Direct simulation of plastocyanin and cytochrome f interactions in solution

Abstract

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.

Computer Simulation of Protein-Protein Association in Photosynthesis

“…Though it does not clearly consider conformational changes and electron transport, it can help to reveal the effect of electrostatic potential changes upon the kinetic parameters of protein interaction and to evaluate the rate constant values of complex formation. For the Pc-Cyt f and Fd-FNR complex formation in solution the simulated dependencies of the reaction rate constant on the ionic strength for different plastocyanin and FNR mutants are in good agreement with the experiments (see [14,18]). It indicates that for these reactions electrostatic forces play specific and very important role.…”

“…The docking distance is a model parameter defined as a distance between particular atoms involved in complex formation. Usually, these atoms are proteins redox centers (cofactors), but for some protein pairs (for example, plastocyanin-cytochrome f ) we additionally measure distances between contacting amino acid residues in order to reduce the number of possible initial complexes [14].…”

“…The most negative charge density of a membrane σ = −42 mC/m 2 in the simulation corresponds to a membrane consisting only of lipids (about 17% of membrane area is occupied by charged lipids). Ionic strength dependences for PcCyt f reaction for various Pc mutants are presented in [14]. Spinach Pc and turnip Cyt f molecular structures were taken from PDB ID 2PCF, docking distance values are given in [14], probability of final complex formation was taken as p = 0.01.…”

“…Ionic strength dependences for PcCyt f reaction for various Pc mutants are presented in [14]. Spinach Pc and turnip Cyt f molecular structures were taken from PDB ID 2PCF, docking distance values are given in [14], probability of final complex formation was taken as p = 0.01.…”

“…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].…”