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Cytochrome c oxidase (CcO) is the terminal enzyme in the respiratory electron transport chain of aerobic organisms. It is a redox-driven proton pump that converts atmospheric oxygen to water and couples the oxygen reduction, generating a membrane proton gradient that subsequently drives ATP synthesis. The function of CcO as a biomolecular nanomachine that transforms the energy of redox reaction into protonmotive force across a biological membrane has been the subject of intense research, debate, and controversy. For a long time, the molecular mechanism of electron transfer coupled to proton pumping in CcO has been one of the central unsolved problems in biochemistry, molecular biology, and bioenergetics. The enzyme structure has been solved for several organisms; however, details of its molecular mechanism of proton pumping still remain elusive. Mainly, the nature and position of the proton-loading site, a key element of the mechanism, are under dispute. However, nowadays, many essential details and principles have emerged with the accelerating progress in this field. Recent calculations indicate that one of the histidine ligands of the CuB center, His291, may play the role of the pumping element. In this chapter, we review the first principles calculation used to study models of the catalytic center of CcO and calculate the pKa of the His291 residue for both the reduced and oxidized states of the enzyme catalytic center. The combined density functional theory (DFT) and continuum electrostatic calculations (QM/CE method) are employed to explore the coupling of the conformational changes of Glu242 residue, the primary proton donor of both chemical and pump protons, to its pKa, and the pKa of His291, a putative proton-loading site of the pumping model. The pKa values of His291 and Glu242, the two crucial residues of the model, are calculated for different redox states of the enzyme, and the influence of various factors on the pKas is analyzed in detail. To understand how different factors affect the apparent pKa values of His291 and Glu242, we have considered several computational QM/CE models of the membrane‒enzyme‒cavities‒solvent system and tested different dielectric properties of the water-filled cavities. In addition, the DFT is applied to two different sizes of quantum-mechanical (QM) systems of interest. We also review the structure and function of CcO, describe the proposed mechanism of proton pumping, identify the fundamental problems that can be addressed computationally in this area and describe the methods for their solution. The outstanding theoretical and computational challenges of the area are also discussed.
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Keywords: bioenergetics, heme-copper oxidases, nitric-oxide reductase, copper center, heme, binuclear complex, histidine ligand, bovine, proton pumping, molecular mechanism, redox-coupled pKa, pKa calculations, DFT, reaction and protein field.
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