title: 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.
authors.affiliation: Biological Faculty, Lomonosov Moscow State University, Leninskie Gory, Moscow 119992, Russia. kovalenko78@mail.ru
authors.forename: I B
authors.initials: IB
authors.lastname: Kovalenko
authors.forename: A M
authors.initials: AM
authors.lastname: Abaturova
authors.forename: P A
authors.initials: PA
authors.lastname: Gromov
authors.forename: D M
authors.initials: DM
authors.lastname: Ustinin
authors.forename: E A
authors.initials: EA
authors.lastname: Grachev
authors.forename: G Yu
authors.initials: GY
authors.lastname: Riznichenko
authors.forename: A B
authors.initials: AB
authors.lastname: Rubin
mesh_terms: D003198:Computer Simulation; D045348:Cytochromes f / Q000737:chemistry*; D007700:Kinetics; D008956:Models, Chemical; D008958:Models, Molecular; D010788:Photosynthesis; D010970:Plastocyanin / Q000737:chemistry*; D011485:Protein Binding; D011487:Protein Conformation; D055672:Static Electricity
chemical_list: D010970:Plastocyanin; D045348:Cytochromes f