Mathematical and computer modeling of primary photosynthetic processes

Riznichenko, G. Yu.; Belyaeva, N. E.; Kovalenko, I. B.; Rubin, A. B.

doi:10.1134/s0006350909010035

Cited by 22 publications

(12 citation statements)

References 16 publications

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“…Our model reproduces the non-monotonic dependence of the association second order rate constant of protein binding on the ionic strength taking into account only electrostatic interactions [13,14,15,16,17,18,25,26,27]. Our calculations confirm the theory [21,30] which supposes that a decrease in the rate constant at low values of the ionic strength is caused by the shift of equilibrium to an ensemble of complexes that are not optimal for the electron transfer.…”

Section: Resultssupporting

confidence: 75%

“…Besides, this method was applied for prediction of binding areas and possible complex structures for several pairs of test proteins [16]. The results are summarized in reviews [25,26,27]. This review presents the results of our works on the simulation of protein-protein complex formation rate constant dependence on the ionic strength.…”

Section: Introductionmentioning

confidence: 99%

“…In BD simulations the interaction of two individual proteins is investigated in solution, the proteins are treated as rigid or semi-rigid bodies, their geometric shape is considered at the atomic resolution, and electrostatic interactions of the proteins are presented in great details. There are BD models for the association of a pair of individual molecules Pc and Cyt f [23,25,32]. Currently there are no BD models of Fd-FNR reaction, although a model of association between ferredoxin and hydrogenase from Chlamydomonas reinhardtii has been presented recently [19].…”

Section: Introductionmentioning

confidence: 99%

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Computer Simulation of Protein-Protein Association in Photosynthesis

Kovalenko

Abaturova

Diakonova

et al. 2011

Math. Model. Nat. Phenom.

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Abstract. The paper is devoted to the method of computer simulation of protein interactions taking part in photosynthetic electron transport reactions. Using this method we have studied kinetic characteristics of protein-protein complex formation for four pairs of proteins involved in photosynthesis at a variety of ionic strength values. Computer simulations describe non-monotonic dependences of complex formation rates on the ionic strength as the result of long-range electrostatic interactions. Calculations confirm that the decrease in the association second order rate constant at low values of the ionic strength is caused by the protein pairs spending more time in "wrong" orientations which do not satisfy the docking conditions and so do not form the final complex capable of the electron transfer.

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Section: Resultssupporting

confidence: 75%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Computer Simulation of Protein-Protein Association in Photosynthesis

Kovalenko

Abaturova

Diakonova

et al. 2011

Math. Model. Nat. Phenom.

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“…Методы математического моделирования широко используются при изучении первичных процессов фотосинтеза, в том числе механизмов световой индукции ФХ [4,[6][7][8][9][10][11][12]. В основе большинства существующих моделей OJIP кривых лежит представление о том, что характер ИКФ определяется быстрыми фотохимическими процессами в ФС2, а также реакциями переноса электронов с донорной стороны ФС2 в ПХ пул.…”

Section: Introductionunclassified

Mathematical Modeling of Photosynthetic Electron Transport Chain Considering Spatial Heterogeneity of the Thylakoid Membrane

Макаров¹

2012

Math.Biol.Bioinf.

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“…One powerful approach is to develop computational models to explore the holistic behavior of the biological network (Kitano, 2002). Although many computational models of PETC in C3 plants have been published in recent years (Riznichenko et al, 2009;Ebenhöh et al, 2011;Zaks et al, 2012;Tikhonov and Vershubskii, 2014;Matuszy nska et al, 2016), they have been predominantly focused on specific mechanisms rather than on the interactions among mechanisms. For example, several models developed to study NPQ (Ebenhöh et al, 2011;Zaks et al, 2012;Matuszy nska et al, 2016) simplify the transport of electrons from PSII to NADPH and do not include any description of the metabolism that consumes ATP and NADPH.…”

mentioning

confidence: 99%

In Silico Analysis of the Regulation of the Photosynthetic Electron Transport Chain in C3 Plants

et al. 2017

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ORCID IDs: 0000-0002-6129-4570 (A.M.); 0000-0001-8273-8022 (X.Y); 0000-0002-0607-4508 (J.H.); 0000-0003-4144-6028 (S.M.D.); 0000-0001-6011-7487 (J.M.); 0000-0003-2196-547X (P.C.S.).We present a new simulation model of the reactions in the photosynthetic electron transport chain of C3 species. We show that including recent insights about the regulation of the thylakoid proton motive force, ATP/NADPH balancing mechanisms (cyclic and noncyclic alternative electron transport), and regulation of Rubisco activity leads to emergent behaviors that may affect the operation and regulation of photosynthesis under different dynamic environmental conditions. The model was parameterized with experimental results in the literature, with a focus on Arabidopsis (Arabidopsis thaliana). A dataset was constructed from multiple sources, including measurements of steady-state and dynamic gas exchange, chlorophyll fluorescence, and absorbance spectroscopy under different light intensities and CO 2 , to test predictions of the model under different experimental conditions. Simulations suggested that there are strong interactions between cyclic and noncyclic alternative electron transport and that an excess capacity for alternative electron transport is required to ensure adequate redox state and lumen pH. Furthermore, the model predicted that, under specific conditions, reduction of ferredoxin by plastoquinol is possible after a rapid increase in light intensity. Further analysis also revealed that the relationship between ATP synthesis and proton motive force was highly regulated by the concentrations of ATP, ADP, and inorganic phosphate, and this facilitated an increase in nonphotochemical quenching and proton motive force under conditions where metabolism was limiting, such as low CO 2 , high light intensity, or combined high CO 2 and high light intensity. The model may be used as an in silico platform for future research on the regulation of photosynthetic electron transport.Plants face highly variable environmental conditions, with fluctuations of light intensity, temperature, humidity, and CO 2 that occur over a wide range of time scales, from seconds to seasons. Imbalances between the rate of light capture and CO 2 assimilation can lead to an excess of energy in the system. Under such conditions, photosynthesis faces three main challenges:1. To dissipate the excess of energy that could otherwise result in the production of reactive oxygen species (Foyer et al., 2011); 2. To couple the production and demand of ATP and NADPH in chloroplasts under a fluctuating environment (Noctor and Foyer, 2000); 3. To maintain an adequate redox state (Allen, 2004) of the photosynthetic electron transport chain (PETC).In this study, we use the term regulation to indicate those mechanisms that allow photosynthesis to achieve these goals. These goals must be met simultaneously, and several mechanisms have been identified as contributing (Kramer et al., 2004), including:1. Nonphotochemical quenching (NPQ) of excess energy absorbed by photosynthetic...

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Mathematical and computer modeling of primary photosynthetic processes

Cited by 22 publications

References 16 publications

Computer Simulation of Protein-Protein Association in Photosynthesis

Computer Simulation of Protein-Protein Association in Photosynthesis

Mathematical Modeling of Photosynthetic Electron Transport Chain Considering Spatial Heterogeneity of the Thylakoid Membrane

In Silico Analysis of the Regulation of the Photosynthetic Electron Transport Chain in C3 Plants

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