The identification of intermediate states of the electron-transfer proteins plastocyanin and cytochrome f diffusional encounters

Abstract

The Brownian dynamics method was used for qualitative analysis of the events that lead to the formation of a functionally active plastocyanin–cytochrome f complex. The intermediate states of this process were identified by density-based hierarchical clustering. Diffusive entrapment of plastocyanin by cytochrome f is the key point of the suggested putative scenario of protein–protein encounter. The motion of plastocyanin was characterized for different values of protein–protein electrostatic interaction energy.