Protein–protein docking of electron transfer complexes: Cytochromecoxidase and cytochromec

Abstract

Electron transferring protein complexes form only transiently and the crystal structures of electron transfer protein--protein complexes involving cytochrome c could so far be determined only for the pairs of yeast cytochrome c peroxidase (CcP) with iso-1-cytochrome c (iso-1-cyt c) and with horse heart cytochrome c (cyt c). This article presents models from computational docking for complexes of cytochrome c oxidase (COX) from Paracoccus denitrificans with horse heart cytochrome c, and with its physiological counterpart cytochrome c552 (c552). Initial docking is performed with the FTDOCK program, which permits an exhaustive search of translational and rotational space. A filtering procedure is then applied to reduce the number of complexes to a manageable number. In a final step of structural and energetic refinement, the complexes are optimized by rigid-body energy minimization with the molecular mechanics package CHARMM. This methodology was first tested on the CcP:iso-1-cyt c complex, in which the complex with the lowest CHARMM energy has an RMSD from the crystal structure of only 1.8 A (C(alpha) carbon atoms). Notably, the crystal conformation has an even lower energy. The same procedure was then applied to COX:cyt c and COX:c552. The lowest-energy COX:cyt c complex is very similar to a docking model previously described for the complex of bovine cytochrome c oxidase with horse heart cytochrome c. For the COX:c552 complex, cytochrome c552 is found in two different orientations, depending on whether it is docked against COX from a two-subunit or from a four-subunit crystal structure, respectively. Both conformations are discussed critically in the light of the available experimental data.

Different Interaction Modes of Two Cytochrome-c Oxidase Soluble CuA Fragments with Their Substrates

“…This indicates that two to three effective charges of opposite sign on each protein interface interact in the bimolecular electron transfer reaction, which is totally consistent with recent protein-protein docking calculations (33). The extrapolated rates at I ϭ 0 (k 0 ϭ 1.2*10 7 and 5.6*10 7 M Ϫ1 s Ϫ1 for the forward and reverse reactions, respectively) indicate that the ET reactions approach the limit imposed by diffusion, as observed with wild-type aa 3 (13).…”

Adaptive evolution of cytochrome c oxidase: Infrastructure for a carnivorous plant radiation

“…2). Surprisingly, when we least-squares fitted (29) the C ␣ coordinates of the transmembrane helical segments of subunits I and II of the Paracoccus denitrificans oxidase (1ar1.pdb)͞ cytochrome c docked complex (18) to the corresponding subunits of bovine COX, the C-terminal tail of subunit VIIa (residue 58) touched the surface loops of the electron donor (residues 45-47). As such, the dissociation kinetics of cytochrome c could be modulated in part by this tripod-like interaction region.…”

“…Comparison with the structure of bovine COX (17) implicates a 2-aa motif, absent from Ϸ99.9% of all other cellular organisms studied, that may alter the dissociation kinetics of cytochrome c docking to the COX holoenzyme (18).…”

Long-range electron transfer

“…Cu A , a binuclear site with bridging S(Cys) atoms, is the primary electron acceptor from cyt c. Studies with Ru-modified cyt c reveal rapid (6 ϫ 10 4 s Ϫ1 ) (84) electron injection from Fe(II) into Cu A at low driving force (⌬G°ϭ Ϫ0.03 eV) (85). Modeling suggests that cyt c binds to the enzyme at an acidic patch on subunit II (86,87). The cyt c heme is very near the Trp-104 (subunit II) indole ring, a residue that appears from mutagenesis experiments to be critical for rapid cyt c 3 Cu A ET (88)(89)(90)(91).…”