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

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. (C) 2004 Elsevier B.V. All rights reserved.