A molecular dynamics study of water chain formation in the proton-conducting K channel of cytochrome c oxidase

Abstract

The formation of water chains in cytochrome c oxidase (CcO) is studied by molecular dynamics (MD). Focus is on water chains in the K channel that can supply a proton to the binuclear center (the heme a 3 Fe/Cu B region), the site of O 2 reduction. By assessing the presence of chains of any length on a short time scale (0.1 ps), a view of the kinds of chains and their persistence is obtained. Chains from the entry of the channel on the inner membrane to Thr359 ( Rhodobacter sphaeroides numbering) are often present but are blocked at that point until a rotation of the Thr359 side chain occurs, permitting formation of chains from Thr359 towards the binuclear center. No continuous hydrogen-bonded water chains are found connecting Thr359 and the binuclear center. Instead, waters hydrogen bond from Thr359 to the hydroxyl of the heme a 3 farnesyl and then continue to the binuclear center via Tyr288, which has been identified as a source of a proton for O 2 reduction. Three hydrogen-bonded waters are found to be present in the binuclear center after a sufficiently long simulation time. One is ligated to the Cu B and could be associated with a water (or hydroxyl) identified in the crystal structure as the fourth ligand of Cu B. The water hydrogen-bonded to the hydroxyl of Tyr288 is extremely persistent and well positioned to participate in O 2 reduction. The third water is located where O 2 is often suggested to reside in mechanistic studies of O 2 reduction.