Analysis of the rate of electron transport through photosynthetic cytochrome $b_6 f$ complex

Khruschev S.S., Fursova P.V., Plusnina T.Yu., Riznichenko G.Yu., Rubin A.B.
 pdf (1538K) / Supplementary information

We consider an approach based on linear algebra methods to analyze the rate of electron transport through the cytochrome $b_6 f$ complex. In the proposed approach, the dependence of the quasi-stationary electron flux through the complex on the degree of reduction of pools of mobile electron carriers is considered a response function characterizing this process. We have developed software in the Python programming language that allows us to construct the master equation for the complex according to the scheme of elementary reactions and calculate quasi-stationary electron transport rates through the complex and the dynamics of their changes during the transition process. The calculations are performed in multithreaded mode, which makes it possible to efficiently use the resources of modern computing systems and to obtain data on the functioning of the complex in a wide range of parameters in a relatively short time. The proposed approach can be easily adapted for the analysis of electron transport in other components of the photosynthetic and respiratory electron-transport chain, as well as other processes in multienzyme complexes containing several reaction centers. Cryo-electron microscopy and redox titration data were used to parameterize the model of cytochrome $b_6 f$ complex. We obtained dependences of the quasi-stationary rate of plastocyanin reduction and plastoquinone oxidation on the degree of reduction of pools of mobile electron carriers and analyzed the dynamics of rate changes in response to changes in the redox state of the plastoquinone pool. The modeling results are in good agreement with the available experimental data.

Keywords: photosynthesis, electron transport, master equation, response function, cytochrome complex
Citation in English: Khruschev S.S., Fursova P.V., Plusnina T.Yu., Riznichenko G.Yu., Rubin A.B. Analysis of the rate of electron transport through photosynthetic cytochrome $b_6 f$ complex // Computer Research and Modeling, 2024, vol. 16, no. 4, pp. 997-1022
Citation in English: Khruschev S.S., Fursova P.V., Plusnina T.Yu., Riznichenko G.Yu., Rubin A.B. Analysis of the rate of electron transport through photosynthetic cytochrome $b_6 f$ complex // Computer Research and Modeling, 2024, vol. 16, no. 4, pp. 997-1022
DOI: 10.20537/2076-7633-2024-16-4-997-1022
URL: http://crm-en.ics.org.ru/journal/article/3505/

 

Supplementary information:

 

Model of a cytochrome complex and examples of the Python software code.

SI_Khruschev_et_al_2024.zip

 

 

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