Photosynthetic membrane is a subcellular system, which converts light energy into the chemical energy of ATP and energy of the reducing compounds, necessary for carbon fixation cycle and biosynthesis. We propose new approach of modeling photosynthetic electron transport and coupled processes taking into account the shape of interacting proteins and geometrical organization of photosynthetic membrane. The model simulates processes on the membrane “scene”, which includes stroma, lumen and intramembrane compartments constructed according to structural data. Submodels, describing the evolution in time of the state probabilities of photosynthetic complexes (PSI, PSII, Cyt b6f, ATP-synthase) by ODE, are coupled with the multiparticle Brownian dynamics description of mobile carrier interactions and with the description of proton gradient creation by means of reaction-diffusion equations. Proteins are simulated as solid bodies, we take into account electrostatical interaction of proteins with each other and electric field of the membrane. For calculation of the rate constants of bimolecular reactions we simulated protein-protein complex formation for Pc-Cytf, Pc-PSI, PSI-Fd, FD-FNR in solution and compared dependences of rate constants on ionic strength and pH with experimental ones. Thus different stages of primary photosynthetic processes are simulated using different mathematical approaches, which are integrated into a combined model. We implemented this model as software which utilizes parallel computations on high-performance clusters and GPUs for better performance. The fluorescence induction curves, P700 redox transformations and dynamics of ATP production similar to experimental ones were simulated. The model reveals the role of physical mechanisms and geometry of reaction volume in regulation of photosynthetic electron transport and coupled processes of energy transformation. The work was supported by grants of the RFBR (14-04-00302, 14-04-00326).
Rubin A., Riznichenko G. Mathethematical Biophysics. Springer, 2013
Riznichenko G., I.Kovalenko, A.Abaturova, D.Ustinin, A.Rubin. New direct dynamic models of protein interactions coupled to photosynthetic electron transport// Biophys. Rev. 2010, 2, 101-110