Exploring O(2) Diffusion in A-Type Cytochrome c Oxidases: Molecular Dynamics Simulations Uncover Two Alternative Channels towards the Binuclear Site

Cytochrome c oxidases (Ccoxs) are the terminal enzymes of the respiratory chain in mitochondria and most bacteria. These enzymes couple dioxygen (O(2)) reduction to the generation of a transmembrane electrochemical proton gradient. Despite decades of research and the availability of a large amount of structural and biochemical data available for the A-type Ccox family, little is known about the channel(s) used by O(2) to travel from the solvent/membrane to the heme a(3)-Cu(B) binuclear center (BNC). Moreover, the identification of all possible O(2) channels as well as the atomic details of O(2) diffusion is essential for the understanding of the working mechanisms of the A-type Ccox. In this work, we determined the O(2) distribution within Ccox from Rhodobacter sphaeroides, in the fully reduced state, in order to identify and characterize all the putative O(2) channels leading towards the BNC. For that, we use an integrated strategy combining atomistic molecular dynamics (MD) simulations (with and without explicit O(2) molecules) and implicit ligand sampling (ILS) calculations. Based on the 3D free energy map for O(2) inside Ccox, three channels were identified, all starting in the membrane hydrophobic region and connecting the surface of the protein to the BNC. One of these channels corresponds to the pathway inferred from the X-ray data available, whereas the other two are alternative routes for O(2) to reach the BNC. Both alternative O(2) channels start in the membrane spanning region and terminate close to Y288(I). These channels are a combination of multiple transiently interconnected hydrophobic cavities, whose opening and closure is regulated by the thermal fluctuations of the lining residues. Furthermore, our results show that, in this Ccox, the most likely (energetically preferred) routes for O(2) to reach the BNC are the alternative channels, rather than the X-ray inferred pathway.