Electronation-dependent structural change at the proton exit side of cytochrome c oxidase as revealed by site-directed fluorescence labeling.
conformational change
cytochrome c oxidase
fluorescence spectroscopy
hydration
site-directed fluorescence labeling
Journal
The FEBS journal
ISSN: 1742-4658
Titre abrégé: FEBS J
Pays: England
ID NLM: 101229646
Informations de publication
Date de publication:
03 2020
03 2020
Historique:
received:
05
07
2019
revised:
17
08
2019
accepted:
04
10
2019
pubmed:
10
10
2019
medline:
20
1
2021
entrez:
10
10
2019
Statut:
ppublish
Résumé
Cytochrome c oxidase (CcO), the terminal enzyme of the respiratory chain of mitochondria and many aerobic prokaryotes that function as a redox-coupled proton pump, catalyzes the reduction of molecular oxygen to water. As part of the respiratory chain, CcO contributes to the proton motive force driving ATP synthesis. While many aspects of the enzyme's catalytic mechanisms have been established, a clear picture of the proton exit pathway(s) remains elusive. Here, we aim to gain insight into the molecular mechanisms of CcO through the development of a new homologous mutagenesis/expression system in Paracoccus denitrificans, which allows mutagenesis of CcO subunits 1, 2, and 3. Our system provides true single thiol-reactive CcO variants in a three-subunit base variant with unique labeling sites for the covalent attachment of reporter groups sensitive to nanoenvironmental factors like protonation, polarity, and hydration. To this end, we exchanged six residues on both membrane sides of CcO for cysteines. We show redox-dependent wetting changes at the proton uptake channel and increased polarity at the proton exit side of CcO upon electronation. We suggest an electronation-dependent conformational change to play a role in proton exit from CcO.
Substances chimiques
Protons
0
Adenosine Triphosphate
8L70Q75FXE
Electron Transport Complex IV
EC 1.9.3.1
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
1232-1246Informations de copyright
© 2019 Federation of European Biochemical Societies.
Références
Brzezinski P & Gennis RB (2008) Cytochrome c oxidase: exciting progress and remaining mysteries. J Bioenerg Biomembr 40, 521-531.
Koepke J, Olkhova E, Angerer H, Muller H, Peng G & Michel H (2009) High resolution crystal structure of Paracoccus denitrificans cytochrome c oxidase: new insights into the active site and the proton transfer pathways. Biochim Biophys Acta 1787, 635-645.
Rak M, Benit P, Chretien D, Bouchereau J, Schiff M, El-Khoury R, Tzagoloff A & Rustin P (2016) Mitochondrial cytochrome c oxidase deficiency. Clin Sci 130, 393-407.
Arnold S (2012) Cytochrome c oxidase and its role in neurodegeneration and neuroprotection. Adv Exp Med Biol 748, 305-339.
Timon-Gomez A, Nyvltova E, Abriata LA, Vila AJ, Hosler J & Barrientos A (2018) Mitochondrial cytochrome c oxidase biogenesis: Recent developments. Semin Cell Dev Biol 76, 163-178.
Nicoletti F, Witt H, Ludwig B, Brunori M & Malatesta F (1998) Paracoccus denitrificans cytochrome c oxidase: a kinetic study on the two- and four-subunit complexes. Biochim Biophys Acta Bioenerg 1365, 393-403.
Solioz M, Carafoli E & Ludwig B (1982) The cytochrome-c oxidase of Paracoccus denitrificans pumps protons in a reconstituted system. J Biol Chem 257, 1579-1582.
Iwata S, Ostermeier C, Ludwig B & Michel H (1995) Structure at 2.8-angstrom resolution of cytochrome-c-oxidase from Paracoccus denitrificans. Nature 376, 660-669.
Michel H (1999) Cytochrome c oxidase: catalytic cycle and mechanisms of proton pumping-A discussion. Biochemistry 38, 15129-15140.
Kaila VR, Verkhovsky MI & Wikstrom M (2010) Proton-coupled electron transfer in cytochrome oxidase. Chem Rev 110, 7062-7081.
Konstantinov AA, Siletsky S, Mitchell D, Kaulen A & Gennis RB (1997) The roles of the two proton input channels in cytochrome c oxidase from Rhodobacter sphaeroides probed by the effects of site-directed mutations on time-resolved electrogenic intraprotein proton transfer. Proc Natl Acad Sci USA 94, 9085-9090.
Belevich I, Verkhovsky MI & Wikstrom M (2006) Proton-coupled electron transfer drives the proton pump of cytochrome c oxidase. Nature 440, 829-832.
Supekar S, Gamiz-Hernandez AP & Kaila VRI (2016) A protonated water cluster as a transient proton-loading site in cytochrome c oxidase. Angew Chem Int Ed Engl 55, 11940-11944.
Schmidt B, McCracken J & Ferguson-Miller S (2003) A discrete water exit pathway in the membrane protein cytochrome c oxidase. Proc Natl Acad Sci USA 100, 15539-15542.
Sharpe MA, Krzyaniak MD, Xu SJ, McCracken J & Ferguson-Miller S (2009) EPR evidence of cyanide binding to the Mn(Mg) center of cytochrome c oxidase: support for Cu-A-Mg involvement in proton pumping. Biochemistry 48, 328-335.
Mills DA, Tan Z, Ferguson-Miller S & Hosler J (2003) A role for subunit III in proton uptake into the D pathway and a possible proton exit pathway in Rhodobacter sphaeroides cytochrome c oxidase. Biochemistry 42, 7410-7417.
Popovic DM & Stuchebrukhov AA (2005) Proton exit channels in bovine cytochrome c oxidase. J Phys Chem B 109, 1999-2006.
Sugitani R & Stuchebrukhov AA (2009) Molecular dynamics simulation of water in cytochrome c oxidase reveals two water exit pathways and the mechanism of transport. Biochim Biophys Acta Bioenerg 1787, 1140-1150.
Kirchberg K, Michel H & Alexiev U (2012) Net proton uptake is preceded by multiple proton transfer steps upon electron injection into cytochrome c oxidase. J Biol Chem 287, 8187-8193.
Son CY, Yethiraj A & Cui Q (2017) Cavity hydration dynamics in cytochrome c oxidase and functional implications. Proc Natl Acad Sci USA 114, E8830-E8836.
Woelke AL, Galstyan G & Knapp EW (2014) Lysine 362 in cytochrome c oxidase regulates opening of the K-channel via changes in pKa and conformation. Biochim Biophys Acta Bioenerg 1837, 1998-2003.
Witt H, Zickermann V & Ludwig B (1995) Site-directed mutagenesis of cytochrome-C-Oxidase reveals 2 acidic residues involved in the binding of cytochrome-C. Biochim Biophys Acta Bioenerg 1230, 74-76.
Kirchberg K, Michel H & Alexiev U (2013) Exploring the entrance of proton pathways in cytochrome c oxidase from Paracoccus denitrificans: Surface charge, buffer capacity and redox-dependent polarity changes at the internal surface. Biochim Biophys Acta Bioenerg 1827, 276-284.
Hilbers F, von der Hocht I, Ludwig B & Michel H (2013) True wild type and recombinant wild type cytochrome c oxidase from Paracoccus denitrificans show a 20-fold difference in their catalase activity. Biochim Biophys Acta Bioenerg 1827, 319-327.
de Gier JWL, Lubben M, Reijnders WNM, Tipker CA, Slotboom DJ, Vanspanning RJM, Stouthamer AH & Vanderoost J (1994) The terminal oxidases of Paracoccus denitrificans. Mol Microbiol 13, 183-196.
Schimo S, Wittig I, Pos KM & Ludwig B (2017) Cytochrome c oxidase biogenesis and metallochaperone interactions: steps in the assembly pathway of a bacterial complex. PLoS ONE 12, e0170037.
Bundschuh FA, Hoffmeier K & Ludwig B (2008) Two variants of the assembly factor Surf1 target specific terminal oxidases in Paracoccus denitrificans. Biochim Biophys Acta 1777, 1336-1343.
Dash BP, Alles M, Bundschuh FA, Richter OH & Ludwig B (2015) Protein chaperones mediating copper insertion into the CuA site of the aa3-type cytochrome c oxidase of Paracoccus denitrificans. Biochim Biophys Acta 1847, 202-211.
de Vries GE, Harms N, Hoogendijk J & Stouthamer AH (1989) Isolation and characterization of Paracoccus denitrificans mutants with increased conjugation frequencies and pleiotropic loss of a (Ngatcn) DNA-modifying property. Arch Microbiol 152, 52-57.
Goodhew CF, Pettigrew GW, Devreese B, VanBeeumen J, VanSpanning RJM, Baker SC, Saunders N, Ferguson SJ & Thompson IP (1996) The cytochromes c-550 of Paracoccus denitrificans and Thiosphaera pantotropha: a need for re-evaluation of the history of Paracoccus cultures. FEMS Microbiol Lett 137, 95-101.
Raitio M, Jalli T & Saraste M (1987) Isolation and analysis of the genes for cytochrome-c-oxidase in Paracoccus denitrificans. EMBO J 6, 2825-2833.
Raitio M & Wikstrom M (1994) An alternative cytochrome-oxidase of Paracoccus-denitrificans functions as a proton pump. Biochim Biophys Acta Bioenerg 1186, 100-106.
Boja ES & Fales HM (2001) Overalkylation of a protein digest with iodoacetamide. Anal Chem 73, 3576-3582.
Witt H, Malatesta F, Nicoletti F, Brunori M & Ludwig B (1998) Tryptophan 121 of subunit II is the electron entry site to cytochrome-c oxidase in Paracoccus denitrificans - Involvement of a hydrophobic patch in the docking reaction. J Biol Chem 273, 5132-5136.
Shimada S, Shinzawa-Itoh K, Baba J, Aoe S, Shimada A, Yamashita E, Kang JY, Tateno M, Yoshikawa S & Tsukihara T (2017) Complex structure of cytochrome c-cytochrome c oxidase reveals a novel protein-protein interaction mode. EMBO J 36, 291-300.
Owenius R, Osterlund M, Lindgren M, Svensson M, Olsen OH, Persson E, Freskgard PO & Carlsson U (1999) Properties of spin and fluorescent labels at a receptor-ligand interface. Biophys J 77, 2237-2250.
Fischermeier E, Pospisil P, Sayed A, Hof M, Solioz M & Fahmy K (2017) Dipolar relaxation dynamics at the active site of an ATPase regulated by membrane lateral pressure. Angew Chem Int Ed Engl 56, 1269-1272.
Alexiev U, Marti T, Heyn MP, Khorana HG & Scherrer P (1994) Covalently bound Ph-indicator dyes at selected extracellular or cytoplasmic sites in bacteriorhodopsin. 2. Rotational orientation of helix-D and helix-E and kinetic correlation between M-formation and proton release in bacteriorhodopsin micelles. Biochemistry 33, 13693-13699.
Klonis N & Sawyer WH (1996) Spectral properties of the prototropic forms of fluorescein in aqueous solution. J Fluoresc 6, 147-157.
Koehorst RBM, Spruijt RB & Hemminga MA (2008) Site-directed fluorescence labeling of a membrane protein with BADAN: probing protein topology and local environment. Biophys J 94, 3945-3955.
Wolf A, Schneider C, Kim TY, Kirchberg K, Volz P & Alexiev U (2016) A simulation-guided fluorescence correlation spectroscopy tool to investigate the protonation dynamics of cytochrome c oxidase. Phys Chem Chem Phys 18, 12877-12885.
Chandran K, Aggarwal D, Migrino RQ, Joseph J, McAllister D, Konorev EA, Antholine WE, Zielonka J, Srinivasan S, Avadhani NG et al. (2009) Doxorubicin inactivates myocardial cytochrome c oxidase in rats: cardioprotection by Mito-Q. Biophys J 96, 1388-1398.
Balke J, Volz P, Neumann F, Brodwolf R, Wolf A, Pischon H, Radbruch M, Mundhenk L, Gruber AD, Ma N et al. (2018) Visualizing oxidative cellular stress induced by nanoparticles in the subcytotoxic range using fluorescence lifetime imaging. Small 14, e1800310.
Gibson DG, Young L, Chuang RY, Venter JC, Hutchison CA & Smith HO (2009) Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat Methods 6, 343-345.
Ludwig B (1986) Cytochrome c oxidase from Paracoccus denitrificans. Methods Enzymol 126, 153-159.
Margoliash E & Frohwirt N (1959) Spectrum of horse-heart cytochrome c. Biochem J 71, 570-572.
Wikstrom M & Sharma V (2018) Proton pumping by cytochrome c oxidase - A 40 year anniversary. Biochim Biophys Acta Bioenerg 1859, 692-698.