Ferredoxin reduced by Photosystem I in light serves as an electron donor for the reduction of NADP(+) to NADPH, and this reaction is catalyzed by enzyme ferredoxin:NADP(+)-reductase (FNR). Kinetics and mechanisms of this reaction have been extensively studied experimentally by site-specific mutagenesis, laser flash photolysis and stopped-flow methods. We have applied a method of multiparticle computer simulation to study the effects of electrostatic interactions upon the reaction rate of Fd-FNR complex formation. Using the model we calculated rate constants of Fd-FNR complex formation for the wild-type proteins and some mutant forms of FNR at different values of ionic strength. Simulation revealed that electrostatic interactions play an important role in Fd-FNR complex formation and define its specificity.

Белок-белковые взаимодействия являются основой большинства биологических процессов. Компьютерное моделирование динамики связывания белков дает важную информацию для понимания механизмов их функционирования. Разработана компьютерная программа ProKSim (Protein Kinetics Simulator), предназначенная для моделирования взаимодействия макромолекул методом многочастичной броуновской динамики с учетом дальнодействующих электростатических взаимодействий. Проведено исследование диффузионностолкновительных комплексов для трех пар белков: ферредоксин и ферредоксин:НАДФ +-редуктаза, пластоцианин и цитохром f, барназа и барстар. Исследована роль электростатических взаимодействий во взаимной ориентации молекул белков при образовании диффузионно-столкновительных комплексов. Ключевые слова: многочастичная броуновская динамика, белок-белковые взаимодействия, механизмы молекулярного распознавания

Ferredoxin (Fd) protein transfers electrons from photosystem I (PSI) to ferredoxin:NADP-reductase (FNR) in the photosynthetic electron transport chain, as well as other metabolic pathways. In some photosynthetic organisms including cyanobacteria and green unicellular algae under anaerobic conditions Fd transfers electrons not only to FNR but also to hydrogenase-an enzyme which catalyzes reduction of atomic hydrogen to H. One of the questions posed by this competitive relationship between proteins is which characteristics of thylakoid stroma media allow switching of the electron flow between the linear path PSI-Fd-FNR-NADP and the path PSI-Fd-hydrogenase-H. The study was conducted using direct multiparticle simulation approach. In this method protein molecules are considered as individual objects that experience Brownian motion and electrostatic interaction with the surrounding media and each other. Using the model we studied the effects of pH and ionic strength (I) upon complex formation between ferredoxin and FNR and ferredoxin and hydrogenase. We showed that the rate constant of Fd-FNR complex formation is constant in a wide range of physiologically significant pH values. Therefore it can be argued that regulation of FNR activity doesn't involve pH changes in stroma. On the other hand, in the model rate constant of Fd-hydrogenase interaction dramatically depends upon pH: in the range 7-9 it increases threefold. It may seem that because hydrogenase reduces protons it should be more active when pH is acidic. Apparently, regulation of hydrogenase's affinity to both her reaction partners (H and Fd) is carried out by changes in its electrostatic properties. In the dark, the protein is inactive and in the light it is activated and starts to interact with both Fd and H. Therefore, we can conclude that in chloroplasts the rate of hydrogen production is regulated by pH through the changes in the affinity between hydrogenase and ferredoxin.

No abstract

Abstract. The paper is devoted to the method of computer simulation of protein interactions taking part in photosynthetic electron transport reactions. Using this method we have studied kinetic characteristics of protein-protein complex formation for four pairs of proteins involved in photosynthesis at a variety of ionic strength values. Computer simulations describe non-monotonic dependences of complex formation rates on the ionic strength as the result of long-range electrostatic interactions. Calculations confirm that the decrease in the association second order rate constant at low values of the ionic strength is caused by the protein pairs spending more time in "wrong" orientations which do not satisfy the docking conditions and so do not form the final complex capable of the electron transfer.