[Mathematical modeling of group of neurons and astrocytes in ischemic stroke].

The mathematical model of group of neurons and astrocytes in the ischemic stroke is discussed. The model includes the description of synaptic signal transmission between the neurons, calcium signaling in astrocytes, ionic currents between the cells and extracellular space and the diffusion through extracellular space. The new modeling approach, based on the creation of appropriate graph, is developed to describe the structure of the system. Using the model, we have analyze the influence of inhibitory synapses on system functioning. We also have shown how the use of medications supporting the activity of inhibitory synapses affects the system behavior in ischemic stroke.

[Multiparticle computer simulation of diffusion and interaction of plastocyanin with cytochrome f in the electrostatic field of the thylakoid membrane].

A multiparticle computer model of plastocyanin-cytochrome f complex formation in the thylakoid lumen has been designed, which takes electrostatic interactions of proteins and the thylakoid membrane into account. The Poisson-Boltzmann formalism was used to determine the electrostatic potential field generated by the electrical charges of the proteins and the thylakoid membrane for different ionic strength values. The role of electrostatic field of the thylakoid membrane in plastocyanin-cytochrome f complex formation was determined. Using the model, the rate constant of plastocyanin-cytochrome f reaction for different values of ionic strength and membrane surface charge were calculated.

[Computer simulation of complex formation between plastocyanine and cytochrome f in thylakoid lumen].

The diffusion of the protein plastocyanine and complex formation between plastocyanine and cytochrome f (a subunit of a cytochrome b6/f complex) in the chloroplast thylakoid lumen has been studied. A 3D computer simulation model of diffusion and binding of plastocyanine and cytochrome f has been constructed, which considers their electrostatic interaction. Based on the experimental data, the parameters of the model for complex formation between plastocyanine and cytochrome f in solution have been estimated. The dependence of the rate of plastocyanine-cytochrome f reaction on the size of the luminal space has been studied. It was shown that the contraction of the luminal space leads to a decrease in the reaction rate, which is in agreement with the experimental data on the inhibition of the reaction under hyperosmotic stress.

[Effect of the tissue architecture on cell-to-cell calcium signaling].

A novel approach based on the approximation of tissue structure by the Voronoi diagram has been elaborated to study cell-to-cell signaling in a tissue mediated by gap junctions. This methodology was applied for the analysis of Ca2+ signaling in the airway epithelium, where adjacent cells were taken to be coupled by gap junctions whose permeability depended on Ca2+ concentration in their cytoplasm. The number of junctional channels connecting a given pair of cells was postulated to be directly proportional to the length of the boundary between them. In a certain range of parameters, a modeled cell generate intracellular Ca2+ oscillations upon the stimulation with the purinergic agonist ATP, and the Ca2+ signal propagated through the tissue due to a Ca2+ rise in adjacent connected cells. The influence of variable sensitivity of cells to ATP on Ca2+ signaling in the tissue was also examined. The model also showed that a mechanical disturbance of a single airway epithelial cell resulted in a prolonged increase in Ca2+ concentration in its cytoplasm, which entailed the spreading of a Ca2+ wave along the tissue.

[Multiparticle computer simulation of photosynthetic electron transport in a thylakoid membrane].

A method for multiparticle computer simulation of photosynthetic electron transport in a thylakoid membrane has been developed. The basic principles of this method were described previously. The method is used to describe the cyclic electron flow around photosystem I. The effects of size and shape of the reaction volume on the kinetics of interaction of a mobile carrier with a protein complex and the limited diffusion of reactants were studied. It was shown that the kinetic parameters of photosynthetic electron transport processes depend on the distribution of protein complexes in the membrane. It was shown that the limited nature of diffusion of plastoquinone molecules in the membrane leads to a tenfold decrease in the efficient diffusion coefficient. It was shown that the occurrence of two phases of dark reduction of photooxidized P700+ is due to a heterogeneous spatial organization of the thylakoid membrane of a chloroplast.

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.

[Experimental and theoretical study of processes of cyclical electron transport around photosystem I]. / Ekspeirmental'noe i teoreticheskoe issledovanie protsessov tsiklicheskgo élektronnogo transporta vokrug fotosistemy I.

The kinetics of photoinduced EPR I signals at different concentrations of ferredoxin was studied on isolated pea chloroplasts. A kinetic model of ferredoxin-dependent electron transport around photosystem I was suggested. A multiparticle model was constructed, which makes it possible to "directly" model the processes of electron transfer in multiprotein complexes and limited diffusion in different compartments of the system (stroma, lumen, and intermembrane space). A comparison of the kinetic and "direct" models revealed an important role of spatial organization of the system in the kinetics of redox turnover of P700.