The Proton Translocation Mechanisms of the Cytochrome bo₃-Type Ubiquinol Oxidase Complex and the Mitochondrial Cytochrome c Oxidase Complex

Every organism contains a respiratory chain that enables it to convert the energy obtained from food molecules into adenosine triphosphate (ATP), the universal energy currency which drives a multitude of life-giving biochemical reactions. A typical respiratory chain contains a series of integral membrane protein complexes that produce a transmembrane proton gradient as a result of sequential electron transfers through these complexes. The energy stored in this proton gradient, a biological battery, is utilized to synthesize ATP. In the oxygenic respiratory process functioning in mitochondria, dioxygen is fully reduced to water by the cytochrome c oxidase (CcO) complex. This molecular machine couples the highly exergonic reduction of dioxygen to the pumping of protons against a transmembrane electrochemical gradient. Another structurally similar enzyme, the cytochrome bo3 complex from Escherichia coli, catalyzes the reduction of dioxygen to water using the same heme-copper dioxygen activating site and also catalyzes the translocation of protons. However, whereas the electron donor for the CcO complex is the water-soluble one-electron carrier cytochrome c, two-electron-donating ubiquinol molecules within the lipid bilayer input electrons into the cytochrome bo3 complex. The dramatically different electron input mechanisms dictated by these electron-donating substrates led to the hypothesis that the proton translocation machineries for these two terminal oxidases are completely disparate. Based on the available data, it is concluded that the cytochrome bo3 complex translocates protons via a quinone(quinol)-loop (Q(H2)-loop) mechanism. In a Q(H2)-loop proton translocation mechanism, proton uptake/release follows electron input to/output from two Q(H2) binding sites and protein conformational cycling is not required. On the other hand, the more complicated redox-linked proton pump of the CcO complex functions by forcing protons through the protein matrix as a result of a series of conformational rearrangements and is successful only through careful control of both electron and proton transfer reactions. This thesis focuses on deciphering the proton translocation capabilities of these two enzymes and contrasts the simplicity of a Q(H2)-loop mechanism with the more evolutionarily advanced CcO proton pump.