title: Linking chemical electron-proton transfer to proton pumping in cytochrome c oxidase: broken-symmetry DFT exploration of intermediates along the catalytic reaction pathway of the iron-copper dinuclear complex.
abstract: After a summary of the problem of coupling electron and proton transfer to proton pumping in cytochrome c oxidase, we present the results of our earlier and recent density functional theory calculations for the dinuclear Fe-a3-CuB reaction center in this enzyme. A specific catalytic reaction wheel diagram is constructed from the calculations, based on the structures and relative energies of the intermediate states of the reaction cycle. A larger family of tautomers/protonation states is generated compared to our earlier work, and a new lowest-energy pathway is proposed. The entire reaction cycle is calculated for the new smaller model (about 185-190 atoms), and two selected arcs of the wheel are chosen for calculations using a larger model (about 205 atoms). We compare the structural and redox energetics and protonation calculations with available experimental data. The reaction cycle map that we have built is positioned for further improvement and testing against experiment.
authors: Department of Integrative Structural and Computational Biology, The Scripps Research Institute , 10550 North Torrey Pines Road, TPC15, La Jolla, California 92037, United States.
authors: Louis
authors: L
authors: Noodleman
authors: Wen-Ge
authors: WG
authors: Han Du
authors: James A
authors: JA
authors: Fee
authors: Andreas W
authors: AW
authors: Götz
authors: Ross C
authors: RC
authors: Walker
mesh_terms: D000255:Adenosine Triphosphate / Q000096:biosynthesis; D001419:Bacteria / Q000201:enzymology; D002384:Catalysis; D003300:Copper / Q000737:chemistry*; D004579:Electron Transport; D003576:Electron Transport Complex IV / Q000737:chemistry*; D007501:Iron / Q000737:chemistry*; D008958:Models, Molecular; D010100:Oxygen / Q000737:chemistry; D017494:Proton Pumps / Q000737:chemistry*; D016963:Thermus thermophilus / Q000201:enzymology
chemical_list: D017494:Proton Pumps; D003300:Copper; D000255:Adenosine Triphosphate; D007501:Iron; D003576:Electron Transport Complex IV; D010100:Oxygen