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Mathematical Simulation of Electron Transport in the Primary Photosynthetic Processes

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Abstract

Summarized results of investigation of regulation of electron transport and associated processes in the photosynthetic membrane using methods of mathematical and computer modeling carried out at the Department of Biophysics, Faculty of Biology, Lomonosov Moscow State University, are presented in this review. Detailed kinetic models of processes in the thylakoid membrane were developed using the apparatus of differential equations. Fitting of the model curves to the data of spectral measurements allowed us to estimate the values of parameters that were not determined directly in experiments. The probabilistic method of agent-based Monte Carlo modeling provides ample opportunities for studying dynamics of heterogeneous systems based on the rules for the behavior of individual elements of the system. Algorithms for simplified representation of Big Data make it possible to monitor changes in the photosynthetic apparatus in the course of culture growth in a photobioreactor and for the purpose of environmental monitoring. Brownian and molecular models describe movement and interaction of individual electron carrier proteins and make it possible to study electrostatic, hydrophobic, and other interactions leading to regulation of conformational changes in the reaction complexes. Direct multiparticle models explicitly simulate Brownian diffusion of the mobile protein carriers and their electrostatic interactions with multienzyme complexes both in solution and in heterogeneous interior of a biomembrane. The combined use of methods of kinetic and Brownian multiparticle and molecular modeling makes it possible to study the mechanisms of regulation of an integral system of electron transport processes in plants and algae at molecular and subcellular levels.

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Abbreviations

Cyt b 6 f :

cytochrome complexes

Fd:

ferredoxin

FNR:

ferredoxin-NADP+-reductase

MEA:

multiexponential approximation method

Pc:

plastocyanin

PQ:

plastoquinone

PSI and PSII:

multienzyme complexes of photosystems I and II

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Acknowledgments

The authors express their gratitude to the staff and graduate students of the Department of Biophysics, whose long-term joint work made it possible to obtain the results presented in this article.

Funding

The work was financially supported by the State Budget Projects of Moscow State University (nos. 16-116021660040-7, 121032500060-0). The work was partially funded by the Russian Foundation for Basic Research (grant no. 20-04-00465) and by the Russian Science Foundation (grants nos. 20-64-46018 and 22-11-00009).

We are grateful to the Russian Foundation for Basic Research for many years of support for research on photosynthesis.

The research was carried out using the equipment of the shared research facilities of HPC computing resources at Lomonosov Moscow State University.

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Authors and Affiliations

  1. Faculty of Biology, Lomonosov Moscow State University, 119234, Moscow, Russia

    Galina Yu. Riznichenko, Natalya E. Belyaeva, Ilya B. Kovalenko, Sergei N. Goryachev, Aleksei S. Maslakov, Tatiana Yu. Plyusnina, Vladimir A. Fedorov, Sergei S. Khruschev, Olga V. Yakovleva & Andrew B. Rubin

  2. Pskov State University, 180000, Pskov, Russia

    Taras K. Antal

Authors
  1. Galina Yu. Riznichenko
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  2. Natalya E. Belyaeva
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  3. Ilya B. Kovalenko
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  5. Sergei N. Goryachev
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  6. Aleksei S. Maslakov
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  7. Tatiana Yu. Plyusnina
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  8. Vladimir A. Fedorov
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  9. Sergei S. Khruschev
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  10. Olga V. Yakovleva
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Contributions

G. Yu. Riznichenko, A. B. Rubin – conception and work management; N. E. Belyaeva, I. B. Kovalenko, T. K. Antal, S. N. Goryachev, A. S. Maslakov, T. Yu. Plyusnina, V. A. Fedorov, S. S. Khruschev, O. V. Yakovleva – research; G. Yu. Riznichenko – writing the text.

Corresponding author

Correspondence to Galina Yu. Riznichenko.

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The authors declare no conflict of interest in financial or any other sphere. This article does not contain any studies with human participants or animals performed by any of the authors.

Additional information

Detailed materials on kinetic models of primary photosynthetic processes and associated processes can be provided upon request by the co-author of this review, Natalya E. Belyaeva, e-mail: natalmurav@yandex.ru. Detailed description of the stochastic model algorithm is given in the original article by the author of the code Alexey S. Maslakov [72], co-author of this review. Additional details can be provided upon request, e-mail: alexei.maslakov@gmail.com. ProKSim software for Brownian Dynamics simulation of protein–protein interactions can be provided upon request by the author Sergei S. Khruschev, e-mail: styx@biophys.msu.ru. Cyt f–Pc protein–protein complexes obtained by molecular dynamics methods for green plants, green algae, and cyananobacteria can be provided upon request by the co-author of this review, Vladimir A. Fedorov, e-mail: xbgth@yandex.ru.

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Riznichenko, G.Y., Belyaeva, N.E., Kovalenko, I.B. et al. Mathematical Simulation of Electron Transport in the Primary Photosynthetic Processes. Biochemistry Moscow 87, 1065–1083 (2022). https://doi.org/10.1134/S0006297922100017

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