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Volumn 47, Issue 16, 2008, Pages 4657-4665

Crystallographic studies of Xe and Kr binding within the large internal cavity of cytochrome ba3 from Thermus thermophilus: Structural analysis and role of oxygen transport channels in the heme-Cu oxidases

Author keywords

[No Author keywords available]

Indexed keywords

CELLULAR RESPIRATION; DIOXYGEN TENSIONS; OXYGEN TRANSPORT CHANNELS;

EID: 42349083650     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi800045y     Document Type: Article
Times cited : (86)

References (60)
  • 1
    • 0000021902 scopus 로고    scopus 로고
    • Heme/Copper Terminal Oxidases
    • Ferguson-Miller, S., and Babcock, G. T. (1996) Heme/Copper Terminal Oxidases. Chem. Rev. 96, 2889-2908.
    • (1996) Chem. Rev , vol.96 , pp. 2889-2908
    • Ferguson-Miller, S.1    Babcock, G.T.2
  • 2
    • 0015955554 scopus 로고
    • Description of Thermus thermophilus Comb-Nov, a nonsporulating thermophilic bacterium from a Japanese thermal spa
    • Oshima, T., and Imahori, K. (1974) Description of Thermus thermophilus Comb-Nov, a nonsporulating thermophilic bacterium from a Japanese thermal spa. Int. J. Syst. Bacteriol. 24, 102-112.
    • (1974) Int. J. Syst. Bacteriol , vol.24 , pp. 102-112
    • Oshima, T.1    Imahori, K.2
  • 5
    • 0028890031 scopus 로고
    • Structure at 2.8 Å resolution of cytochrome c oxidase from Paracoccus denitrificans
    • Iwata, S., Ostermeier, C., Ludwig, B., and Michel, H. (1995) Structure at 2.8 Å resolution of cytochrome c oxidase from Paracoccus denitrificans. Nature 376, 660-669.
    • (1995) Nature , vol.376 , pp. 660-669
    • Iwata, S.1    Ostermeier, C.2    Ludwig, B.3    Michel, H.4
  • 6
    • 33750807024 scopus 로고    scopus 로고
    • 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, R. M., and Ferguson-Miller, S. (2006) Identification of conserved lipid/detergent-binding sites in a high-resolution structure of the membrane protein cytochrome c oxidase. Proc. Natl. Acad. Sci. U.S.A. 103, 16117-16122.
    • (2006) Proc. Natl. Acad. Sci. U.S.A , vol.103 , pp. 16117-16122
    • Qin, L.1    Hiser, C.2    Mulichak, A.3    Garavito, R.M.4    Ferguson-Miller, S.5
  • 7
    • 0036382724 scopus 로고    scopus 로고
    • The X-ray crystal structures of wildtype and EQ(I-286) mutant cytochrome c oxidases from Rhodobacter sphaeroides
    • Svensson-Ek, M., Abramson, J., Larsson, G., Tornroth, S., Brzezinski, P., and Iwata, S. (2002) The X-ray crystal structures of wildtype and EQ(I-286) mutant cytochrome c oxidases from Rhodobacter sphaeroides. J. Mol. Biol. 321, 329-339.
    • (2002) J. Mol. Biol , vol.321 , pp. 329-339
    • Svensson-Ek, M.1    Abramson, J.2    Larsson, G.3    Tornroth, S.4    Brzezinski, P.5    Iwata, S.6
  • 11
    • 0026530174 scopus 로고
    • Oxygen activation and the conservation of energy in cell respiration
    • Babcock, G. T., and Wikstrom, M. (1992) Oxygen activation and the conservation of energy in cell respiration. Nature 356, 301-309.
    • (1992) Nature , vol.356 , pp. 301-309
    • Babcock, G.T.1    Wikstrom, M.2
  • 13
    • 33748460871 scopus 로고    scopus 로고
    • Cohen, J., Arkhipov, A., Braun, R., and Schulten, K. (2006) Imaging the migration pathways for O-2, CO, NO, and Xe inside myoglobin. Biophys. J. 91, 1844-1857.
    • Cohen, J., Arkhipov, A., Braun, R., and Schulten, K. (2006) Imaging the migration pathways for O-2, CO, NO, and Xe inside myoglobin. Biophys. J. 91, 1844-1857.
  • 15
    • 0013851845 scopus 로고
    • Binding of xenon to horse haemoglobin
    • Schoenborn, B. P. (1965) Binding of xenon to horse haemoglobin. Nature 208, 760-762.
    • (1965) Nature , vol.208 , pp. 760-762
    • Schoenborn, B.P.1
  • 17
    • 0020180559 scopus 로고
    • Effects of media and electrode materials on the electrochemical reduction of dioxygen
    • Sawyer, D. T., Chlericato, G., Angelis, C. T., Nanni, E. J., and Tsuchiya, T. (1982) Effects of media and electrode materials on the electrochemical reduction of dioxygen. Anal. Chem. 54, 1720-1724.
    • (1982) Anal. Chem , vol.54 , pp. 1720-1724
    • Sawyer, D.T.1    Chlericato, G.2    Angelis, C.T.3    Nanni, E.J.4    Tsuchiya, T.5
  • 18
    • 20544433165 scopus 로고
    • van der Waals volumes and radii
    • Bondi, A. (1964) van der Waals volumes and radii. J. Phys. Chem. 68, 441-451.
    • (1964) J. Phys. Chem , vol.68 , pp. 441-451
    • Bondi, A.1
  • 19
    • 0001481729 scopus 로고
    • Molecular charge distributions and chemical binding
    • Bader, R. F. W., Henneker, W. H., and Cade, P. E. (1967) Molecular charge distributions and chemical binding. J. Chem. Phys. 46, 3341.
    • (1967) J. Chem. Phys , vol.46 , pp. 3341
    • Bader, R.F.W.1    Henneker, W.H.2    Cade, P.E.3
  • 20
    • 0031973948 scopus 로고    scopus 로고
    • Oxygen and proton pathways in cytochrome c oxidase
    • Hofacker, I., and Schulten, K. (1998) Oxygen and proton pathways in cytochrome c oxidase. Proteins 30, 100-107.
    • (1998) Proteins , vol.30 , pp. 100-107
    • Hofacker, I.1    Schulten, K.2
  • 24
    • 0033212815 scopus 로고    scopus 로고
    • Integration of macromolecular diffraction data
    • Leslie, A. G. (1999) Integration of macromolecular diffraction data. Acta Crystallogr. D55, 1696-1702.
    • (1999) Acta Crystallogr , vol.D55 , pp. 1696-1702
    • Leslie, A.G.1
  • 25
    • 0028103275 scopus 로고
    • The CCP4 suite: Programs for protein crystallography
    • Collaborative Computational Project Number 4
    • Collaborative Computational Project Number 4 (1994) The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D50, 760-763.
    • (1994) Acta Crystallogr , vol.D50 , pp. 760-763
  • 26
    • 13244281317 scopus 로고    scopus 로고
    • Coot: Model-building tools for molecular graphics
    • Emsley, P., and Cowtan, K. (2004) Coot: Model-building tools for molecular graphics. Acta Crystallogr. D60, 2126-2132.
    • (2004) Acta Crystallogr , vol.D60 , pp. 2126-2132
    • Emsley, P.1    Cowtan, K.2
  • 27
    • 0030924992 scopus 로고    scopus 로고
    • Refinement of macromolecular structures by the maximum-likelihood method
    • Murshudov, G. N., Vagin, A. A., and Dodson, E. J. (1997) Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D53, 240-255.
    • (1997) Acta Crystallogr , vol.D53 , pp. 240-255
    • Murshudov, G.N.1    Vagin, A.A.2    Dodson, E.J.3
  • 28
    • 33646260450 scopus 로고    scopus 로고
    • Optimal description of a protein structure in terms of multiple groups undergoing TLS motion
    • Painter, J., and Merritt, E. A. (2006) Optimal description of a protein structure in terms of multiple groups undergoing TLS motion. Acta Crystallogr. D62, 439-450.
    • (2006) Acta Crystallogr , vol.D62 , pp. 439-450
    • Painter, J.1    Merritt, E.A.2
  • 31
    • 0027968068 scopus 로고
    • CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
    • Thompson, J. D., Higgins, D. G., and Gibson, T. J. (1994) CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22, 4673-4680.
    • (1994) Nucleic Acids Res , vol.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 32
    • 0033531970 scopus 로고    scopus 로고
    • Human glutathione transferase A4-4 crystal structures and mutagenesis reveal the basis of high catalytic efficiency with toxic lipid peroxidation products
    • Bruns, C. M., Hubatsch, I., Ridderstrom, M., Mannervik, B., and Tainer, J. A. (1999) Human glutathione transferase A4-4 crystal structures and mutagenesis reveal the basis of high catalytic efficiency with toxic lipid peroxidation products. J. Mol. Biol. 288, 427-439.
    • (1999) J. Mol. Biol , vol.288 , pp. 427-439
    • Bruns, C.M.1    Hubatsch, I.2    Ridderstrom, M.3    Mannervik, B.4    Tainer, J.A.5
  • 33
    • 0027995683 scopus 로고
    • Detection, delineation, measurement and display of cavities in macromolecular structures
    • Kleywegt, G. J., and Jones, T. A. (1994) Detection, delineation, measurement and display of cavities in macromolecular structures. Acta Crystallogr. D50, 178-185.
    • (1994) Acta Crystallogr , vol.D50 , pp. 178-185
    • Kleywegt, G.J.1    Jones, T.A.2
  • 34
    • 0035371783 scopus 로고    scopus 로고
    • A novel scenario for the evolution of haem-copper oxygen reductases
    • Pereira, M. M., Santana, M., and Teixeira, M. (2001) A novel scenario for the evolution of haem-copper oxygen reductases. Biochim. Biophys. Acta 1505, 185-208.
    • (2001) Biochim. Biophys. Acta , vol.1505 , pp. 185-208
    • Pereira, M.M.1    Santana, M.2    Teixeira, M.3
  • 35
    • 28044463816 scopus 로고    scopus 로고
    • Cooperative water filling of a nonpolar protein cavity observed by high-pressure crystallography and simulation
    • Collins, M. D., Hummer, G., Quillin, M. L., Matthews, B. W., and Gruner, S. M. (2005) Cooperative water filling of a nonpolar protein cavity observed by high-pressure crystallography and simulation. Proc. Natl. Acad. Sci. U.S.A. 102, 16668-16671.
    • (2005) Proc. Natl. Acad. Sci. U.S.A , vol.102 , pp. 16668-16671
    • Collins, M.D.1    Hummer, G.2    Quillin, M.L.3    Matthews, B.W.4    Gruner, S.M.5
  • 36
    • 0015977588 scopus 로고
    • The interpretation of protein structures: Total volume, group volume distributions and packing density
    • Richards, F. M. (1974) The interpretation of protein structures: Total volume, group volume distributions and packing density. J. Mol. Biol. 82, 1-14.
    • (1974) J. Mol. Biol , vol.82 , pp. 1-14
    • Richards, F.M.1
  • 37
    • 0027522362 scopus 로고
    • Estimation of the maximum change in stability of globular proteins upon mutation of a hydrophobic residue to another of smaller size
    • Lee, B. (1993) Estimation of the maximum change in stability of globular proteins upon mutation of a hydrophobic residue to another of smaller size. Protein Sci. 2, 733-738.
    • (1993) Protein Sci , vol.2 , pp. 733-738
    • Lee, B.1
  • 38
    • 4143060405 scopus 로고    scopus 로고
    • A single-amino-acid lid renders a gas-tight compartment within a membrane-bound transporter
    • Salomonsson, L., Lee, A., Gennis, R. B., and Brzezinski, P. (2004) A single-amino-acid lid renders a gas-tight compartment within a membrane-bound transporter. Proc. Natl. Acad. Sci. U.S.A. 101, 11617-11621.
    • (2004) Proc. Natl. Acad. Sci. U.S.A , vol.101 , pp. 11617-11621
    • Salomonsson, L.1    Lee, A.2    Gennis, R.B.3    Brzezinski, P.4
  • 40
    • 0030745897 scopus 로고    scopus 로고
    • 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
    • Konstantinov, A. A., Siletsky, S., Mitchell, D., Kaulen, A., and Gennis, R. B. (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. U.S.A. 94, 9085-9090.
    • (1997) Proc. Natl. Acad. Sci. U.S.A , vol.94 , pp. 9085-9090
    • Konstantinov, A.A.1    Siletsky, S.2    Mitchell, D.3    Kaulen, A.4    Gennis, R.B.5
  • 41
    • 0042307434 scopus 로고    scopus 로고
    • Direct observation of protonation reactions during the catalytic cycle of cytochrome c oxidase
    • Nyquist, R. M., Heitbrink, D., Bolwien, C., Gennis, R. B., and Heberle, J. (2003) Direct observation of protonation reactions during the catalytic cycle of cytochrome c oxidase. Proc. Natl. Acad. Sci. U.S.A. 100, 8715-8720.
    • (2003) Proc. Natl. Acad. Sci. U.S.A , vol.100 , pp. 8715-8720
    • Nyquist, R.M.1    Heitbrink, D.2    Bolwien, C.3    Gennis, R.B.4    Heberle, J.5
  • 42
    • 0344071850 scopus 로고
    • Reaction of oxygen with respiratory chain in cells and tissues
    • Chance, B. (1965) Reaction of oxygen with respiratory chain in cells and tissues. J. Gen. Physiol. 49, 163-195.
    • (1965) J. Gen. Physiol , vol.49 , pp. 163-195
    • Chance, B.1
  • 43
    • 0028955899 scopus 로고
    • Fast reactions of cytochrome oxidase
    • Einarsdottir, O. (1995) Fast reactions of cytochrome oxidase. Biochim. Biophys. Acta 1229, 129-147.
    • (1995) Biochim. Biophys. Acta , vol.1229 , pp. 129-147
    • Einarsdottir, O.1
  • 44
    • 0016709349 scopus 로고
    • Functional intermediates in reaction of membrane-bound cytochrome-oxidase with oxygen
    • Chance, B., Saronio, C., and Leigh, J. S. (1975) Functional intermediates in reaction of membrane-bound cytochrome-oxidase with oxygen. J. Biol. Chem. 250, 9226-9237.
    • (1975) J. Biol. Chem , vol.250 , pp. 9226-9237
    • Chance, B.1    Saronio, C.2    Leigh, J.S.3
  • 45
    • 0025096278 scopus 로고
    • Cytochrome c oxidase: Decay of the primary oxygen intermediate involves direct electron transfer from cytochrome a
    • Han, S., Ching, Y. C., and Rousseau, D. L. (1990) Cytochrome c oxidase: Decay of the primary oxygen intermediate involves direct electron transfer from cytochrome a. Proc. Natl. Acad. Sci. U.S.A. 87, 8408-8412.
    • (1990) Proc. Natl. Acad. Sci. U.S.A , vol.87 , pp. 8408-8412
    • Han, S.1    Ching, Y.C.2    Rousseau, D.L.3
  • 46
    • 0016782319 scopus 로고
    • Oxygen diffusion in biological and artificial membranes determined by the fluorochrome pyrene
    • Fischkoff, S., and Vanderkooi, J. M. (1975) Oxygen diffusion in biological and artificial membranes determined by the fluorochrome pyrene. J. Gen. Physiol. 65, 663-676.
    • (1975) J. Gen. Physiol , vol.65 , pp. 663-676
    • Fischkoff, S.1    Vanderkooi, J.M.2
  • 47
    • 0016542177 scopus 로고
    • Solvation of oxygen in lechtin bilayers
    • Kimmich, R., and Peters, A. (1975) Solvation of oxygen in lechtin bilayers. Chem. Phys. Lipids 14, 350-362.
    • (1975) Chem. Phys. Lipids , vol.14 , pp. 350-362
    • Kimmich, R.1    Peters, A.2
  • 48
    • 0017918326 scopus 로고
    • Heterogeneous solubility of oxygen in aqueous lecithin dispersions and its relation to chain mobility: NMR relaxation and wide-line study
    • Peters, A., and Kimmich, R. (1978) Heterogeneous solubility of oxygen in aqueous lecithin dispersions and its relation to chain mobility: NMR relaxation and wide-line study. Biophys. Struct. Mech. 4, 67-85.
    • (1978) Biophys. Struct. Mech , vol.4 , pp. 67-85
    • Peters, A.1    Kimmich, R.2
  • 49
    • 0023869404 scopus 로고
    • The oxygen dpendence of mitochondrial oxidative phosphorylation measured by a new optical method for measuring oxygen concentration
    • Wilson, D. F., Rumsey, W. L., Green, T. J., and Vanderkooi, J. M. (1988) The oxygen dpendence of mitochondrial oxidative phosphorylation measured by a new optical method for measuring oxygen concentration. J. Biol. Chem. 263, 2712-2718.
    • (1988) J. Biol. Chem , vol.263 , pp. 2712-2718
    • Wilson, D.F.1    Rumsey, W.L.2    Green, T.J.3    Vanderkooi, J.M.4
  • 50
    • 0037617781 scopus 로고
    • Oxygen transport parameter in membranes as deduced by saturation recovery measurements of spin-lattice relaxation times of spin labels
    • Kusumi, A., Subczynski, W. K., and Hyde, J. S. (1982) Oxygen transport parameter in membranes as deduced by saturation recovery measurements of spin-lattice relaxation times of spin labels. Proc. Natl. Acad. Sci. U.S.A. 79, 1854-1858.
    • (1982) Proc. Natl. Acad. Sci. U.S.A , vol.79 , pp. 1854-1858
    • Kusumi, A.1    Subczynski, W.K.2    Hyde, J.S.3
  • 53
    • 0041806720 scopus 로고    scopus 로고
    • Myoglobin: The hydrogen atom of biology and a paradigm of complexity
    • Frauenfelder, H., McMahon, B. H., and Fenimore, P. W. (2003) Myoglobin: The hydrogen atom of biology and a paradigm of complexity. Proc. Natl. Acad. Sci. U.S.A. 100, 8615-8617.
    • (2003) Proc. Natl. Acad. Sci. U.S.A , vol.100 , pp. 8615-8617
    • Frauenfelder, H.1    McMahon, B.H.2    Fenimore, P.W.3
  • 54
    • 0020490364 scopus 로고
    • 3Fe and CuB in cytochrome c oxidase in beef heart mitochondria studied by Fourier-transform infrared spectroscopy at low temperatures
    • 3Fe and CuB in cytochrome c oxidase in beef heart mitochondria studied by Fourier-transform infrared spectroscopy at low temperatures. J. Biol. Chem. 257, 1639-1650.
    • (1982) J. Biol. Chem , vol.257 , pp. 1639-1650
    • Fiamingo, F.G.1    Altschuld, R.A.2    Moh, P.P.3    Alben, J.O.4
  • 56
    • 0027308712 scopus 로고
    • Coordination dynamics of heme-copper oxidases: The ligand shuttle and the control and coupling of electron transfer and proton translocation
    • Woodruff, W. H. (1993) Coordination dynamics of heme-copper oxidases: The ligand shuttle and the control and coupling of electron transfer and proton translocation. J. Bioenerg. Biomembr. 25, 177-188.
    • (1993) J. Bioenerg. Biomembr , vol.25 , pp. 177-188
    • Woodruff, W.H.1
  • 58
    • 0344961407 scopus 로고    scopus 로고
    • Ligand binding in a docking site of cytochrome c oxidase: A time-resolved step-scan Fourier transform infrared study
    • Koutsoupakis, C., Soulimane, T., and Varotsis, C. (2003) Ligand binding in a docking site of cytochrome c oxidase: A time-resolved step-scan Fourier transform infrared study. J. Am. Chem. Soc. 125, 14728-14732.
    • (2003) J. Am. Chem. Soc , vol.125 , pp. 14728-14732
    • Koutsoupakis, C.1    Soulimane, T.2    Varotsis, C.3
  • 60
    • 0027359220 scopus 로고
    • The gateway to the active site of heme copper oxidases
    • Lemon, D. D., Calhoun, M. W., Gennis, R. B., and Woodruff, W. H. (1993) The gateway to the active site of heme copper oxidases. Biochemistry 32, 11953-11956.
    • (1993) Biochemistry , vol.32 , pp. 11953-11956
    • Lemon, D.D.1    Calhoun, M.W.2    Gennis, R.B.3    Woodruff, W.H.4


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