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The K-pathway revisited: a computational study on cytochrome c oxidase
Anne Tuukkanen1, Michael I Verkhovsky, Liisa Laakkonen
1Helsinki Bioenergetics Group, Institute of Biotechnology, University of Helsinki, FIN-00014 University of Helsinki, Helsinki, Finland.
Biochimica Et Biophysica Acta
|July 18, 2006
Summary
The K-pathway in cytochrome c oxidase facilitates proton transfer for water formation. Lysine-319 is significantly protonated at neutral pH, with its pKa influenced by the redox state of the binuclear site.
Area of Science:
- Biochemistry and Biophysics
- Molecular Biology
- Computational Chemistry
Background:
- Cytochrome c oxidase is a crucial enzyme in cellular respiration, responsible for catalyzing the reduction of oxygen to water.
- Two proton pathways, D and K, are known to exist within the enzyme, with the K-pathway implicated in water formation.
- Previous studies suggested Lysine-319 (Lys(I)-319) remains neutral across various pH and redox conditions.
Purpose of the Study:
- To investigate the protonation behavior of Lys(I)-319 in cytochrome c oxidase under different redox states.
- To elucidate the role of explicit water molecules and electrostatic interactions in the K-pathway's function.
- To determine how the redox state of the binuclear heme a3/Cu(B) site affects the K-pathway's protonation.
Main Methods:
- Construction of cytochrome c oxidase models in various redox states.
- Utilization of quantum-chemically derived charge parameters for redox metal centers.
- Application of continuum electrostatics to define protonation states of titratable sites, including explicit treatment of a key water molecule.
Main Results:
- Substantial protonation of Lys(I)-319 was observed at neutral pH when a nearby crystallographic water molecule was explicitly included in calculations.
- The local environment of Lys(I)-319 remained structurally consistent across different redox states.
- The pKa of Lys(I)-319 was found to be redox-dependent, specifically when redox changes were electrically uncompensated, and it interacts electrostatically with Glu(II)-62.
Conclusions:
- The explicit inclusion of a water molecule significantly alters the protonation state of Lys(I)-319, challenging previous assumptions.
- Lys(I)-319's protonation is sensitive to the redox state of the binuclear site, suggesting a dynamic role in proton transfer.
- These findings provide new insights into the mechanism of the K-pathway and its contribution to cytochrome c oxidase function.
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