Computer simulation of plastocyanin-cytochrome f complex formation in the thylakoid lumen

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.…”

“…Our approach makes it possible to simulate reaction kinetics and obtain reaction time courses directly from the computer simulation. This method was used to study Pc-Cyt f complex formation for wild type (wt) and mutant Pc at a variety of ionic strength values in solution [14] and in the chloroplast thylakoid lumen [15]. The method was further developed to take into account the electrostatic interactions of proteins with the thylakoid membrane in the thylakoid lumen [13].…”

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

“…In Fig. 13 Dependence of the protein binding rate constant of the Pc-cyt f reaction divided by cyt f concentration in the thylakoid lumen on the distance z between the membranes at constant number of molecules (Kovalenko et al 2008a) Fig. 12 The model scene visualization (the thylakoid lumen bounded by the thylakoid membranes) with proteins plastocyanin (Pc) and cytochrome f (Cyt f ) the current version of DMSM, these processes are included implicitly with the parameter of probability of interaction.…”

“…b Ionic strength is 80 mM interactions of mobile carrier Pc and cyt f as part of the cytochrome complex protruding into the lumen space (see Fig. 12) (Kovalenko et al 2008a). The model scene of the luminal space was presented as a rectangular parallelepiped, bounded by membranes at the top and bottom, while at the butt ends, the mirror boundary conditions were assumed (Fig.…”

“…To simulate the behavior of such complex subcellular systems in vivo, it is necessary to consider not only a single pair of molecules but rather a great number of them interacting in the constrained reaction volumes of cell organelles. Below we shall briefly describe the "direct" multiparticle simulation method (DMSM) we developed to solve this problem (Kovalenko et al 2003(Kovalenko et al , 2006(Kovalenko et al , 2008a(Kovalenko et al , b, 2009Riznichenko et al 2009;Rubin and Riznichenko 2009).…”