| Abstract
| - Cytochrome c oxidase is a redox-driven proton pump that creates a membrane proton gradient responsiblefor driving ATP synthesis in aerobic cells. The crystal structure of the enzyme has been recently solved;however, the details of the mechanism of its proton pumping remain unknown. The enzyme internal watermolecules play a key role in proton translocation through the enzyme. Here, we examine the thermodynamicproperties of internal water in a hydrophobic cavity around the catalytic center of the enzyme. The crystalstructure does not show any water molecules in this region; it is believed, however, that, since protons aredelivered to the catalytic center, where the reduction of molecular oxygen occurs, at least some water moleculesmust be present there. The goal of the present study was to examine how many water molecules are presentin the catalytic center cavity and why these water molecules are not observed in the crystal structure of theenzyme. The behavior of water molecules is discussed in the context of redox-coupled proton translocationin the enzyme.
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