title: Expanding the view of proton pumping in cytochrome c oxidase through computer simulation.
abstract: In cytochrome c oxidase (CcO), a redox-driven proton pump, protons are transported by the Grotthuss shuttling via hydrogen-bonded water molecules and protonatable residues. Proton transport through the D-pathway is a complicated process that is highly sensitive to alterations in the amino acids or the solvation structure in the channel, both of which can inhibit proton pumping and enzymatic activity. Simulations of proton transport in the hydrophobic cavity showed a clear redox state dependence. To study the mechanism of proton pumping in CcO, multi-state empirical valence bond (MS-EVB) simulations have been conducted, focusing on the proton transport through the D-pathway and the hydrophobic cavity next to the binuclear center. The hydration structures, transport pathways, effects of residues, and free energy surfaces of proton transport were revealed in these MS-EVB simulations. The mechanistic insight gained from them is herein reviewed and placed in context for future studies.
authors.affiliation: Department of Chemistry, University of Chicago, Chicago, IL, USA.
authors.forename: Yuxing
authors.initials: Y
authors.lastname: Peng
authors.forename: Gregory A
authors.initials: GA
authors.lastname: Voth
mesh_terms: D000465:Algorithms; D001426:Bacterial Proteins / Q000737:chemistry* / Q000378:metabolism; D001665:Binding Sites; D001692:Biological Transport; D003198:Computer Simulation; D018360:Crystallography, X-Ray; D003576:Electron Transport Complex IV / Q000737:chemistry* / Q000378:metabolism; D006418:Heme / Q000031:analogs & derivatives / Q000737:chemistry / Q000378:metabolism; D006860:Hydrogen Bonding; D057927:Hydrophobic and Hydrophilic Interactions; D007700:Kinetics; D008954:Models, Biological; D008958:Models, Molecular; D010084:Oxidation-Reduction; D017434:Protein Structure, Tertiary; D011522:Protons; D012196:Review Literature as Topic; D012242:Rhodobacter sphaeroides / Q000201:enzymology / Q000378:metabolism; D014867:Water / Q000737:chemistry / Q000378:metabolism
chemical_list: D001426:Bacterial Proteins; D011522:Protons; D014867:Water; C027728:heme a; D006418:Heme; D003576:Electron Transport Complex IV