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

Abstract

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.

Computer Simulation of Protein-Protein Association in Photosynthesis

“…Our model reproduces the non-monotonic dependence of the association second order rate constant of protein binding on the ionic strength taking into account only electrostatic interactions [13,14,15,16,17,18,25,26,27]. Our calculations confirm the theory [21,30] which supposes that a decrease in the rate constant at low values of the ionic strength is caused by the shift of equilibrium to an ensemble of complexes that are not optimal for the electron transfer.…”

“…Besides, this method was applied for prediction of binding areas and possible complex structures for several pairs of test proteins [16]. The results are summarized in reviews [25,26,27]. This review presents the results of our works on the simulation of protein-protein complex formation rate constant dependence on the ionic strength.…”

Combination of different simulation techniques in the complex model of photosynthetic membrane

“…По формуле (1) получаем, что среднее расстояние между комплексами переносчик будет преодолевать за время порядка 2.5 · 10 −7 с. Метод броуновской динамики позволяет моделировать электростатическое взаимодействие между белками и связывание одного подвижного переносчика с мультиферментным комплексом [Ullmann et al, 1997;Pearson, Gross, 1998;Ubbink et al, 1998;De Rienzo et al, 2001;Gross, Pearson, 2003]. В последние годы мы развиваем метод многочастичного прямого моделирования на основе броуновской динамики, позволяющий моделировать диффузию мобильных переносчиков в люмене и взаимодействие с пигмент-белковыми комплексами с учетом реалистичной геометрии белков и электростатических взаимодействий между ними [Riznichenko et al, 2010;Коваленко и др., 2009;Абатурова и др., 2009].…”