Theoretical studies on association/dissociation process of plastocyanin and cytochrome f in photosynthesis

Abstract

We investigate the association/dissociation process of plastocyanin with cytochrome f before/after the reaction of the electron transfer from cytochrome f to plastocyanin by using all-atom molecular dynamics simulation and our coarse-grained model simulation. The force field parameters of the oxidized and reduced plastocyanin are estimated by quantum chemical calculations and are summarized in this paper. The free energy profiles corresponding to the association/dissociation process are calculated by the thermodynamic integration method with the all-atom molecular dynamics simulations. A flat free energy landscape in the middle range of the association/dissociation process for both cases before and after the reaction is observed. The radial distribution function of the case before the reaction is calculated by the coarse-grained model with the Langevin equation of motion. We estimate the free energy landscape from the radial distribution function. The results by the coarse-grained model may reproduce similar results by all-atom molecular dynamics simulation. We discuss the association/dissociation process of the complex of plastocyanin and cytochrome f in relation to the free energy landscape with some physical properties such as the binding free energy, the activation free energy, the energy of the reaction, and so on.