed to describe how interacting charged particles diffuse near the membrane in low-ionic-strength media for which the common assumption of electroneutrality is invalid. Analysis of this model - constructed to take into account the presence a self-consistent field - shows that the latter contributes to the emergence of bistability, localized structures with highly heterogeneous spatial distributions of charges, and spatially and temporally aperiodic modes.

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