MD Simulations Reveal an Alternative Pathway for Dioxygen Diffusion in Aa3 Cytochrome C Oxidases

Abstract

Cytochrome c oxidases (CCOX) are members of the heme-copper oxidase superfamily and they are the terminal enzymes of the respiratory chain. These proteins are membrane-bound multi-subunit redox-driven proton pumps, which couple the reduction of molecular dioxygen to water with the creation of a transmembrane electrochemical proton gradient.Over the last 20 years, most of the CCOX research focused on the mechanisms and energetics of reduction and/or proton pumping and little emphasis has been given to the pathways used by dioxygen to reach the binuclear site. The main objective of this work is to identify possible alternative dioxygen pathways in the reduced CCOX from Rhodobacter sphaeroides [1] using extensive Molecular Dynamics (MD) simulations. Our simulations allowed the identification of two possible dioxygen channels, whose entrances are both located in the membrane region. The first channel is a Y-shaped hydrophobic cavity with a constriction point near F282(I) and W172(I), and it corresponds to the oxygen pathway previously identified in the X-ray structure [2]. The second channel follows the hydroxylfarnesyl tail of haem a3 and ends near the Y288(I) (which is covalently linked to the H284(I) imidazole group).[1] Qin et al. (2009) Biochemistry 48, 5121-5130.[2] Svensson-EK et al. (2002) J.Mol.Biol.321, 329-339.