Paper Citing NAMD - Abstract
Tuukkanen, Anne; Verkhovsky, Michael I.; Laakkonen, Liisa; Wikstrom, Marten
The K-pathway revisited: A computational study on cytochrome c oxidase
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS, 1757:1117-1121, SEP-OCT 2006
Cytochrome c oxidase contains two established proton-conducting structures, the D- and K-pathways. The role of the K-pathway appears to be to conduct the first two protons to be used in water formation, which are taken up on reduction of the oxidized enzyme. Previous computational work has suggested that Lys(I)-319 is neutral over a large pH range and in various redox states. We have constructed oxidase models in different redox states using quantum-chemically derived charge parameters for the redox metal centers. The protonation behaviour of titratable sites in the two-subunit enzyme was defined by continuum electrostatics. The calculations reported here show substantial protonation of Lys(I)-319 at neutral pH once the stable X-ray crystallographic water molecule found immediately next to it is treated explicitly. The immediate structure of the Lys(I)319 environment is independent of redox state, but the pK(a) value of this residue changes with the redox state of the binuclear heme a(3)/Cu-B site whenever that change is electrically uncompensated. Lys(I)-319 is also found to interact electrostatically with the conserved residue Glu(II)-62 in subunit II. These results are discussed in relation to the role of the K-pathway in oxidase function. (c) 2006 Elsevier B.V. All rights reserved.
