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Toward a Chemical Mechanism of Proton Pumping by the B-Type Cytochrome c Oxidases: Application of Density Functional Theory to Cytochrome ba3 of Thermus thermophilus

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posted on 12.11.2008, 00:00 by James A. Fee, David A. Case, Louis Noodleman
A mechanism for proton pumping by the B-type cytochrome c oxidases is presented in which one proton is pumped in conjunction with the weakly exergonic, two-electron reduction of Fe-bound O2 to the Fe−Cu bridging peroxodianion and three protons are pumped in conjunction with the highly exergonic, two-electron reduction of Fe(III)−O−O−Cu(II) to form water and the active oxidized enzyme, Fe(III)−OH,Cu(II). The scheme is based on the active-site structure of cytochrome ba3 from Thermus thermophilus, which is considered to be both necessary and sufficient for coupled O2 reduction and proton pumping when appropriate gates are in place (not included in the model). Fourteen detailed structures obtained from density functional theory (DFT) geometry optimization are presented that are reasonably thought to occur during the four-electron reduction of O2. Each proton-pumping step takes place when a proton resides on the imidazole ring of I-His376 and the large active-site cluster has a net charge of +1 due to an uncompensated, positive charge formally associated with CuB. Four types of DFT were applied to determine the energy of each intermediate, and standard thermochemical approaches were used to obtain the reaction free energies for each step in the catalytic cycle. This application of DFT generally conforms with previously suggested criteria for a valid model (Siegbahn, P. E. M.; Blomberg, M. A. R. Chem. Rev. 2000, 100, 421−437) and shows how the chemistry of O2 reduction in the heme a3−CuB dinuclear center can be harnessed to generate an electrochemical proton gradient across the lipid bilayer.