Long-range regulation of cytochrome c binding to bc1 complex.

Abstract

The cytochrome bc1 complex (Complex III, ubiquinol-cytochrome c oxidoreductase) is a highly conserved multi-subunit protein found in the mitochondria and is a key complex in the electron transport chain. During oxidative phosphorylation, cytochrome (cyt) c, a mobile electron carrier, binds to one cyt c1 subunit of a bc1 complex dimer and shuttles electrons from Complex III to Complex IV. X-ray crystallographic studies revealed that only one molecule of cyt c binds to one bc1 complex dimer, despite two cytochrome c1 subunits available for binding, pointing toward the existence of a regulation mechanism preventing the docking of a second cyt c substrate. However, the structural basis for such a mechanism of long-range (>30 Å) regulation of substrate binding is not clear from static structural studies. We employed all-atom molecular dynamics simulations to uncover a possible mechanism of regulation. Our results reveal that a finger-like extended domain of the vacant cyt c1 subunit undergoes a conformational change with its tip moving towards cyt c, transferring mechanical motion and causing distortion of the vacant cyt c binding site. In addition, we explored the role of naturally occurring methylated Lys-72 residue of cyt c in substrate binding and its likely role in the regulation of the bc1 complex activity. Finally, our results of experimental verification of computational predictions are presented.