Structural and functional studies of cytochrome c oxidase

Abstract

Cytochrome c oxidase (CcO) reduces oxygen with electrons passed down the electron transport chain and conserves the energy by pumping protons against the electrochemical potential across the membrane. A complete mechanism including the intramolecular electron transfer to the active center, the oxygen reduction chemistry and the coupled proton pumping remains to be revealed. This thesis set out to understand the structural nature of this enzyme under various conditions with the aid of spectroscopic methods.;We found a new protein conformational change that modulates the electron redistribution among the redox centers in the reversed electron transfer initiated by photodissociating the CO molecule from the CO-bound mixed-valence C cO. This conformational change involves the transition from a high energy P1 state, under which various metable species accumulate to a significant amount, to a relaxed P2 state, which destabilizes all the metable states with one-electron in the binuclear center. As a result, the redox equilibrium is perturbed, and the electrons are redistributed.;We also studied structural changes associated with the alkaline transition in both the ferric and ferrous states of CcO and clearly observed the Schiff base formation between formyl groups of both hemes and amino acid residues of the protein with hemes remaining in the protein matrix at pH 12.0. Time resolved pH jump spectra indicate the change of the ligation state of the hemes and the relative mobility of the nearby amino acids.;With an oxygen isotope experiment, we successfully proved that the O-O bond is broken in PCO/O2, which is a structural analog of P R, the reaction intermediate remaining to be determined.;In the mutagenesis studies, two conformers (the alpha/beta form) were detected in the ferrous CO adduct and were attributed to different active site conformations including the conformational change of the macrocycle of heme a3. The equilibrium between the conformers is very sensitive to the subtle structural changes over a wide range and some of this information is translated through a heme-to-heme communication. The structural features associated with each conformer are suggested to play functional roles in the catalytic cycle, such as delicately regulating the proton pumping.