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Riznichenko GY, Belyaeva NE, Kovalenko IB, Antal TK, Goryachev SN, Maslakov AS, Plyusnina TY, Fedorov VA, Khruschev SS, Yakovleva OV, Rubin AB. Mathematical Simulation of Electron Transport in the Primary Photosynthetic Processes. BIOCHEMISTRY (MOSCOW) 2022; 87:1065-1083. [DOI: 10.1134/s0006297922100017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Riznichenko GY, Belyaeva NE, Diakonova AN, Kovalenko IB, Maslakov AS, Antal TK, Goryachev SN, Plyusnina TY, Fedorov VA, Khruschev SS, Rubin AB. Models of Photosynthetic Electron Transport. Biophysics (Nagoya-shi) 2020. [DOI: 10.1134/s0006350920050152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Fedorov VA, Kovalenko IB, Khruschev SS, Ustinin DM, Antal TK, Riznichenko GY, Rubin AB. Comparative analysis of plastocyanin-cytochrome f complex formation in higher plants, green algae and cyanobacteria. PHYSIOLOGIA PLANTARUM 2019; 166:320-335. [PMID: 30740703 DOI: 10.1111/ppl.12940] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 02/05/2019] [Indexed: 06/09/2023]
Abstract
Mechanisms of the complex formation between plastocyanin and cytochrome f in higher plants (Spinacia oleracea and Brassica rapa), green microalgae Chlamydomonas reinhardtii and two species of cyanobacteria (Phormidium laminosum and Nostoc sp.) were investigated using combined Brownian and molecular dynamics simulations and hierarchical cluster analysis. In higher plants and green algae, electrostatic interactions force plastocyanin molecule close to the heme of cytochrome f. In the subsequent rotation of plastocyanin molecule around the point of electrostatic contact in the vicinity of cytochrome f, copper (Cu) atom approaches cytochrome heme forming a stable configuration where cytochrome f molecule behaves as a rather rigid body without conformational changes. In Nostoc plastocyanin molecule approaches cytochrome f in a different orientation (head-on) where the stabilization of the plastocyanin-cytochrome f complex is accompanied by the conformational changes of the G188E189D190 loop that stabilizes the whole complex. In cyanobacterium P. laminosum, electrostatic preorientation of the approaching molecules was not detected, thus indicating that random motions rather than long-range electrostatic interactions are responsible for the proper mutual orientation. We demonstrated that despite the structural similarity of the investigated electron transport proteins in different photosynthetic organisms, the complexity of molecular mechanisms of the complex formation increases in the following sequence: non-heterocystous cyanobacteria - heterocystous cyanobacteria - green algae - flowering plants.
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Affiliation(s)
- Vladimir A Fedorov
- Biology Faculty, Lomonosov Moscow State University, Moscow, 119992, Russia
| | - Ilya B Kovalenko
- Biology Faculty, Lomonosov Moscow State University, Moscow, 119992, Russia
- Institute of Physics and Mathematics, Astrakhan State University, Astrakhan, 414056, Russia
- Scientific and Technological Center of Unique Instrumentation of the Russian Academy of Sciences, Moscow, 117342, Russia
- Peoples' Friendship University of Russia (RUDN University), Moscow, 117198, Russia
| | - Sergei S Khruschev
- Biology Faculty, Lomonosov Moscow State University, Moscow, 119992, Russia
| | - Dmitry M Ustinin
- Keldysh Institute of Applied Mathematics RAS, Moscow, 125047, Russia
| | - Taras K Antal
- Biology Faculty, Lomonosov Moscow State University, Moscow, 119992, Russia
| | | | - Andrei B Rubin
- Biology Faculty, Lomonosov Moscow State University, Moscow, 119992, Russia
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Riznichenk G, Kovalenko I, Fedorov V, Khruschev S, Rubin A. Photosynthetic Electron Transfer by Dint of Protein Mobile Carriers. Multi-particle Brownian and Molecular Modeling. EPJ WEB OF CONFERENCES 2019. [DOI: 10.1051/epjconf/201922403008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The paper presents the review of works on modeling the interaction of photosynthetic proteins using the multiparticle Brownian dynamics method developed at the Department of Biophysics, Biological Faculty, Lomonosov Moscow State University. The method describes the displacement of individual macromolecules – mobile electron carriers, and their electrostatic interactions between each other and with pigment-protein complexes embedded in photosynthetic membrane. Three-dimensional models of the protein molecules were constructed on the basis of the data from the Protein Data Bank. We applied the Brownian methods coupled to molecular dynamic simulations to reveal the role of electrostatic interactions and conformational motions in the transfer of an electron from the cytochrome complex Cyt b6f) membrane we developed the model which combines events of proteins Pc diffusion along the thylakoid membrane, electrostatic interactions of Pc with the membrane charges, formation of Pc super-complexes with multienzyme complexes of Photosystem I and to the molecule of the mobile carrier plastocyanin (Pc) in plants, green algae and cyanic bacteria. Taking into account the interior of photosynthetic membrane we developed the model which combines events of proteins Pc diffusion along the thylakoid membrane, electrostatic interactions of Pc with the membrane charges, formation of Pc super-complexes with multienzyme complexes of Photosystem I and Cyt b6f, embedded in photosynthetic membrane, electron transfer and complex dissociation. Multiparticle Brownian simulation method can be used to consider the processes of protein interactions in subcellular systems in order to clarify the role of individual stages and the biophysical mechanisms of these processes.
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Nakagawa S, Kurniawan I, Kodama K, Arwansyah MS, Kawaguchi K, Nagao H. Theoretical study on interaction of cytochrome f and plastocyanin complex by a simple coarse-grained model with molecular crowding effect. Mol Phys 2017. [DOI: 10.1080/00268976.2017.1406160] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Satoshi Nakagawa
- Faculty of Mathematics and Physics, Institute of Science and Engineering, Kanazawa University, Kanazawa, Japan
| | - Isman Kurniawan
- Faculty of Mathematics and Physics, Institute of Science and Engineering, Kanazawa University, Kanazawa, Japan
| | - Koichi Kodama
- Faculty of Mathematics and Physics, Institute of Science and Engineering, Kanazawa University, Kanazawa, Japan
| | - Muhammad Saleh Arwansyah
- Faculty of Mathematics and Physics, Institute of Science and Engineering, Kanazawa University, Kanazawa, Japan
| | - Kazutomo Kawaguchi
- Faculty of Mathematics and Physics, Institute of Science and Engineering, Kanazawa University, Kanazawa, Japan
| | - Hidemi Nagao
- Faculty of Mathematics and Physics, Institute of Science and Engineering, Kanazawa University, Kanazawa, Japan
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Kovalenko IB, Knyazeva OS, Antal TK, Ponomarev VY, Riznichenko GY, Rubin AB. Multiparticle Brownian dynamics simulation of experimental kinetics of cytochrome bf oxidation and photosystem I reduction by plastocyanin. PHYSIOLOGIA PLANTARUM 2017; 161:88-96. [PMID: 28369912 DOI: 10.1111/ppl.12570] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 01/22/2017] [Accepted: 02/22/2017] [Indexed: 06/07/2023]
Abstract
A model of electron transport from cytochrome f to photosystem I mediated by plastocyanin was designed on the basis of the multiparticle Brownian dynamics method. The model combines events which occur over a wide time range, including protein diffusion along the thylakoid membrane, long-distance interactions between proteins, formation of a multiprotein complex, electron transfer within a complex and complex dissociation. Results of the modeling were compared with the experimental kinetics measured in chloroplast thylakoids. Computer simulation demonstrated that the complex interior of the photosynthetic membrane, electrostatic interactions and Brownian diffusion provide physical conditions for the directed electron flow along the photosynthetic electron transport chain.
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Affiliation(s)
- Ilya B Kovalenko
- Biology Faculty, Lomonosov Moscow State University, Moscow, 119992, Russia
| | - Olga S Knyazeva
- Physical Faculty, Lomonosov Moscow State University, Moscow, 119992, Russia
| | - Taras K Antal
- Biology Faculty, Lomonosov Moscow State University, Moscow, 119992, Russia
| | | | | | - Andrei B Rubin
- Biology Faculty, Lomonosov Moscow State University, Moscow, 119992, Russia
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Diakonova AN, Khrushchev SS, Kovalenko IB, Riznichenko GY, Rubin AB. Influence of pH and ionic strength on electrostatic properties of ferredoxin, FNR, and hydrogenase and the rate constants of their interaction. Phys Biol 2016; 13:056004. [PMID: 27716644 DOI: 10.1088/1478-3975/13/5/056004] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Ferredoxin (Fd) protein transfers electrons from photosystem I (PSI) to ferredoxin:NADP+-reductase (FNR) in the photosynthetic electron transport chain, as well as other metabolic pathways. In some photosynthetic organisms including cyanobacteria and green unicellular algae under anaerobic conditions Fd transfers electrons not only to FNR but also to hydrogenase-an enzyme which catalyzes reduction of atomic hydrogen to H2. One of the questions posed by this competitive relationship between proteins is which characteristics of thylakoid stroma media allow switching of the electron flow between the linear path PSI-Fd-FNR-NADP+ and the path PSI-Fd-hydrogenase-H2. The study was conducted using direct multiparticle simulation approach. In this method protein molecules are considered as individual objects that experience Brownian motion and electrostatic interaction with the surrounding media and each other. Using the model we studied the effects of pH and ionic strength (I) upon complex formation between ferredoxin and FNR and ferredoxin and hydrogenase. We showed that the rate constant of Fd-FNR complex formation is constant in a wide range of physiologically significant pH values. Therefore it can be argued that regulation of FNR activity doesn't involve pH changes in stroma. On the other hand, in the model rate constant of Fd-hydrogenase interaction dramatically depends upon pH: in the range 7-9 it increases threefold. It may seem that because hydrogenase reduces protons it should be more active when pH is acidic. Apparently, regulation of hydrogenase's affinity to both her reaction partners (H+ and Fd) is carried out by changes in its electrostatic properties. In the dark, the protein is inactive and in the light it is activated and starts to interact with both Fd and H+. Therefore, we can conclude that in chloroplasts the rate of hydrogen production is regulated by pH through the changes in the affinity between hydrogenase and ferredoxin.
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Diakonova AN, Khruschev SS, Kovalenko IB, Riznichenko GY, Rubin AB. The role of electrostatic interactions in the formation of ferredoxin–ferredoxin NADP+ reductase and ferredoxin–hydrogenase complexes. Biophysics (Nagoya-shi) 2016. [DOI: 10.1134/s0006350916040060] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Khruschev SS, Abaturova AM, Fedorov VA, Kovalenko IB, Riznichenko GY, Rubin AB. The identification of intermediate states of the electron-transfer proteins plastocyanin and cytochrome f diffusional encounters. Biophysics (Nagoya-shi) 2015. [DOI: 10.1134/s0006350915040156] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Khruschev SS, Abaturova AM, Diakonova AN, Fedorov VA, Ustinin DM, Kovalenko IB, Riznichenko GY, Rubin AB. Brownian-dynamics simulations of protein–protein interactions in the photosynthetic electron transport chain. Biophysics (Nagoya-shi) 2015. [DOI: 10.1134/s0006350915020086] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Kovalenko IB, Knyazeva OS, Riznichenko GY, Rubin AB. Computer simulation of plastocyanin interaction with cytochrome f and photosystem I in cyanobacterium Phormidium laminosum. Biophysics (Nagoya-shi) 2014. [DOI: 10.1134/s0006350914010047] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Vershubskii AV, Tikhonov AN. Electron transport and transmembrane proton transfer in photosynthetic systems of oxygenic type in Silico. Biophysics (Nagoya-shi) 2013. [DOI: 10.1134/s000635091301017x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Riznichenko GY, Kovalenko IB, Abaturova AM, Diakonova AN, Knyazeva OS, Ustinin DM, Khruschev SS, Rubin AB. Multiparticle computer simulation of protein interactions in the photosynthetic membrane. Biophysics (Nagoya-shi) 2011. [DOI: 10.1134/s0006350911050162] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Kovalenko IB, Abaturova AM, Riznichenko GY, Rubin AB. Computer simulation of interaction of photosystem 1 with plastocyanin and ferredoxin. Biosystems 2011; 103:180-7. [DOI: 10.1016/j.biosystems.2010.09.013] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2010] [Revised: 09/23/2010] [Accepted: 09/27/2010] [Indexed: 11/25/2022]
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