Molecular simulation studies of the orientation and conformation of cytochrome c adsorbed on self-assembled monolayers

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 a charged surface. Lysine residues Lys25, Lys27, Lys72, and Lys79 are responsible for the strong electrostatic interactions with the surface. A possible electron-transfer pathway is proposed (i.e., iron-His18-Cys17-Gln16-surface and iron-Met80-Lys79-surface). The effect of the strength of negatively charged surfaces on the conformation of adsorbed Cyt-c is studied. Although higher surface charge density of a negatively charged surface favors its preferred orientation, too high a surface charge density will cause a severe conformational change of the adsorbed protein, resulting in the loss of bioactivity of the adsorbed protein.