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.
Highlights
Photosynthetic electron transport forms the basis of light energy transduction into energy of chemical compounds, ATP and NADPH, used for metabolic needs, firstly, for CO2 assimilation in the chloroplast of leaves and algae
Methods of mathematical and computer modeling significantly contribute to the research of the mechanisms underlying the different steps of photosynthetic electron flow to enrich the knowledge on the physic-chemical basis of energy transduction
The method describes the displacement of individual macromolecules – mobile electron carriers, and their interaction between each other and with pigment-protein complexes embedded in photosynthetic membrane
Summary
Photosynthetic electron transport forms the basis of light energy transduction into energy of chemical compounds, ATP and NADPH, used for metabolic needs, firstly, for CO2 assimilation in the chloroplast of leaves and algae. The structure of the photosynthetic membrane (Fig 1) shows that in areas where electron transport is carried out by mobile carriers (molecules of the PQ pool, Pc in the lumen, Fd on the stromal side of the PSI) their interaction with multi-enzyme complexes does not correspond to the concepts of free diffusion and random collisions. The method describes the displacement of individual macromolecules – mobile electron carriers, and their interaction between each other and with pigment-protein complexes embedded in photosynthetic membrane. Molecules of electron carrier proteins perform Brownian motion in a medium and undergo electrostatic interactions with each other and with the surface of a photosynthetic membrane. With the help of the multi-particle Brownian dynamics, the interaction of the Pc molecule with the cytochrome f cofactor in a solution [7, 18] and in the lumen of the thylakoid [14, 16], the interaction of Pc with the PSI donor part and the interaction of Fd with the PSI acceptor part [9] and Fd with subsequent electron acceptors, FNR [8], and hydrogenase [19,20,21]) were simulated (Fig. 2.)
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