Molecular Simulation Studies of the Orientation and Conformation of Cytochrome c Adsorbed on Self-Assembled Monolayers

Abstract

Cytochrome c (Cyt-c) is an important membrane electron-transfer protein. To maximize its electron transfer, adsorbed Cyt-c should have a preferred orientation with its heme ring close and perpendicular to the surface. Moreover, the adsorbed Cyt-c should keep its native conformation. In this work, the orientation and conformation of Cyt-c adsorbed on carboxyl-terminated self-assembled monolayers (SAMs) are investigated by a combined Monte Carlo and molecular dynamics simulation approach. The root-mean-square deviation, radius of gyration, eccentricity, dipole moment, heme orientation, and superimposed structures of Cyt-c were calculated. Simulation results show that the desired orientation of Cyt-c with its heme group perpendicular to the surface could be obtained on a negatively charged surface. The direction of the dipole of Cyt-c, contributed significantly by both lysine residues near the surface and glutamic acid residues far away from the surface, determines the final orientation of Cyt-c adsorbed on ...