Cytochrome c oxidase is the final electron acceptor in the respiratory chain and catalyzes the highly exergonic oxygen reduction reaction to water and forms a transmembrane electrochemical proton gradient. This transmembrane gradient is used by ATP synthase to produce ATP. The oxygen chemistry reaction of the enzyme is coupled to a proton pump, which substantially contributes to the transmembrane electrochemical gradient. Two proton entry pathways, D pathway and K pathway, have been resolved in X-ray crystal structures. But the exit pathway for the pumped proton and its mechanism is not well understood. The work in this thesis presents extensive studies in proton translocation in both the D-pathway and putative exit pathway. The mutations in the highly conserved R481 confirmed that the residue itself and the hydrogen bonds it forms with the heme propionates are not critical for proton pumping ability and the environmental changes of the hemes were detected on the R481 mutant oxidases. The putative exit pathway is very complicated to define due to the network of many water molecules and hydrophilic residues in the area. But clearly, changing the charge status in some of the residues in putative exit pathway affected the function of the oxidases and the environment of hemes. The D-pathway proton translocation study reveals that the waters do not necessarily need to be hydrogen-bonded to conserved serines in the middle of the pathway. However, the serine mutations caused changes in the pKa of E286 (branch point for substrate proton and pumped proton), which led to the conclusion that the pKa of E286 is not directly related to proton pumping ability.
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The study of aa3-type cytochrome c oxidase in Rhodobacter sphaeroides
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