Proton transfer in uncoupled variants of cytochrome c oxidase

Cytochrome c oxidase is a membrane‐bound redox‐driven proton pump that harbors two proton‐transfer pathways, D and K, which are used at different stages of the reaction cycle. Here, we address the question if a D pathway with a modified energy landscape for proton transfer could take over the role of the K pathway when the latter is blocked by a mutation. Our data indicate that structural alterations near the entrance of the D pathway modulate energy barriers that influence proton transfer to the proton‐loading site. The data also suggest that during reduction of the catalytic site, its protonation has to occur via the K pathway and that this proton transfer to the catalytic site cannot take place through the D pathway.

[1]  C. Hiser,et al.  The K-path entrance in cytochrome c oxidase is defined by mutation of E101 and controlled by an adjacent ligand binding domain. , 2018, Biochimica et biophysica acta. Bioenergetics.

[2]  K. Krab,et al.  Oxygen Activation and Energy Conservation by Cytochrome c Oxidase , 2018, Chemical reviews.

[3]  C. Hiser,et al.  Role of conformational change and K-path ligands in controlling cytochrome c oxidase activity. , 2017, Biochemical Society transactions.

[4]  M. Blomberg Mechanism of Oxygen Reduction in Cytochrome c Oxidase and the Role of the Active Site Tyrosine. , 2016, Biochemistry.

[5]  M. Blomberg,et al.  How cytochrome c oxidase can pump four protons per oxygen molecule at high electrochemical gradient. , 2015, Biochimica et biophysica acta.

[6]  Ville R. I. Kaila,et al.  New perspectives on proton pumping in cellular respiration. , 2015, Chemical reviews.

[7]  E. Knapp,et al.  Lysine 362 in cytochrome c oxidase regulates opening of the K-channel via changes in pKA and conformation. , 2014, Biochimica et biophysica acta.

[8]  R. Gennis,et al.  Proton pumping by an inactive structural variant of cytochrome c oxidase. , 2014, Journal of inorganic biochemistry.

[9]  M. Blomberg,et al.  Proton pumping in cytochrome c oxidase: energetic requirements and the role of two proton channels. , 2014, Biochimica et biophysica acta.

[10]  Per E M Siegbahn,et al.  Mutations in the D‐channel of cytochrome c oxidase causes leakage of the proton pump , 2014, FEBS letters.

[11]  P. Rich,et al.  Functions of the hydrophilic channels in protonmotive cytochrome c oxidase , 2013, Journal of The Royal Society Interface.

[12]  C. Hiser,et al.  Gating and regulation of the cytochrome c oxidase proton pump. , 2012, Biochimica et biophysica acta.

[13]  R. Gennis,et al.  Proton transfer in ba(3) cytochrome c oxidase from Thermus thermophilus. , 2012, Biochimica et biophysica acta.

[14]  M. Wikström,et al.  The D-channel of cytochrome oxidase: an alternative view. , 2011, Biochimica et biophysica acta.

[15]  E. Fadda,et al.  Molecular basis of proton uptake in single and double mutants of cytochrome c oxidase , 2011, Journal of physics. Condensed matter : an Institute of Physics journal.

[16]  A. Warshel,et al.  Exploration of the cytochrome c oxidase pathway puzzle and examination of the origin of elusive mutational effects. , 2011, Biochimica et biophysica acta.

[17]  L. Qin,et al.  Crystallographic and online spectral evidence for role of conformational change and conserved water in cytochrome oxidase proton pump , 2011, Proceedings of the National Academy of Sciences.

[18]  Ville R. I. Kaila,et al.  Proton-coupled electron transfer in cytochrome oxidase. , 2010, Chemical reviews.

[19]  A. Stuchebrukhov,et al.  Similarity of cytochrome c oxidases in different organisms , 2010, Proteins.

[20]  A. Johansson,et al.  Variable proton-pumping stoichiometry in structural variants of cytochrome c oxidase. , 2010, Biochimica et biophysica acta.

[21]  B. Ludwig,et al.  Electron transfer and energy transduction in the terminal part of the respiratory chain - lessons from bacterial model systems. , 2009, Biochimica et biophysica acta.

[22]  R. Pomès,et al.  Functional hydration and conformational gating of proton uptake in cytochrome c oxidase. , 2009, Journal of molecular biology.

[23]  J. Koepke,et al.  A D-pathway mutation decouples the Paracoccus denitrificans cytochrome c oxidase by altering the side-chain orientation of a distant conserved glutamate. , 2008, Journal of molecular biology.

[24]  R. Gennis,et al.  Cytochrome c oxidase: exciting progress and remaining mysteries , 2008, Journal of bioenergetics and biomembranes.

[25]  M. Wikström,et al.  The proton donor for OO bond scission by cytochrome c oxidase , 2008, Proceedings of the National Academy of Sciences.

[26]  R. Gennis,et al.  Impaired proton pumping in cytochrome c oxidase upon structural alteration of the D pathway. , 2008, Biochimica et biophysica acta.

[27]  Ville R. I. Kaila,et al.  Glutamic acid 242 is a valve in the proton pump of cytochrome c oxidase , 2008, Proceedings of the National Academy of Sciences.

[28]  P. Brzezinski,et al.  Charge transfer in the K proton pathway linked to electron transfer to the catalytic site in cytochrome c oxidase. , 2008, Biochemistry.

[29]  I. Belevich,et al.  Molecular mechanism of proton translocation by cytochrome c oxidase. , 2008, Antioxidants & redox signaling.

[30]  M. Wikström,et al.  The K-pathway revisited: a computational study on cytochrome c oxidase. , 2006, Biochimica et biophysica acta.

[31]  S. Yoshikawa,et al.  Proton pumping mechanism of bovine heart cytochrome c oxidase. , 2006, Biochimica et biophysica acta.

[32]  S. Ferguson-Miller,et al.  Energy transduction: proton transfer through the respiratory complexes. , 2006, Annual review of biochemistry.

[33]  T. Soulimane,et al.  ba3‐Cytochrome c Oxidase From Thermus Thermophilus , 2006 .

[34]  P. Brzezinski,et al.  Structural elements involved in electron‐coupled proton transfer in cytochrome c oxidase , 2004, FEBS letters.

[35]  A. Stuchebrukhov,et al.  Proton pumping mechanism and catalytic cycle of cytochrome c oxidase: Coulomb pump model with kinetic gating , 2004, FEBS letters.

[36]  R. Gennis,et al.  Redox-coupled proton translocation in biological systems: Proton shuttling in cytochrome c oxidase , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[37]  P. Brzezinski,et al.  Redox-driven proton pumping by heme-copper oxidases. , 2003, Biochimica et biophysica acta.

[38]  G. Hummer,et al.  Water-gated mechanism of proton translocation by cytochrome c oxidase. , 2003, Biochimica et biophysica acta.

[39]  J. Swanson,et al.  Computer simulation of water in cytochrome c oxidase. , 2003, Biochimica et biophysica acta.

[40]  R. Gennis,et al.  A mutation in subunit I of cytochrome oxidase from Rhodobacter sphaeroides results in an increase in steady-state activity but completely eliminates proton pumping. , 2002, Biochemistry.

[41]  P. Brzezinski,et al.  Zinc ions inhibit oxidation of cytochrome c oxidase by oxygen , 2001, FEBS letters.

[42]  R. Gennis,et al.  On the role of the K-proton transfer pathway in cytochrome c oxidase , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[43]  A. Puustinen,et al.  The role of the D- and K-pathways of proton transfer in the function of the haem-copper oxidases. , 2000, Biochimica et biophysica acta.

[44]  E. Bamberg,et al.  Tracing the D-pathway in reconstituted site-directed mutants of cytochrome c oxidase from Paracoccus denitrificans. , 2000, Biochemistry.

[45]  L. Florens,et al.  Where is 'outside' in cytochrome c oxidase and how and when do protons get there? , 2000, Biochimica et biophysica acta.

[46]  E. Bamberg,et al.  Single-electron reduction of the oxidized state is coupled to proton uptake via the K pathway in Paracoccus denitrificans cytochrome c oxidase. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[47]  H. Michel,et al.  Functional properties of the heme propionates in cytochrome c oxidase from Paracoccus denitrificans. Evidence from FTIR difference spectroscopy and site-directed mutagenesis. , 2000, Biochemistry.

[48]  R. Gennis,et al.  Aspartate-132 in cytochrome c oxidase from Rhodobacter sphaeroides is involved in a two-step proton transfer during oxo-ferryl formation. , 1999, Biochemistry.

[49]  N. Fisher,et al.  Effects of mutation of the conserved glutamic acid-286 in subunit I of cytochrome c oxidase from Rhodobacter sphaeroides. , 1999, Biochemistry.

[50]  H. Michel,et al.  The mechanism of proton pumping by cytochrome c oxidasex127e [comments]. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[51]  S. Ferguson-Miller,et al.  Overexpression and purification of cytochrome c oxidase from Rhodobacter sphaeroides. , 1998, Protein expression and purification.

[52]  G. Hummer,et al.  Structure and dynamics of a proton shuttle in cytochrome c oxidase , 1998 .

[53]  R. Gennis,et al.  Mechanism of inhibition of electron transfer by amino acid replacement K362M in a proton channel of Rhodobacter sphaeroides cytochrome c oxidase. , 1998, Biochemistry.

[54]  R. Gennis,et al.  Role of the pathway through K(I-362) in proton transfer in cytochrome c oxidase from R. sphaeroides. , 1998, Biochemistry.

[55]  P. Brzezinski,et al.  Pathways of Proton Transfer in Cytochrome c Oxidase , 1998, Journal of bioenergetics and biomembranes.

[56]  G. Hummer,et al.  Bound water in the proton translocation mechanism of the haem‐copper oxidases , 1997, FEBS letters.

[57]  R. Gennis,et al.  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. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[58]  P. Brzezinski,et al.  Kinetic coupling between electron and proton transfer in cytochrome c oxidase: simultaneous measurements of conductance and absorbance changes. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[59]  R. Gennis,et al.  Polar residues in helix VIII of subunit I of cytochrome c oxidase influence the activity and the structure of the active site. , 1996, Biochemistry.

[60]  R. Gennis,et al.  Rapid purification of wildtype and mutant cytochrome c oxidase from Rhodobacter sphaeroides by Ni2+‐NTA affinity chromatography , 1995, FEBS letters.

[61]  R. Gennis,et al.  Possible proton relay pathways in cytochrome c oxidase. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[62]  D. Kobayashi,et al.  Improved broad-host-range plasmids for DNA cloning in gram-negative bacteria. , 1988, Gene.

[63]  P. Brzezinski,et al.  The reduction of cytochrome c oxidase by carbon monoxide , 1985, FEBS letters.

[64]  W. Vanneste The stoichiometry and absorption spectra of components a and a-3 in cytochrome c oxidase. , 1966, Biochemistry.