Galina Riznichenko

Modeling of the Primary Processes in a Photosynthetic Membrane

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Direct simulation of plastocyanin and cytochrome f interactions in solution

Most biological functions, including photosynthetic activity, are mediated by protein interactions. The proteins plastocyanin and cytochrome f are reaction partners in a photosynthetic electron transport chain. We designed a 3D computer simulation model of diffusion and interaction of spinach plastocyanin and turnip cytochrome f in solution. It is the first step in simulating the electron transfer from cytochrome f to photosystem 1 in the lumen of thylakoid. The model is multiparticle and it can describe the interaction of several hundreds of proteins. In our model the interacting proteins are represented as rigid bodies with spatial fixed charges. Translational and rotational motion of proteins is the result of the effect of stochastic Brownian force and electrostatic force. The Poisson-Boltzmann formalism is used to determine the electrostatic potential field generated around the proteins. Using this model we studied the kinetic characteristics of plastocyanin-cytochrome f complex formation for plastocyanin mutants at pH 7 and a variety of ionic strength values.

Kinetic mechanisms of biological regulation in photosynthetic organisms.

Principles of regulation on different levels of photosynthetic apparatus are discussed. Mathematical models of isolated photosynthetic reaction centers and general system of energy transduction in chloroplast are developed. A general approach to model these complex metabolic systems is suggested. Regulatory mechanisms in plant cell are correlated with the different patterns of fluorescence induction curve at different internal physiological states of the cells and external (environmental) conditions. Light regulation inside photosynthetic reaction centers, diffusion processes in thylakoid membrane, generation of transmembrane electrochemical potential, coupling with processes of CO2 fixation in Calvin Cycle are considered as stages of control of energy transformation in chloroplasts in their connection with kinetic patterns of fluorescence induction curves and other spectrophotometric data.

New direct dynamic models of protein interactions coupled to photosynthetic electron transport reactions

This review covers the methods of computer simulation of protein interactions taking part in photosynthetic electron transport reactions. A direct multiparticle simulation method that simulates reactions describing interactions of ensembles of molecules in the heterogeneous interior of a cell is developed. In the models, protein molecules move according to the laws of Brownian dynamics, mutually orient themselves in the electrical field, and form complexes in the 3D scene. The method allows us to visualize the processes of molecule interactions and to calculate the rate constants for protein complex formation reactions in the solution and in the photosynthetic membrane. Three-dimensional multiparticle computer models for simulating the complex formation kinetics for plastocyanin with photosystem I and cytochrome bf complex, and ferredoxin with photosystem I and ferredoxin:NADP+-reductase are considered. Effects of ionic strength are featured for wild type and mutant proteins. The computer multiparticle models describe nonmonotonic dependences of complex formation rates on the ionic strength as the result of long-range electrostatic interactions.

Fluorescence induction curves registered from individual microalgae cenobiums in the process of population growth.

Registration of chlorophyll fluorescence induction curves (IC) from individual microalgae cenobiums was performed during Scenedesmus quadricauda culture growth. Emphasis was placed on the analysis of patterns of the slow phase of IC, since these slow fluorescence transitions reflect complex interactions between primary and secondary photosynthetic processes. A classification was performed of the ICs obtained according to the patterns of their slow phase. Four different types of such patterns were distinguished. The microalgae population structure with respect to IC patterns was investigated at different stages of culture growth. The distribution of microalgae cenobiums over the patterns of IC was found to change in accordance with the stage of population development. At the stage of the population growth enhancement, nonmonotonous IC dominated with a high steady-state level of fluorescence. The stage of linear growth was characterized by IC with monotonous decay kinetics and low steady-state level of fluorescence. At the third stage including the phases of growth inhibition, stationary state and the beginning of cell death the population structure was the most heterogeneous, with all IC patterns observed.

Multiparticle Direct Simulation of Photosynthetic Electron Transport Processes

In our previous study [3] we described the method for a direct three-dimensional (3D) computer simulation of ferredoxin-dependent cyclic electron transport around the photosystem 1 pigment-protein complex. Simulations showed that the spatial organization of the system plays a significant role in shaping the kinetics of the redox turnover of P700 (the reaction center of a photosystem 1 pigment-protein complex). In this paper we develop the direct 3D model of cyclic electron transport and apply it to study the nature of fast and slow components of the P700+ dark reduction process. We demonstrate that the slow phase of this process is diffusion controlled and is determined by the diffusion of reduced plastoquinone and plastocyanin molecules from the granal to the stromal areas of the thylakoid membrane.

Multiparticle Brownian dynamics simulation of experimental kinetics of cytochrome bf oxidation and photosystem I reduction by plastocyanin

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.

Nonlinear Models of DNA Dynamics DNA dynamics

To understand the mechanisms that mediate the activity of biological systems at the molecular and subcellular levels, it is necessary to study the physical processes involving biological macromolecules. Following this approach, application of the ideas and methods of modern nonlinear physics turns out to be especially productive. Up-to-date nonlinear DNA physics is a special field of scientific research that makes it possible to considerably promote our understanding of the laws underlying the function of this molecule of life.

Models of Photosynthetic Electron Transport: Electron Transfer in a Multienzyme Complex multienzyme complex

This chapter is devoted to the modeling of electron transport processes, which are the basis of the primary photosynthetic light stage where the transformation of solar energy into the energy of chemical bonds takes place. We shall discuss the structure and main functional mechanisms operating in a system as well as the problem of adequate mathematical apparatus for the description of the primary photosynthetic processes and the formulation and analysis of related kinetic models.

The stoichiometry and energetics of oxygenic phototrophic growth

The values of gross metabolic flows in cells are essentially interconnected due to conservation laws of chemical elements and interrelations of biochemical coupling. Therefore, the overall stoichiometry of cellular metabolism, such as the biomass quantum yield, the ratio between linear and circular flows via the electron transport chain, etc., can be calculated using balances of metabolic flows in the network branching points and coupling ratios related to ATP formation and expenditures. This work has studied the energetic stoichiometry of photosynthetic cells by considering the transfer of reductivity in the course of biochemical reactions. This approach yielded rigorous mathematical expressions for biomass quantum yield and other integral bioenergetic indices of cellular growth as functions of ATP balance parameters. The effect of cellular substance turnover has been taken into account. The obtained theoretical estimation of biomass quantum yield is rather close to experimental data which confirms the predictive capacity of this approach.