Direct simulation of interaction of the proteins plastocyanin and cytochrome f
"Математика. Компьютер. Образование". Cб. трудов XII международной конференции. Под общей редакцией Г.Ю. Ризниченко Ижевск: Научно-издательский центр "Регулярная и хаотическая динамика", 2005. Vol. 3, 344pp. Pp. 955-966.
The paper is devoted to a novel approach for direct computer simulation of protein diffusion and interaction in a 3D space. The interacting molecules are considered as rigid bodies with spatial fixed partial charges. We consider 3D translational and rotational Brownian motion of proteins and electrostatic interactions. This approach is a further development of the method of direct 3D simulation of electron transport in photosynthetic membrane. We built a 3D computer model for the interaction of mobile electron carrier protein plastocyanin with cytochrome f, one of the subunits of cytochrome bf complex, in solution. Using this model we studied the dependence of the kinetic parameters of protein-protein interactions on the ionic strength.