1v54 Citations

The low-spin heme of cytochrome c oxidase as the driving element of the proton-pumping process.

Abstract

Mitochondrial cytochrome c oxidase plays an essential role in aerobic cellular respiration, reducing dioxygen to water in a process coupled with the pumping of protons across the mitochondrial inner membrane. An aspartate residue, Asp-51, located near the enzyme surface, undergoes a redox-coupled x-ray structural change, which is suggestive of a role for this residue in redox-driven proton pumping. However, functional or mechanistic evidence for the involvement of this residue in proton pumping has not yet been obtained. We report that the Asp-51 --> Asn mutation of the bovine enzyme abolishes its proton-pumping function without impairment of the dioxygen reduction activity. Improved x-ray structures (at 1.8/1.9-A resolution in the fully oxidized/reduced states) show that the net positive charge created upon oxidation of the low-spin heme of the enzyme drives the active proton transport from the interior of the mitochondria to Asp-51 across the enzyme via a water channel and a hydrogen-bond network, located in tandem, and that the enzyme reduction induces proton ejection from the aspartate to the mitochondrial exterior. A peptide bond in the hydrogen-bond network critically inhibits reverse proton transfer through the network. A redox-coupled change in the capacity of the water channel, induced by the hydroxyfarnesylethyl group of the low-spin heme, suggests that the channel functions as an effective proton-collecting region. Infrared results indicate that the conformation of Asp-51 is controlled only by the oxidation state of the low-spin heme. These results indicate that the low-spin heme drives the proton-pumping process.

Reviews - 1v54 mentioned but not cited (11)

  1. Copper active sites in biology. Solomon EI, Heppner DE, Johnston EM, Ginsbach JW, Cirera J, Qayyum M, Kieber-Emmons MT, Kjaergaard CH, Hadt RG, Tian L. Chem Rev 114 3659-3853 (2014)
  2. Cardiac mitochondrial matrix and respiratory complex protein phosphorylation. Covian R, Balaban RS. Am J Physiol Heart Circ Physiol 303 H940-66 (2012)
  3. Mitochondria-targeted disruptors and inhibitors of cytochrome c/cardiolipin peroxidase complexes: a new strategy in anti-apoptotic drug discovery. Kagan VE, Bayir A, Bayir H, Stoyanovsky D, Borisenko GG, Tyurina YY, Wipf P, Atkinson J, Greenberger JS, Chapkin RS, Belikova NA. Mol Nutr Food Res 53 104-114 (2009)
  4. Darwin at the molecular scale: selection and variance in electron tunnelling proteins including cytochrome c oxidase. Moser CC, Page CC, Dutton PL. Philos Trans R Soc Lond B Biol Sci 361 1295-1305 (2006)
  5. Functions of the hydrophilic channels in protonmotive cytochrome c oxidase. Rich PR, Maréchal A. J R Soc Interface 10 20130183 (2013)
  6. Yeast cytochrome c oxidase: a model system to study mitochondrial forms of the haem-copper oxidase superfamily. Maréchal A, Meunier B, Lee D, Orengo C, Rich PR. Biochim Biophys Acta 1817 620-628 (2012)
  7. Molecular and Supramolecular Structure of the Mitochondrial Oxidative Phosphorylation System: Implications for Pathology. Nesci S, Trombetti F, Pagliarani A, Ventrella V, Algieri C, Tioli G, Lenaz G. Life (Basel) 11 242 (2021)
  8. Maturation of the respiratory complex II flavoprotein. Sharma P, Maklashina E, Cecchini G, Iverson TM. Curr Opin Struct Biol 59 38-46 (2019)
  9. Carbon Monoxide Signaling: Examining Its Engagement with Various Molecular Targets in the Context of Binding Affinity, Concentration, and Biologic Response. Yuan Z, De La Cruz LK, Yang X, Wang B. Pharmacol Rev 74 823-873 (2022)
  10. Recent progress in experimental studies on the catalytic mechanism of cytochrome c oxidase. Shimada A, Tsukihara T, Yoshikawa S. Front Chem 11 1108190 (2023)
  11. Cytochrome c Oxidase at Full Thrust: Regulation and Biological Consequences to Flying Insects. Mesquita RD, Gaviraghi A, Gonçalves RLS, Vannier-Santos MA, Mignaco JA, Fontes CFL, Machado LESF, Oliveira MF. Cells 10 470 (2021)

Articles - 1v54 mentioned but not cited (78)

  1. The low-spin heme of cytochrome c oxidase as the driving element of the proton-pumping process. Tsukihara T, Shimokata K, Katayama Y, Shimada H, Muramoto K, Aoyama H, Mochizuki M, Shinzawa-Itoh K, Yamashita E, Yao M, Ishimura Y, Yoshikawa S. Proc Natl Acad Sci U S A 100 15304-15309 (2003)
  2. The adaptive evolution of the mammalian mitochondrial genome. da Fonseca RR, Johnson WE, O'Brien SJ, Ramos MJ, Antunes A. BMC Genomics 9 119 (2008)
  3. Identification of conserved lipid/detergent-binding sites in a high-resolution structure of the membrane protein cytochrome c oxidase. Qin L, Hiser C, Mulichak A, Garavito RM, Ferguson-Miller S. Proc Natl Acad Sci U S A 103 16117-16122 (2006)
  4. Drug off-target effects predicted using structural analysis in the context of a metabolic network model. Chang RL, Xie L, Xie L, Bourne PE, Palsson BØ. PLoS Comput Biol 6 e1000938 (2010)
  5. Exploring the proton pump mechanism of cytochrome c oxidase in real time. Belevich I, Bloch DA, Belevich N, Wikström M, Verkhovsky MI. Proc Natl Acad Sci U S A 104 2685-2690 (2007)
  6. Multiscale Simulations of Biological Membranes: The Challenge To Understand Biological Phenomena in a Living Substance. Enkavi G, Javanainen M, Kulig W, Róg T, Vattulainen I. Chem Rev 119 5607-5774 (2019)
  7. Adaptive antioxidant methionine accumulation in respiratory chain complexes explains the use of a deviant genetic code in mitochondria. Bender A, Hajieva P, Moosmann B. Proc Natl Acad Sci U S A 105 16496-16501 (2008)
  8. Glutamic acid 242 is a valve in the proton pump of cytochrome c oxidase. Kaila VR, Verkhovsky MI, Hummer G, Wikström M. Proc Natl Acad Sci U S A 105 6255-6259 (2008)
  9. Structure of yeast cytochrome c oxidase in a supercomplex with cytochrome bc1. Hartley AM, Lukoyanova N, Zhang Y, Cabrera-Orefice A, Arnold S, Meunier B, Pinotsis N, Maréchal A. Nat Struct Mol Biol 26 78-83 (2019)
  10. Structural insights into electron transfer in caa3-type cytochrome oxidase. Lyons JA, Aragão D, Slattery O, Pisliakov AV, Soulimane T, Caffrey M. Nature 487 514-518 (2012)
  11. The identification of mitochondrial DNA variants in glioblastoma multiforme. Yeung KY, Dickinson A, Donoghue JF, Polekhina G, White SJ, Grammatopoulos DK, McKenzie M, Johns TG, St John JC. Acta Neuropathol Commun 2 1 (2014)
  12. The elusive nature of adaptive mitochondrial DNA evolution of an arctic lineage prone to frequent introgression. Melo-Ferreira J, Vilela J, Fonseca MM, da Fonseca RR, Boursot P, Alves PC. Genome Biol Evol 6 886-896 (2014)
  13. Knowledge-based potential for positioning membrane-associated structures and assessing residue-specific energetic contributions. Schramm CA, Hannigan BT, Donald JE, Keasar C, Saven JG, Degrado WF, Samish I. Structure 20 924-935 (2012)
  14. A designed functional metalloenzyme that reduces O2 to H2O with over one thousand turnovers. Miner KD, Mukherjee A, Gao YG, Null EL, Petrik ID, Zhao X, Yeung N, Robinson H, Lu Y. Angew Chem Int Ed Engl 51 5589-5592 (2012)
  15. Analysis of complete mitochondrial genomes from extinct and extant rhinoceroses reveals lack of phylogenetic resolution. Willerslev E, Gilbert MT, Binladen J, Ho SY, Campos PF, Ratan A, Tomsho LP, da Fonseca RR, Sher A, Kuznetsova TV, Nowak-Kemp M, Roth TL, Miller W, Schuster SC. BMC Evol Biol 9 95 (2009)
  16. Alternative RNA editing produces a novel protein involved in mitochondrial DNA maintenance in trypanosomes. Ochsenreiter T, Anderson S, Wood ZA, Hajduk SL. Mol Cell Biol 28 5595-5604 (2008)
  17. Computer simulation of explicit proton translocation in cytochrome c oxidase: the D-pathway. Xu J, Voth GA. Proc Natl Acad Sci U S A 102 6795-6800 (2005)
  18. Gating of proton and water transfer in the respiratory enzyme cytochrome c oxidase. Wikström M, Ribacka C, Molin M, Laakkonen L, Verkhovsky M, Puustinen A. Proc Natl Acad Sci U S A 102 10478-10481 (2005)
  19. Molecular evolution of a widely-adopted taxonomic marker (COI) across the animal tree of life. Pentinsaari M, Salmela H, Mutanen M, Roslin T. Sci Rep 6 35275 (2016)
  20. Parallel Structural Evolution of Mitochondrial Ribosomes and OXPHOS Complexes. van der Sluis EO, Bauerschmitt H, Becker T, Mielke T, Frauenfeld J, Berninghausen O, Neupert W, Herrmann JM, Beckmann R. Genome Biol Evol 7 1235-1251 (2015)
  21. Assessing the fitness consequences of mitonuclear interactions in natural populations. Hill GE, Havird JC, Sloan DB, Burton RS, Greening C, Dowling DK. Biol Rev Camb Philos Soc 94 1089-1104 (2019)
  22. Conservative and compensatory evolution in oxidative phosphorylation complexes of angiosperms with highly divergent rates of mitochondrial genome evolution. Havird JC, Whitehill NS, Snow CD, Sloan DB. Evolution 69 3069-3081 (2015)
  23. Storage of an excess proton in the hydrogen-bonded network of the d-pathway of cytochrome C oxidase: identification of a protonated water cluster. Xu J, Sharpe MA, Qin L, Ferguson-Miller S, Voth GA. J Am Chem Soc 129 2910-2913 (2007)
  24. Loop recognition and copper-mediated disulfide reduction underpin metal site assembly of CuA in human cytochrome oxidase. Morgada MN, Abriata LA, Cefaro C, Gajda K, Banci L, Vila AJ. Proc Natl Acad Sci U S A 112 11771-11776 (2015)
  25. Photolabeling of cardiolipin binding subunits within bovine heart cytochrome c oxidase. Sedlák E, Panda M, Dale MP, Weintraub ST, Robinson NC. Biochemistry 45 746-754 (2006)
  26. Snapshot of an oxygen intermediate in the catalytic reaction of cytochrome c oxidase. Ishigami I, Lewis-Ballester A, Echelmeier A, Brehm G, Zatsepin NA, Grant TD, Coe JD, Lisova S, Nelson G, Zhang S, Dobson ZF, Boutet S, Sierra RG, Batyuk A, Fromme P, Fromme R, Spence JCH, Ros A, Yeh SR, Rousseau DL. Proc Natl Acad Sci U S A 116 3572-3577 (2019)
  27. Adaptive evolution of cytochrome c oxidase: Infrastructure for a carnivorous plant radiation. Jobson RW, Nielsen R, Laakkonen L, Wikström M, Albert VA. Proc Natl Acad Sci U S A 101 18064-18068 (2004)
  28. Female and male gamete mitochondria are distinct and complementary in transcription, structure, and genome function. de Paula WB, Agip AN, Missirlis F, Ashworth R, Vizcay-Barrena G, Lucas CH, Allen JF. Genome Biol Evol 5 1969-1977 (2013)
  29. A unified hydrophobicity scale for multispan membrane proteins. Koehler J, Woetzel N, Staritzbichler R, Sanders CR, Meiler J. Proteins 76 13-29 (2009)
  30. Proton-coupled electron transfer and the role of water molecules in proton pumping by cytochrome c oxidase. Sharma V, Enkavi G, Vattulainen I, Róg T, Wikström M. Proc Natl Acad Sci U S A 112 2040-2045 (2015)
  31. Computational study of the activated O(H) state in the catalytic mechanism of cytochrome c oxidase. Sharma V, Karlin KD, Wikström M. Proc Natl Acad Sci U S A 110 16844-16849 (2013)
  32. TMKink: a method to predict transmembrane helix kinks. Meruelo AD, Samish I, Bowie JU. Protein Sci 20 1256-1264 (2011)
  33. Differential Expression of Genes that Control Respiration Contribute to Thermal Adaptation in Redband Trout (Oncorhynchus mykiss gairdneri). Garvin MR, Thorgaard GH, Narum SR. Genome Biol Evol 7 1404-1414 (2015)
  34. Molecular dynamics simulation of water in cytochrome c oxidase reveals two water exit pathways and the mechanism of transport. Sugitani R, Stuchebrukhov AA. Biochim Biophys Acta 1787 1140-1150 (2009)
  35. Water molecule reorganization in cytochrome c oxidase revealed by FTIR spectroscopy. Maréchal A, Rich PR. Proc Natl Acad Sci U S A 108 8634-8638 (2011)
  36. Naja naja oxiana Cobra Venom Cytotoxins CTI and CTII Disrupt Mitochondrial Membrane Integrity: Implications for Basic Three-Fingered Cytotoxins. Gasanov SE, Shrivastava IH, Israilov FS, Kim AA, Rylova KA, Zhang B, Dagda RK. PLoS One 10 e0129248 (2015)
  37. Non-bilayer structures in mitochondrial membranes regulate ATP synthase activity. Gasanov SE, Kim AA, Yaguzhinsky LS, Dagda RK. Biochim Biophys Acta Biomembr 1860 586-599 (2018)
  38. Naja mossambica mossambica Cobra Cardiotoxin Targets Mitochondria to Disrupt Mitochondrial Membrane Structure and Function. Zhang B, Li F, Chen Z, Shrivastava IH, Gasanoff ES, Dagda RK. Toxins (Basel) 11 E152 (2019)
  39. Redox-coupled proton pumping in cytochrome c oxidase: further insights from computer simulation. Xu J, Voth GA. Biochim Biophys Acta 1777 196-201 (2008)
  40. A Database of Predicted Binding Sites for Cholesterol on Membrane Proteins, Deep in the Membrane. Lee AG. Biophys J 115 522-532 (2018)
  41. Phenol-Induced O-O Bond Cleavage in a Low-Spin Heme-Peroxo-Copper Complex: Implications for O2 Reduction in Heme-Copper Oxidases. Schaefer AW, Kieber-Emmons MT, Adam SM, Karlin KD, Solomon EI. J Am Chem Soc 139 7958-7973 (2017)
  42. Direct regulation of cytochrome c oxidase by calcium ions. Vygodina T, Kirichenko A, Konstantinov AA. PLoS One 8 e74436 (2013)
  43. Molecular Mechanism by which Cobra Venom Cardiotoxins Interact with the Outer Mitochondrial Membrane. Li F, Shrivastava IH, Hanlon P, Dagda RK, Gasanoff ES. Toxins (Basel) 12 E425 (2020)
  44. Molecular characterization of a complex of apoptosis-inducing factor 1 with cytochrome c oxidase of the mitochondrial respiratory chain. Hevler JF, Zenezeni Chiozzi R, Cabrera-Orefice A, Brandt U, Arnold S, Heck AJR. Proc Natl Acad Sci U S A 118 e2106950118 (2021)
  45. Characterization of the structure of RAMP1 by mutagenesis and molecular modeling. Simms J, Hay DL, Wheatley M, Poyner DR. Biophys J 91 662-669 (2006)
  46. Letter CyMIRA: The Cytonuclear Molecular Interactions Reference for Arabidopsis. Forsythe ES, Sharbrough J, Havird JC, Warren JM, Sloan DB. Genome Biol Evol 11 2194-2202 (2019)
  47. Insights into functions of the H channel of cytochrome c oxidase from atomistic molecular dynamics simulations. Sharma V, Jambrina PG, Kaukonen M, Rosta E, Rich PR. Proc Natl Acad Sci U S A 114 E10339-E10348 (2017)
  48. Towards accurate residue-residue hydrophobic contact prediction for alpha helical proteins via integer linear optimization. Rajgaria R, McAllister SR, Floudas CA. Proteins 74 929-947 (2009)
  49. Ablation of mitochondrial DNA results in widespread remodeling of the mitochondrial complexome. Guerrero-Castillo S, van Strien J, Brandt U, Arnold S. EMBO J 40 e108648 (2021)
  50. Convergent Evolution of Mitochondrial Genes in Deep-Sea Fishes. Shen X, Pu Z, Chen X, Murphy RW, Shen Y. Front Genet 10 925 (2019)
  51. Stoichiometry of lipid interactions with transmembrane proteins--Deduced from the 3D structures. Páli T, Bashtovyy D, Marsh D. Protein Sci 15 1153-1161 (2006)
  52. Dewetting transitions coupled to K-channel activation in cytochrome c oxidase. Supekar S, Kaila VRI. Chem Sci 9 6703-6710 (2018)
  53. MitImpact 3: modeling the residue interaction network of the Respiratory Chain subunits. Castellana S, Biagini T, Petrizzelli F, Parca L, Panzironi N, Caputo V, Vescovi AL, Carella M, Mazza T. Nucleic Acids Res 49 D1282-D1288 (2021)
  54. The Mitonuclear Dimension of Neanderthal and Denisovan Ancestry in Modern Human Genomes. Sharbrough J, Havird JC, Noe GR, Warren JM, Sloan DB. Genome Biol Evol 9 1567-1581 (2017)
  55. Adaptation of the Mitochondrial Genome in Cephalopods: Enhancing Proton Translocation Channels and the Subunit Interactions. Almeida D, Maldonado E, Vasconcelos V, Antunes A. PLoS One 10 e0135405 (2015)
  56. Differential stability of dimeric and monomeric cytochrome c oxidase exposed to elevated hydrostatic pressure. Stanicová J, Sedlák E, Musatov A, Robinson NC. Biochemistry 46 7146-7152 (2007)
  57. Interheme electron tunneling in cytochrome c oxidase. Kaila VR, Johansson MP, Sundholm D, Wikström M. Proc Natl Acad Sci U S A 107 21470-21475 (2010)
  58. Structure-based validation can drastically underestimate error rate in proteome-wide cross-linking mass spectrometry studies. Yugandhar K, Wang TY, Wierbowski SD, Shayhidin EE, Yu H. Nat Methods 17 985-988 (2020)
  59. Developing a high-quality scoring function for membrane protein structures based on specific inter-residue interactions. Heim AJ, Li Z. J Comput Aided Mol Des 26 301-309 (2012)
  60. Molecular mechanisms involved in the side effects of fatty acid amide hydrolase inhibitors: a structural phenomics approach to proteome-wide cellular off-target deconvolution and disease association. Dider S, Ji J, Zhao Z, Xie L. NPJ Syst Biol Appl 2 16023 (2016)
  61. Automatic structure classification of small proteins using random forest. Jain P, Hirst JD. BMC Bioinformatics 11 364 (2010)
  62. Structure of bovine cytochrome c oxidase crystallized at a neutral pH using a fluorinated detergent. Luo F, Shinzawa-Itoh K, Hagimoto K, Shimada A, Shimada S, Yamashita E, Yoshikawa S, Tsukihara T. Acta Crystallogr F Struct Biol Commun 73 416-422 (2017)
  63. The conserved carboxyl domain of MorC, an inner membrane protein of Aggregatibacter actinomycetemcomitans, is essential for membrane function. Smith KP, Voogt RD, Ruiz T, Mintz KP. Mol Oral Microbiol 31 43-58 (2016)
  64. Bee Venom Melittin Disintegrates the Respiration of Mitochondria in Healthy Cells and Lymphoblasts, and Induces the Formation of Non-Bilayer Structures in Model Inner Mitochondrial Membranes. Gasanoff E, Liu Y, Li F, Hanlon P, Garab G. Int J Mol Sci 22 11122 (2021)
  65. Development of a machine learning method to predict membrane protein-ligand binding residues using basic sequence information. Suresh MX, Gromiha MM, Suwa M. Adv Bioinformatics 2015 843030 (2015)
  66. Structure-Related Differences between Cytochrome Oxidase I Proteins in a Stable Heteroplasmic Mitochondrial System. Skibinski DOF, Ghiselli F, Diz AP, Milani L, Mullins JGL. Genome Biol Evol 9 3265-3281 (2017)
  67. The Possible Role of Nonbilayer Structures in Regulating ATP Synthase Activity in Mitochondrial Membranes. Gasanov SE, Kim AA, Dagda RK. Biophysics (Oxf) 61 596-600 (2016)
  68. A Pilot STEM Curriculum Designed to Teach High School Students Concepts in Biochemical Engineering and Pharmacology. Gasanoff ES, Li F, George EM, Dagda RK. EC Pharmacol Toxicol 7 846-877 (2019)
  69. Structural basis of mammalian complex IV inhibition by steroids. Di Trani JM, Moe A, Riepl D, Saura P, Kaila VRI, Brzezinski P, Rubinstein JL. Proc Natl Acad Sci U S A 119 e2205228119 (2022)
  70. Do angiosperms with highly divergent mitochondrial genomes have altered mitochondrial function? Havird JC, Noe GR, Link L, Torres A, Logan DC, Sloan DB, Chicco AJ. Mitochondrion 49 1-11 (2019)
  71. Electric fields control water-gated proton transfer in cytochrome c oxidase. Saura P, Riepl D, Frey DM, Wikström M, Kaila VRI. Proc Natl Acad Sci U S A 119 e2207761119 (2022)
  72. Genomic Signatures of Mitonuclear Coevolution in Mammals. Weaver RJ, Rabinowitz S, Thueson K, Havird JC. Mol Biol Evol 39 msac233 (2022)
  73. Glutamate transporter homolog-based model predicts that anion-π interaction is the mechanism for the voltage-dependent response of prestin. Lovas S, He DZ, Liu H, Tang J, Pecka JL, Hatfield MP, Beisel KW. J Biol Chem 290 24326-24339 (2015)
  74. Structure of bovine cytochrome c oxidase in the ligand-free reduced state at neutral pH. Luo F, Shinzawa-Itoh K, Hagimoto K, Shimada A, Shimada S, Yamashita E, Yoshikawa S, Tsukihara T. Acta Crystallogr F Struct Biol Commun 74 92-98 (2018)
  75. Calcium-Dependent Interaction of Nitric Oxide Synthase with Cytochrome c Oxidase: Implications for Brain Bioenergetics. Haynes V, Giulivi C. Brain Sci 13 1534 (2023)
  76. Mitochondrial Genome Alterations, Cytochrome C Oxidase Activity, and Oxidative Stress: Implications in Primary Open-angle Glaucoma. Mohanty K, Mishra S, Dada R, Dada T. J Curr Glaucoma Pract 16 158-165 (2022)
  77. SAFlex: A structural alphabet extension to integrate protein structural flexibility and missing data information. Allam I, Flatters D, Caumes G, Regad L, Delos V, Nuel G, Camproux AC. PLoS One 13 e0198854 (2018)
  78. The oxygen-oxygen distance of water in crystallographic data sets. Palese LL. Data Brief 28 105076 (2020)


Reviews citing this publication (43)

  1. Energy transduction: proton transfer through the respiratory complexes. Hosler JP, Ferguson-Miller S, Mills DA. Annu Rev Biochem 75 165-187 (2006)
  2. Regulation of mitochondrial oxidative phosphorylation through cell signaling. Hüttemann M, Lee I, Samavati L, Yu H, Doan JW. Biochim Biophys Acta 1773 1701-1720 (2007)
  3. Regulation of oxidative phosphorylation, the mitochondrial membrane potential, and their role in human disease. Hüttemann M, Lee I, Pecinova A, Pecina P, Przyklenk K, Doan JW. J Bioenerg Biomembr 40 445-456 (2008)
  4. Regulation of mitochondrial respiration and apoptosis through cell signaling: cytochrome c oxidase and cytochrome c in ischemia/reperfusion injury and inflammation. Hüttemann M, Helling S, Sanderson TH, Sinkler C, Samavati L, Mahapatra G, Varughese A, Lu G, Liu J, Ramzan R, Vogt S, Grossman LI, Doan JW, Marcus K, Lee I. Biochim Biophys Acta 1817 598-609 (2012)
  5. Oxygen Activation and Energy Conservation by Cytochrome c Oxidase. Wikström M, Krab K, Sharma V. Chem Rev 118 2469-2490 (2018)
  6. The subunit composition and function of mammalian cytochrome c oxidase. Kadenbach B, Hüttemann M. Mitochondrion 24 64-76 (2015)
  7. Susceptibility of mitochondrial electron-transport complexes to oxidative damage. Focus on cytochrome c oxidase. Musatov A, Robinson NC. Free Radic Res 46 1313-1326 (2012)
  8. Biogenesis of cytochrome c oxidase. Khalimonchuk O, Rödel G. Mitochondrion 5 363-388 (2005)
  9. Mechanism and energetics of proton translocation by the respiratory heme-copper oxidases. Wikström M, Verkhovsky MI. Biochim Biophys Acta 1767 1200-1214 (2007)
  10. Molecular mechanism of proton translocation by cytochrome c oxidase. Belevich I, Verkhovsky MI. Antioxid Redox Signal 10 1-29 (2008)
  11. Structures of membrane proteins. Vinothkumar KR, Henderson R. Q Rev Biophys 43 65-158 (2010)
  12. Proton-pumping mechanism of cytochrome C oxidase. Yoshikawa S, Muramoto K, Shinzawa-Itoh K. Annu Rev Biophys 40 205-223 (2011)
  13. Phosphorylation of mammalian cytochrome c and cytochrome c oxidase in the regulation of cell destiny: respiration, apoptosis, and human disease. Hüttemann M, Lee I, Grossman LI, Doan JW, Sanderson TH. Adv Exp Med Biol 748 237-264 (2012)
  14. Structural elements involved in electron-coupled proton transfer in cytochrome c oxidase. Namslauer A, Brzezinski P. FEBS Lett 567 103-110 (2004)
  15. Tissue- and Condition-Specific Isoforms of Mammalian Cytochrome c Oxidase Subunits: From Function to Human Disease. Sinkler CA, Kalpage H, Shay J, Lee I, Malek MH, Grossman LI, Hüttemann M. Oxid Med Cell Longev 2017 1534056 (2017)
  16. Design principles of proton-pumping haem-copper oxidases. Brzezinski P, Adelroth P. Curr Opin Struct Biol 16 465-472 (2006)
  17. Redox-driven membrane-bound proton pumps. Brzezinski P. Trends Biochem Sci 29 380-387 (2004)
  18. Synthetic Fe/Cu Complexes: Toward Understanding Heme-Copper Oxidase Structure and Function. Adam SM, Wijeratne GB, Rogler PJ, Diaz DE, Quist DA, Liu JJ, Karlin KD. Chem Rev 118 10840-11022 (2018)
  19. Evolution of cytochrome bc complexes: from membrane-anchored dehydrogenases of ancient bacteria to triggers of apoptosis in vertebrates. Dibrova DV, Cherepanov DA, Galperin MY, Skulachev VP, Mulkidjanian AY. Biochim Biophys Acta 1827 1407-1427 (2013)
  20. Proton-pumping mechanism of cytochrome c oxidase: a kinetic master-equation approach. Kim YC, Hummer G. Biochim Biophys Acta 1817 526-536 (2012)
  21. Uncovering channels in photosystem II by computer modelling: current progress, future prospects, and lessons from analogous systems. Ho FM. Photosynth Res 98 503-522 (2008)
  22. Small single transmembrane domain (STMD) proteins organize the hydrophobic subunits of large membrane protein complexes. Zickermann V, Angerer H, Ding MG, Nübel E, Brandt U. FEBS Lett 584 2516-2525 (2010)
  23. Revealing various coupling of electron transfer and proton pumping in mitochondrial respiratory chain. Sun F, Zhou Q, Pang X, Xu Y, Rao Z. Curr Opin Struct Biol 23 526-538 (2013)
  24. Rotary ATPases: models, machine elements and technical specifications. Stewart AG, Sobti M, Harvey RP, Stock D. Bioarchitecture 3 2-12 (2013)
  25. Gaining mass: the structure of respiratory complex I-from bacterial towards mitochondrial versions. Letts JA, Sazanov LA. Curr Opin Struct Biol 33 135-145 (2015)
  26. High efficiency versus maximal performance--the cause of oxidative stress in eukaryotes: a hypothesis. Kadenbach B, Ramzan R, Vogt S. Mitochondrion 13 1-6 (2013)
  27. Amazing structure of respirasome: unveiling the secrets of cell respiration. Guo R, Gu J, Wu M, Yang M. Protein Cell 7 854-865 (2016)
  28. Proteins, chlorophylls and lipids: X-ray analysis of a three-way relationship. Fyfe PK, Hughes AV, Heathcote P, Jones MR. Trends Plant Sci 10 275-282 (2005)
  29. The road to the structure of the mitochondrial respiratory chain supercomplex. Caruana NJ, Stroud DA. Biochem Soc Trans 48 621-629 (2020)
  30. Current advances in research of cytochrome c oxidase. Popović DM. Amino Acids 45 1073-1087 (2013)
  31. Nitrosative/oxidative modifications and ageing. Musci G, Persichini T, Casadei M, Mazzone V, Venturini G, Polticelli F, Colasanti M. Mech Ageing Dev 127 544-551 (2006)
  32. Proton translocation in cytochrome c oxidase: insights from proton exchange kinetics and vibrational spectroscopy. Ishigami I, Hikita M, Egawa T, Yeh SR, Rousseau DL. Biochim Biophys Acta 1847 98-108 (2015)
  33. The mechanism of coupling between oxido-reduction and proton translocation in respiratory chain enzymes. Papa S, Capitanio G, Papa F. Biol Rev Camb Philos Soc 93 322-349 (2018)
  34. Melatonin: Regulation of Prion Protein Phase Separation in Cancer Multidrug Resistance. Loh D, Reiter RJ. Molecules 27 705 (2022)
  35. Lipid conformation in crystalline bilayers and in crystals of transmembrane proteins. Marsh D, Páli T. Chem Phys Lipids 141 48-65 (2006)
  36. Metals in membranes. Liang X, Campopiano DJ, Sadler PJ. Chem Soc Rev 36 968-992 (2007)
  37. Parkin loss-of-function pathology: Premature neuronal senescence induced by high levels of reactive oxygen species? Buhlman LM. Mech Ageing Dev 161 112-120 (2017)
  38. Coupled electron and proton transfer reactions during the O→E transition in bovine cytochrome c oxidase. Popović DM, Stuchebrukhov AA. Biochim Biophys Acta 1817 506-517 (2012)
  39. The two faces of cyanide: an environmental toxin and a potential novel mammalian gasotransmitter. Zuhra K, Szabo C. FEBS J 289 2481-2515 (2022)
  40. Blue Copper Proteins: A rigid machine for efficient electron transfer, a flexible device for metal uptake. Pérez-Henarejos SA, Alcaraz LA, Donaire A. Arch Biochem Biophys 584 134-148 (2015)
  41. The Interplay among Subunit Composition, Cardiolipin Content, and Aggregation State of Bovine Heart Cytochrome c Oxidase. Sedlák E, Kožár T, Musatov A. Cells 9 E2588 (2020)
  42. Role of cooperative H(+)/e(-) linkage (redox bohr effect) at heme a/Cu(A) and heme a(3)/Cu(B) in the proton pump of cytochrome c oxidase. Papa S. Biochemistry (Mosc) 70 178-186 (2005)
  43. The Mitochondrial Genome in Aging and Disease and the Future of Mitochondrial Therapeutics. Saravanan S, Lewis CJ, Dixit B, O'Connor MS, Stolzing A, Boominathan A. Biomedicines 10 490 (2022)

Articles citing this publication (114)

  1. The architecture of respiratory supercomplexes. Letts JA, Fiedorczuk K, Sazanov LA. Nature 537 644-648 (2016)
  2. Structures and physiological roles of 13 integral lipids of bovine heart cytochrome c oxidase. Shinzawa-Itoh K, Aoyama H, Muramoto K, Terada H, Kurauchi T, Tadehara Y, Yamasaki A, Sugimura T, Kurono S, Tsujimoto K, Mizushima T, Yamashita E, Tsukihara T, Yoshikawa S. EMBO J 26 1713-1725 (2007)
  3. Proton-coupled electron transfer drives the proton pump of cytochrome c oxidase. Belevich I, Verkhovsky MI, Wikström M. Nature 440 829-832 (2006)
  4. Genetic ablation of calcium-independent phospholipase A2gamma leads to alterations in mitochondrial lipid metabolism and function resulting in a deficient mitochondrial bioenergetic phenotype. Mancuso DJ, Sims HF, Han X, Jenkins CM, Guan SP, Yang K, Moon SH, Pietka T, Abumrad NA, Schlesinger PH, Gross RW. J Biol Chem 282 34611-34622 (2007)
  5. A mechanistic principle for proton pumping by cytochrome c oxidase. Faxén K, Gilderson G, Adelroth P, Brzezinski P. Nature 437 286-289 (2005)
  6. Identification of cardiolipin binding sites on cytochrome c oxidase at the entrance of proton channels. Arnarez C, Marrink SJ, Periole X. Sci Rep 3 1263 (2013)
  7. A peroxide bridge between Fe and Cu ions in the O2 reduction site of fully oxidized cytochrome c oxidase could suppress the proton pump. Aoyama H, Muramoto K, Shinzawa-Itoh K, Hirata K, Yamashita E, Tsukihara T, Ogura T, Yoshikawa S. Proc Natl Acad Sci U S A 106 2165-2169 (2009)
  8. Redox-dependent conformational changes in cytochrome C oxidase suggest a gating mechanism for proton uptake. Qin L, Liu J, Mills DA, Proshlyakov DA, Hiser C, Ferguson-Miller S. Biochemistry 48 5121-5130 (2009)
  9. Bovine cytochrome c oxidase structures enable O2 reduction with minimization of reactive oxygens and provide a proton-pumping gate. Muramoto K, Ohta K, Shinzawa-Itoh K, Kanda K, Taniguchi M, Nabekura H, Yamashita E, Tsukihara T, Yoshikawa S. Proc Natl Acad Sci U S A 107 7740-7745 (2010)
  10. Adaptive evolution and functional redesign of core metabolic proteins in snakes. Castoe TA, Jiang ZJ, Gu W, Wang ZO, Pollock DD. PLoS One 3 e2201 (2008)
  11. The proton pumping pathway of bovine heart cytochrome c oxidase. Shimokata K, Katayama Y, Murayama H, Suematsu M, Tsukihara T, Muramoto K, Aoyama H, Yoshikawa S, Shimada H. Proc Natl Acad Sci U S A 104 4200-4205 (2007)
  12. A vibrational spectral maker for probing the hydrogen-bonding status of protonated Asp and Glu residues. Nie B, Stutzman J, Xie A. Biophys J 88 2833-2847 (2005)
  13. Higd1a is a positive regulator of cytochrome c oxidase. Hayashi T, Asano Y, Shintani Y, Aoyama H, Kioka H, Tsukamoto O, Hikita M, Shinzawa-Itoh K, Takafuji K, Higo S, Kato H, Yamazaki S, Matsuoka K, Nakano A, Asanuma H, Asakura M, Minamino T, Goto Y, Ogura T, Kitakaze M, Komuro I, Sakata Y, Tsukihara T, Yoshikawa S, Takashima S. Proc Natl Acad Sci U S A 112 1553-1558 (2015)
  14. A histidine residue acting as a controlling site for dioxygen reduction and proton pumping by cytochrome c oxidase. Muramoto K, Hirata K, Shinzawa-Itoh K, Yoko-o S, Yamashita E, Aoyama H, Tsukihara T, Yoshikawa S. Proc Natl Acad Sci U S A 104 7881-7886 (2007)
  15. Electron flow in multiheme bacterial cytochromes is a balancing act between heme electronic interaction and redox potentials. Breuer M, Rosso KM, Blumberger J. Proc Natl Acad Sci U S A 111 611-616 (2014)
  16. Cryo-EM structure of the yeast respiratory supercomplex. Rathore S, Berndtsson J, Marin-Buera L, Conrad J, Carroni M, Brzezinski P, Ott M. Nat Struct Mol Biol 26 50-57 (2019)
  17. Cytochrome c phosphorylation: Control of mitochondrial electron transport chain flux and apoptosis. Kalpage HA, Wan J, Morse PT, Zurek MP, Turner AA, Khobeir A, Yazdi N, Hakim L, Liu J, Vaishnav A, Sanderson TH, Recanati MA, Grossman LI, Lee I, Edwards BFP, Hüttemann M. Int J Biochem Cell Biol 121 105704 (2020)
  18. The Mg2+-containing Water Cluster of Mammalian Cytochrome c Oxidase Collects Four Pumping Proton Equivalents in Each Catalytic Cycle. Yano N, Muramoto K, Shimada A, Takemura S, Baba J, Fujisawa H, Mochizuki M, Shinzawa-Itoh K, Yamashita E, Tsukihara T, Yoshikawa S. J Biol Chem 291 23882-23894 (2016)
  19. Degenerative diseases, oxidative stress and cytochrome c oxidase function. Kadenbach B, Ramzan R, Vogt S. Trends Mol Med 15 139-147 (2009)
  20. Functional hydration and conformational gating of proton uptake in cytochrome c oxidase. Henry RM, Yu CH, Rodinger T, Pomès R. J Mol Biol 387 1165-1185 (2009)
  21. Electronic continuum model for molecular dynamics simulations of biological molecules. Leontyev IV, Stuchebrukhov AA. J Chem Theory Comput 6 1498-1508 (2010)
  22. Combined microspectrophotometric and crystallographic examination of chemically reduced and X-ray radiation-reduced forms of cytochrome ba3 oxidase from Thermus thermophilus: structure of the reduced form of the enzyme. Liu B, Chen Y, Doukov T, Soltis SM, Stout CD, Fee JA. Biochemistry 48 820-826 (2009)
  23. Contribution of peroxidized cardiolipin to inactivation of bovine heart cytochrome c oxidase. Musatov A. Free Radic Biol Med 41 238-246 (2006)
  24. A D-pathway mutation decouples the Paracoccus denitrificans cytochrome c oxidase by altering the side-chain orientation of a distant conserved glutamate. Dürr KL, Koepke J, Hellwig P, Müller H, Angerer H, Peng G, Olkhova E, Richter OM, Ludwig B, Michel H. J Mol Biol 384 865-877 (2008)
  25. Multiple phosphorylations of cytochrome c oxidase and their functions. Helling S, Hüttemann M, Ramzan R, Kim SH, Lee I, Müller T, Langenfeld E, Meyer HE, Kadenbach B, Vogt S, Marcus K. Proteomics 12 950-959 (2012)
  26. Leber's Hereditary Optic Neuropathy-Gene Therapy: From Benchtop to Bedside. Koilkonda RD, Guy J. J Ophthalmol 2011 179412 (2011)
  27. Kinetic gating of the proton pump in cytochrome c oxidase. Kim YC, Wikström M, Hummer G. Proc Natl Acad Sci U S A 106 13707-13712 (2009)
  28. Kinetic models of redox-coupled proton pumping. Kim YC, Wikström M, Hummer G. Proc Natl Acad Sci U S A 104 2169-2174 (2007)
  29. A suggested role for mitochondria in Noonan syndrome. Lee I, Pecinova A, Pecina P, Neel BG, Araki T, Kucherlapati R, Roberts AE, Hüttemann M. Biochim Biophys Acta 1802 275-283 (2010)
  30. A new model for the evolution of carnivory in the bladderwort plant (utricularia): adaptive changes in cytochrome C oxidase (COX) provide respiratory power. Laakkonen L, Jobson RW, Albert VA. Plant Biol (Stuttg) 8 758-764 (2006)
  31. Insights into the mechanism of proton transport in cytochrome c oxidase. Yamashita T, Voth GA. J Am Chem Soc 134 1147-1152 (2012)
  32. Atomic structures of respiratory complex III2, complex IV, and supercomplex III2-IV from vascular plants. Maldonado M, Guo F, Letts JA. Elife 10 e62047 (2021)
  33. Phosphorylation of Cytochrome c Threonine 28 Regulates Electron Transport Chain Activity in Kidney: IMPLICATIONS FOR AMP KINASE. Mahapatra G, Varughese A, Ji Q, Lee I, Liu J, Vaishnav A, Sinkler C, Kapralov AA, Moraes CT, Sanderson TH, Stemmler TL, Grossman LI, Kagan VE, Brunzelle JS, Salomon AR, Edwards BF, Hüttemann M. J Biol Chem 292 64-79 (2017)
  34. Crystal structure of CO-bound cytochrome c oxidase determined by serial femtosecond X-ray crystallography at room temperature. Ishigami I, Zatsepin NA, Hikita M, Conrad CE, Nelson G, Coe JD, Basu S, Grant TD, Seaberg MH, Sierra RG, Hunter MS, Fromme P, Fromme R, Yeh SR, Rousseau DL. Proc Natl Acad Sci U S A 114 8011-8016 (2017)
  35. A single-amino-acid lid renders a gas-tight compartment within a membrane-bound transporter. Salomonsson L, Lee A, Gennis RB, Brzezinski P. Proc Natl Acad Sci U S A 101 11617-11621 (2004)
  36. Stable transformation of CHO Cells and human NARP cybrids confers oligomycin resistance (oli(r)) following transfer of a mitochondrial DNA-encoded oli(r) ATPase6 gene to the nuclear genome: a model system for mtDNA gene therapy. Zullo SJ, Parks WT, Chloupkova M, Wei B, Weiner H, Fenton WA, Eisenstadt JM, Merril CR. Rejuvenation Res 8 18-28 (2005)
  37. Theoretical and computational analysis of the membrane potential generated by cytochrome c oxidase upon single electron injection into the enzyme. Sugitani R, Medvedev ES, Stuchebrukhov AA. Biochim Biophys Acta 1777 1129-1139 (2008)
  38. What limits the allotopic expression of nucleus-encoded mitochondrial genes? The case of the chimeric Cox3 and Atp6 genes. Figueroa-Martínez F, Vázquez-Acevedo M, Cortés-Hernández P, García-Trejo JJ, Davidson E, King MP, González-Halphen D. Mitochondrion 11 147-154 (2011)
  39. pH-dependent transition between delocalized and trapped valence states of a CuA center and its possible role in proton-coupled electron transfer. Hwang HJ, Lu Y. Proc Natl Acad Sci U S A 101 12842-12847 (2004)
  40. Dimer interface of bovine cytochrome c oxidase is influenced by local posttranslational modifications and lipid binding. Liko I, Degiacomi MT, Mohammed S, Yoshikawa S, Schmidt C, Robinson CV. Proc Natl Acad Sci U S A 113 8230-8235 (2016)
  41. Electron spin resonance in membrane research: protein-lipid interactions. Marsh D. Methods 46 83-96 (2008)
  42. Nek5 interacts with mitochondrial proteins and interferes negatively in mitochondrial mediated cell death and respiration. Melo Hanchuk TD, Papa PF, La Guardia PG, Vercesi AE, Kobarg J. Cell Signal 27 1168-1177 (2015)
  43. Charge parameterization of the metal centers in cytochrome c oxidase. Johansson MP, Kaila VR, Laakkonen L. J Comput Chem 29 753-767 (2008)
  44. Context dependence and coevolution among amino acid residues in proteins. Wang ZO, Pollock DD. Methods Enzymol 395 779-790 (2005)
  45. How periplasmic thioredoxin TlpA reduces bacterial copper chaperone ScoI and cytochrome oxidase subunit II (CoxB) prior to metallation. Abicht HK, Schärer MA, Quade N, Ledermann R, Mohorko E, Capitani G, Hennecke H, Glockshuber R. J Biol Chem 289 32431-32444 (2014)
  46. Structural analysis of mitochondrial mutations reveals a role for bigenomic protein interactions in human disease. Lloyd RE, McGeehan JE. PLoS One 8 e69003 (2013)
  47. De Novo Design of Tetranuclear Transition Metal Clusters Stabilized by Hydrogen-Bonded Networks in Helical Bundles. Zhang SQ, Chino M, Liu L, Tang Y, Hu X, DeGrado WF, Lombardi A. J Am Chem Soc 140 1294-1304 (2018)
  48. Forces maintaining organellar genomes: is any as strong as genetic code disparity or hydrophobicity? de Grey AD. Bioessays 27 436-446 (2005)
  49. Monomeric structure of an active form of bovine cytochrome c oxidase. Shinzawa-Itoh K, Sugimura T, Misaki T, Tadehara Y, Yamamoto S, Hanada M, Yano N, Nakagawa T, Uene S, Yamada T, Aoyama H, Yamashita E, Tsukihara T, Yoshikawa S, Muramoto K. Proc Natl Acad Sci U S A 116 19945-19951 (2019)
  50. Properties of Arg481 mutants of the aa3-type cytochrome c oxidase from Rhodobacter sphaeroides suggest that neither R481 nor the nearby D-propionate of heme a3 is likely to be the proton loading site of the proton pump. Lee HJ, Ojemyr L, Vakkasoglu A, Brzezinski P, Gennis RB. Biochemistry 48 7123-7131 (2009)
  51. Quantum chemistry applied to the mechanisms of transition metal containing enzymes -- cytochrome c oxidase, a particularly challenging case. Blomberg MR, Siegbahn PE. J Comput Chem 27 1373-1384 (2006)
  52. Prediction of high- and low-affinity quinol-analogue-binding sites in the aa3 and bo3 terminal oxidases from Bacillus subtilis and Escherichia coli1. Bossis F, De Grassi A, Palese LL, Pierri CL. Biochem J 461 305-314 (2014)
  53. Crystallographic evidence for active-site dynamics in the hydrolytic aldehyde dehydrogenases. Implications for the deacylation step of the catalyzed reaction. Muñoz-Clares RA, González-Segura L, Díaz-Sánchez AG. Chem Biol Interact 191 137-146 (2011)
  54. A candidate complex approach to study functional mitochondrial DNA changes: sequence variation and quaternary structure modeling of Drosophila simulans cytochrome c oxidase. Melvin RG, Katewa SD, Ballard JW. J Mol Evol 66 232-242 (2008)
  55. A common coupling mechanism for A-type heme-copper oxidases from bacteria to mitochondria. Maréchal A, Xu JY, Genko N, Hartley AM, Haraux F, Meunier B, Rich PR. Proc Natl Acad Sci U S A 117 9349-9355 (2020)
  56. Construction of histidine-tagged yeast mitochondrial cytochrome c oxidase for facile purification of mutant forms. Meunier B, Maréchal A, Rich PR. Biochem J 444 199-204 (2012)
  57. Redox-controlled proton gating in bovine cytochrome c oxidase. Egawa T, Yeh SR, Rousseau DL. PLoS One 8 e63669 (2013)
  58. Similarity of cytochrome c oxidases in different organisms. Popovic DM, Leontyev IV, Beech DG, Stuchebrukhov AA. Proteins 78 2691-2698 (2010)
  59. Tryptophan 334 oxidation in bovine cytochrome c oxidase subunit I involves free radical migration. Lemma-Gray P, Weintraub ST, Carroll CA, Musatov A, Robinson NC. FEBS Lett 581 437-442 (2007)
  60. X-ray structures of catalytic intermediates of cytochrome c oxidase provide insights into its O2 activation and unidirectional proton-pump mechanisms. Shimada A, Etoh Y, Kitoh-Fujisawa R, Sasaki A, Shinzawa-Itoh K, Hiromoto T, Yamashita E, Muramoto K, Tsukihara T, Yoshikawa S. J Biol Chem 295 5818-5833 (2020)
  61. Structures of reduced and ligand-bound nitric oxide reductase provide insights into functional differences in respiratory enzymes. Sato N, Ishii S, Sugimoto H, Hino T, Fukumori Y, Sako Y, Shiro Y, Tosha T. Proteins 82 1258-1271 (2014)
  62. Dielectric relaxation of cytochrome c oxidase: Comparison of the microscopic and continuum models. Leontyev IV, Stuchebrukhov AA. J Chem Phys 130 085103 (2009)
  63. Electron transfer interactome of cytochrome C. Volkov AN, van Nuland NA. PLoS Comput Biol 8 e1002807 (2012)
  64. Keeping it complicated: Mitochondrial genome plasticity across diplonemids. Valach M, Moreira S, Hoffmann S, Stadler PF, Burger G. Sci Rep 7 14166 (2017)
  65. Partial steps of charge translocation in the nonpumping N139L mutant of Rhodobacter sphaeroides cytochrome c oxidase with a blocked D-channel. Siletsky SA, Zhu J, Gennis RB, Konstantinov AA. Biochemistry 49 3060-3073 (2010)
  66. Wide turn diversity in protein transmembrane helices implications for G-protein-coupled receptor and other polytopic membrane protein structure and function. Riek RP, Finch AA, Begg GE, Graham RM. Mol Pharmacol 73 1092-1104 (2008)
  67. A Protonated Water Cluster as a Transient Proton-Loading Site in Cytochrome c Oxidase. Supekar S, Gamiz-Hernandez AP, Kaila VR. Angew Chem Int Ed Engl 55 11940-11944 (2016)
  68. Two conformational states of Glu242 and pKas in bovine cytochrome c oxidase. Popovic DM, Stuchebrukhov AA. Photochem Photobiol Sci 5 611-620 (2006)
  69. Inhibition of membrane-bound cytochrome c oxidase by zinc ions: high-affinity Zn2+-binding site at the P-side of the membrane. Vygodina TV, Zakirzianova W, Konstantinov AA. FEBS Lett 582 4158-4162 (2008)
  70. Prediction of buried helices in multispan alpha helical membrane proteins. Adamian L, Liang J. Proteins 63 1-5 (2006)
  71. Structural Changes and Proton Transfer in Cytochrome c Oxidase. Vilhjálmsdóttir J, Johansson AL, Brzezinski P. Sci Rep 5 12047 (2015)
  72. X-ray structural analyses of azide-bound cytochrome c oxidases reveal that the H-pathway is critically important for the proton-pumping activity. Shimada A, Hatano K, Tadehara H, Yano N, Shinzawa-Itoh K, Yamashita E, Muramoto K, Tsukihara T, Yoshikawa S. J Biol Chem 293 14868-14879 (2018)
  73. Cell-free synthesis of cytochrome c oxidase, a multicomponent membrane protein. Katayama Y, Shimokata K, Suematsu M, Ogura T, Tsukihara T, Yoshikawa S, Shimada H. J Bioenerg Biomembr 42 235-240 (2010)
  74. Effective pumping proton collection facilitated by a copper site (CuB) of bovine heart cytochrome c oxidase, revealed by a newly developed time-resolved infrared system. Kubo M, Nakashima S, Yamaguchi S, Ogura T, Mochizuki M, Kang J, Tateno M, Shinzawa-Itoh K, Kato K, Yoshikawa S. J Biol Chem 288 30259-30269 (2013)
  75. Cation binding site of cytochrome c oxidase: progress report. Vygodina TV, Kirichenko A, Konstantinov AA. Biochim Biophys Acta 1837 1188-1195 (2014)
  76. Critical roles of the CuB site in efficient proton pumping as revealed by crystal structures of mammalian cytochrome c oxidase catalytic intermediates. Shimada A, Hara F, Shinzawa-Itoh K, Kanehisa N, Yamashita E, Muramoto K, Tsukihara T, Yoshikawa S. J Biol Chem 297 100967 (2021)
  77. Exploring O2 diffusion in A-type cytochrome c oxidases: molecular dynamics simulations uncover two alternative channels towards the binuclear site. Oliveira AS, Damas JM, Baptista AM, Soares CM. PLoS Comput Biol 10 e1004010 (2014)
  78. Water exit pathways and proton pumping mechanism in B-type cytochrome c oxidase from molecular dynamics simulations. Yang L, Skjevik ÅA, Han Du WG, Noodleman L, Walker RC, Götz AW. Biochim Biophys Acta 1857 1594-1606 (2016)
  79. Characterization of the mitochondrial ATP synthase from yeast Saccharomyces cerevisae. Pagadala V, Vistain L, Symersky J, Mueller DM. J Bioenerg Biomembr 43 333-347 (2011)
  80. Relaxed selection on male mitochondrial genes in DUI bivalves eases the need for mitonuclear coevolution. Maeda GP, Iannello M, McConie HJ, Ghiselli F, Havird JC. J Evol Biol 34 1722-1736 (2021)
  81. Electric field modulated redox-driven protonation and hydration energetics in energy converting enzymes. Saura P, Frey DM, Gamiz-Hernandez AP, Kaila VRI. Chem Commun (Camb) 55 6078-6081 (2019)
  82. Modulation of the active site conformation by site-directed mutagenesis in cytochrome c oxidase from Paracoccus denitrificans. Ji H, Das TK, Puustinen A, Wikström M, Yeh SR, Rousseau DL. J Inorg Biochem 104 318-323 (2010)
  83. Molecular evolution of cytochrome C oxidase-I protein of insects living in Saudi Arabia. Sabir JSM, Rabah S, Yacoub H, Hajrah NH, Atef A, Al-Matary M, Edris S, Alharbi MG, Ganash M, Mahyoub J, Al-Hindi RR, Al-Ghamdi KM, Hall N, Bahieldin A, Kamli MR, Rather IA. PLoS One 14 e0224336 (2019)
  84. Spectroscopic and kinetic investigation of the fully reduced and mixed valence states of ba3-cytochrome c oxidase from Thermus thermophilus: a Fourier transform infrared (FTIR) and time-resolved step-scan FTIR study. Koutsoupakis C, Soulimane T, Varotsis C. J Biol Chem 287 37495-37507 (2012)
  85. Stabilization of the peroxy intermediate in the oxygen splitting reaction of cytochrome cbb(3). Sharma V, Wikström M, Kaila VR. Biochim Biophys Acta 1807 813-818 (2011)
  86. dissectHMMER: a HMMER-based score dissection framework that statistically evaluates fold-critical sequence segments for domain fold similarity. Wong WC, Yap CK, Eisenhaber B, Eisenhaber F. Biol Direct 10 39 (2015)
  87. Effect of a buried ion pair in the hydrophobic core of a protein: An insight from constant pH molecular dynamics study. Pathak AK. Biopolymers 103 148-157 (2015)
  88. IR signatures of the metal centres of bovine cytochrome c oxidase: assignments and redox-linkage. Dodia R, Maréchal A, Bettini S, Iwaki M, Rich PR. Biochem Soc Trans 41 1242-1248 (2013)
  89. Isolated complexes of the amino acid arginine with polyether and polyamine macrocycles, the role of proton transfer. Avilés-Moreno JR, Berden G, Oomens J, Martínez-Haya B. Phys Chem Chem Phys 19 31345-31351 (2017)
  90. Proton-transfer pathways in the mitochondrial S. cerevisiae cytochrome c oxidase. Björck ML, Vilhjálmsdóttir J, Hartley AM, Meunier B, Näsvik Öjemyr L, Maréchal A, Brzezinski P. Sci Rep 9 20207 (2019)
  91. The inhibitory binding site(s) of Zn2+ in cytochrome c oxidase. Francia F, Giachini L, Boscherini F, Venturoli G, Capitanio G, Martino PL, Papa S. FEBS Lett 581 611-616 (2007)
  92. Orientation and conformation of lipids in crystals of transmembrane proteins. Marsh D, Páli T. Eur Biophys J 42 119-146 (2013)
  93. Communication between R481 and Cu(B) in cytochrome bo(3) ubiquinol oxidase from Escherichia coli. Egawa T, Lin MT, Hosler JP, Gennis RB, Yeh SR, Rousseau DL. Biochemistry 48 12113-12124 (2009)
  94. Critical structural role of R481 in cytochrome c oxidase from Rhodobacter sphaeroides. Egawa T, Lee HJ, Gennis RB, Yeh SR, Rousseau DL. Biochim Biophys Acta 1787 1272-1275 (2009)
  95. Circular dichroism spectra of cytochrome c oxidase. Dyuba AV, Arutyunyan AM, Vygodina TV, Azarkina NV, Kalinovich AV, Sharonov YA, Konstantinov AA. Metallomics 3 417-432 (2011)
  96. Cytochrome aa3 Oxygen Reductase Utilizes the Tunnel Observed in the Crystal Structures To Deliver O2 for Catalysis. Mahinthichaichan P, Gennis RB, Tajkhorshid E. Biochemistry 57 2150-2161 (2018)
  97. Evolution of mitochondrial power in vertebrate metazoans. Kitazoe Y, Tanaka M. PLoS One 9 e98188 (2014)
  98. First-principles molecular dynamics study of proton transfer mechanism in bovine cytochrome c oxidase. Kamiya K, Boero M, Tateno M, Shiraishi K, Oshiyama A. J Phys Condens Matter 19 365220 (2007)
  99. Ligand trapping by cytochrome c oxidase: implications for gating at the catalytic center. Parul D, Palmer G, Fabian M. J Biol Chem 285 4536-4543 (2010)
  100. Photobiochemical production of carbon monoxide by Thermus thermophilus ba3 -cytochrome c oxidase. Koutsoupakis C, Soulimane T, Varotsis C. Chemistry 21 4958-4961 (2015)
  101. Ultrafast Backbone Protonation in Channelrhodopsin-1 Captured by Polarization Resolved Fs Vis-pump-IR-Probe Spectroscopy and Computational Methods. Stensitzki T, Adam S, Schlesinger R, Schapiro I, Heyne K. Molecules 25 E848 (2020)
  102. Biochemical and crystallographic studies of monomeric and dimeric bovine cytochrome c oxidase. Shinzawa-Itoh K, Muramoto K. Biophys Physicobiol 18 186-195 (2021)
  103. Crystallographic studies of cytochrome c and cytochrome c oxidase. Tsukihara T. J Biochem 171 13-15 (2022)
  104. Electronic structures of heme a of cytochrome c oxidase in the redox states--charge density migration to the propionate groups of heme a. Takano Y, Nakamura H. J Comput Chem 31 954-962 (2010)
  105. Elucidation of the Correlation between Heme Distortion and Tertiary Structure of the Heme-Binding Pocket Using a Convolutional Neural Network. Kondo HX, Iizuka H, Masumoto G, Kabaya Y, Kanematsu Y, Takano Y. Biomolecules 12 1172 (2022)
  106. The 1.3-Å resolution structure of bovine cytochrome c oxidase suggests a dimerization mechanism. Shinzawa-Itoh K, Hatanaka M, Fujita K, Yano N, Ogasawara Y, Iwata J, Yamashita E, Tsukihara T, Yoshikawa S, Muramoto K. BBA Adv 1 100009 (2021)
  107. Crystallographic cyanide-probing for cytochrome c oxidase reveals structural bases suggesting that a putative proton transfer H-pathway pumps protons. Shimada A, Baba J, Nagao S, Shinzawa-Itoh K, Yamashita E, Muramoto K, Tsukihara T, Yoshikawa S. J Biol Chem 299 105277 (2023)
  108. Congress Homage to Prof. M.G. Replacement: a celebration of structural biology at Purdue University. Abad-Zapatero C. Structure 13 845-848 (2005)
  109. Inhibition of bacterial oxidases by formamide and analogs. Gupta S, Mazumdar S. Biol Chem 389 599-607 (2008)
  110. Molecular characterization and phylogenetic relationships among Rhynchophorus sp. haplotypes in Makkah Al-Mukarramah Region-KSA. Al-Otaibi WM, Alghamdi KM, Mahyoub JA. Saudi J Biol Sci 29 103388 (2022)
  111. Radical Transport Facilitated by a Proton Transfer Network at the Subunit Interface of Ribonucleotide Reductase. Cui C, Song DY, Drennan CL, Stubbe J, Nocera DG. J Am Chem Soc 145 5145-5154 (2023)
  112. Reconstruction of absolute absorption spectrum of reduced heme a in cytochrome C oxidase from bovine heart. Dyuba AV, Vygodina TV, Konstantinov AA. Biochemistry (Mosc) 78 1358-1365 (2013)
  113. Structures of Tetrahymena thermophila respiratory megacomplexes on the tubular mitochondrial cristae. Han F, Hu Y, Wu M, He Z, Tian H, Zhou L. Nat Commun 14 2542 (2023)
  114. Substrate binding-dissociation and intermolecular electron transfer in cytochrome c oxidase are driven by energy-dependent conformational changes in the enzyme and substrate. Ashe D, Alleyne T, Sampson V. Biotechnol Appl Biochem 59 213-222 (2012)