Theoretical Study of Dissociation Process of Plastocyanins by PaCS-MD Simulation

Abstract

Abstract We present a procedure of calculation of free energy landscape of two proteins by using parallel cascade molecular dynamics (PaCS-MD) and multiple independent umbrella sampling (MIUS). The free energy landscape of two plastocyanins for association/dissociation process is investigate by using the present method. We find that binding free energy is around 1 kcal/mol and that the barrier energy at around the middle range between the equilibrium point and the dissociation state becomes about 1 kcal/mol from the association process. The present results suggest that the energy barrier may arise from hydrogen bonds between two plastocyanins. We also find that the effective interaction between two plastocyanins already vanishes at the distance of 2 Å from equilibrium state. The equilibrium point of the complex around 27.9 Å is a good agreement with the experimental result 27.8 Å