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Volumn 91, Issue 6, 2006, Pages 2035-2045

Pathways of H2 toward the active site of [NiFe]-hydrogenase

Author keywords

[No Author keywords available]

Indexed keywords

ALANINE; HYDROGEN; HYDROGENASE; IRON; MUTANT PROTEIN; NICKEL; SOLVENT; VALINE; ION; NICKEL IRON HYDROGENASE; NICKEL-IRON HYDROGENASE;

EID: 33748456960     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1529/biophysj.106.084376     Document Type: Article
Times cited : (65)

References (61)
  • 1
    • 0028568063 scopus 로고
    • Nickel hydrogenases: In search of the active site
    • Albracht, S. P. J. 1994. Nickel hydrogenases: in search of the active site. Biochim. Biophys. Acta. 1188:167-204.
    • (1994) Biochim. Biophys. Acta , vol.1188 , pp. 167-204
    • Albracht, S.P.J.1
  • 2
    • 0001748001 scopus 로고
    • Carbanion mechanism. 6.1 Metallation of arylmethanes by potassium hydride/18-Crown-6 ether in tetrahydrofuran and the acidity of hydrogen
    • Buncel, E., and B. Menon. 1977. Carbanion mechanism. 6.1 Metallation of arylmethanes by potassium hydride/18-Crown-6 ether in tetrahydrofuran and the acidity of hydrogen. J. Am. Chem. Soc. 99:4457-4461.
    • (1977) J. Am. Chem. Soc. , vol.99 , pp. 4457-4461
    • Buncel, E.1    Menon, B.2
  • 3
    • 0000825849 scopus 로고
    • Highly reactive dihydrogen complexes of ruthenium and rhenium: Facile heterolysis of coordinated dihydrogen
    • Chinn, M. S., D. M. Heynekey, N. G. Payne, and C. D. Sofield. 1989. Highly reactive dihydrogen complexes of ruthenium and rhenium: facile heterolysis of coordinated dihydrogen. Organometallics. 8:1824-1826.
    • (1989) Organometallics , vol.8 , pp. 1824-1826
    • Chinn, M.S.1    Heynekey, D.M.2    Payne, N.G.3    Sofield, C.D.4
  • 4
    • 0000420682 scopus 로고
    • Coordination of dihydrogen
    • Heinekey, D. M., and W. J. Oldham. 1993. Coordination of dihydrogen. Chem. Rev. 93:913-926.
    • (1993) Chem. Rev. , vol.93 , pp. 913-926
    • Heinekey, D.M.1    Oldham, W.J.2
  • 6
    • 0036523377 scopus 로고    scopus 로고
    • Hydrogenases: Hydrogen-activating enzymes
    • Frey, M. 2002. Hydrogenases: hydrogen-activating enzymes. ChemBioChem. 3:153-160.
    • (2002) ChemBioChem. , vol.3 , pp. 153-160
    • Frey, M.1
  • 7
    • 0034886919 scopus 로고    scopus 로고
    • Classification and phylogeny of hydrogenases
    • Vignais, P. M., B. Billoud, and J. Meyer. 2001. Classification and phylogeny of hydrogenases. FEMS Microbiol. Rev. 25:455-501.
    • (2001) FEMS Microbiol. Rev. , vol.25 , pp. 455-501
    • Vignais, P.M.1    Billoud, B.2    Meyer, J.3
  • 8
    • 0017899813 scopus 로고
    • Characterization of the periplasmic hydrogenase from Desulfovibrio gigas
    • Hatchikian, E. C., M. Bruschi, and J. LeGall. 1978. Characterization of the periplasmic hydrogenase from Desulfovibrio gigas. Biochem. Biophys. Res. Commun. 82:451-461.
    • (1978) Biochem. Biophys. Res. Commun. , vol.82 , pp. 451-461
    • Hatchikian, E.C.1    Bruschi, M.2    LeGall, J.3
  • 11
    • 0029066353 scopus 로고
    • Infrared-detectable groups sense changes in charge density on the nickel center in hydrogenase from Chromatium vinosum
    • Bagley, K. A., E. C. Duin, W. Roseboom, S. P. J. Albracht, and W. H. Woodruff. 1995. Infrared-detectable groups sense changes in charge density on the nickel center in hydrogenase from Chromatium vinosum. Biochemistry. 34:5527-5535.
    • (1995) Biochemistry , vol.34 , pp. 5527-5535
    • Bagley, K.A.1    Duin, E.C.2    Roseboom, W.3    Albracht, S.P.J.4    Woodruff, W.H.5
  • 13
    • 0033611949 scopus 로고    scopus 로고
    • Theoretical characterization of the reaction intermediates in a model of the nickel-iron hydrogenase of Desulfovibrio gigas
    • Niu, S., L. M. Thomson, and M. B. Hall. 1999. Theoretical characterization of the reaction intermediates in a model of the nickel-iron hydrogenase of Desulfovibrio gigas. J. Am. Chem. Soc. 121:4000-4007.
    • (1999) J. Am. Chem. Soc. , vol.121 , pp. 4000-4007
    • Niu, S.1    Thomson, L.M.2    Hall, M.B.3
  • 15
    • 0021826804 scopus 로고
    • Electron paramagnetic resonance studies on the mechanism of activation and the catalytic cycle of the nickel-containing hydrogenase from Desulfovibrio gigas
    • Teixeira, M., I. Moura, A. V. Xavier, B. H. Huynh, D. V. Der Vartanian, H. D. Peck, Jr., J. LeGall, and J. J. G. Moura. 1985. Electron paramagnetic resonance studies on the mechanism of activation and the catalytic cycle of the nickel-containing hydrogenase from Desulfovibrio gigas. J. Biol. Chem. 260:8942-8950.
    • (1985) J. Biol. Chem. , vol.260 , pp. 8942-8950
    • Teixeira, M.1    Moura, I.2    Xavier, A.V.3    Huynh, B.H.4    Der Vartanian, D.V.5    Peck Jr., H.D.6    LeGall, J.7    Moura, J.J.G.8
  • 16
    • 0014400785 scopus 로고
    • Purification and properties of hydrogenases of different origins
    • Yagi, T., M. Honya, and N. Tamiya. 1968. Purification and properties of hydrogenases of different origins. Biochim. Biophys. Acta. 153:699-705.
    • (1968) Biochim. Biophys. Acta , vol.153 , pp. 699-705
    • Yagi, T.1    Honya, M.2    Tamiya, N.3
  • 19
    • 0022370609 scopus 로고
    • Properties and reactivation of two different deactivated forms of Desulfovibrio gigas hydrogenase
    • Fernandez, V. M., E. Claude Hatchikian, and R. Cammack. 1985. Properties and reactivation of two different deactivated forms of Desulfovibrio gigas hydrogenase. Biochim. Biophys. Acta. 832:69-79.
    • (1985) Biochim. Biophys. Acta , vol.832 , pp. 69-79
    • Fernandez, V.M.1    Claude Hatchikian, E.2    Cammack, R.3
  • 20
    • 0000879509 scopus 로고
    • ESR-detectable nickel and iron-sulphur centers in relation to the reversible activation of Desulfovibrio gigas hydrogenase
    • Fernandez, V. M., E. C. Hatchikian, D. Patil, and R. Cammack. 1986. ESR-detectable nickel and iron-sulphur centers in relation to the reversible activation of Desulfovibrio gigas hydrogenase. Biochim. Biophys. Acta. 883:145-154.
    • (1986) Biochim. Biophys. Acta , vol.883 , pp. 145-154
    • Fernandez, V.M.1    Hatchikian, E.C.2    Patil, D.3    Cammack, R.4
  • 21
    • 0002884165 scopus 로고
    • Nickel and iron-sulphur centers in Desulfovibrio gigas hydrogenase: ESR spectra, redox properties and interactions
    • Cammack, R., D. Patil, E. C. Hatchikian, and V. M. Fernandez. 1987. Nickel and iron-sulphur centers in Desulfovibrio gigas hydrogenase: ESR spectra, redox properties and interactions. Biochim. Biophys. Acta. 912:98-109.
    • (1987) Biochim. Biophys. Acta , vol.912 , pp. 98-109
    • Cammack, R.1    Patil, D.2    Hatchikian, E.C.3    Fernandez, V.M.4
  • 23
    • 0000207156 scopus 로고
    • An x-ray absorption spectroscopy of nickel redox chemistry in hydrogenase
    • Bagyinka, C., J. P. Whitehead, and M. J. Maroney. 1993. An x-ray absorption spectroscopy of nickel redox chemistry in hydrogenase. J. Am. Chem. Soc. 115:3576-3585.
    • (1993) J. Am. Chem. Soc. , vol.115 , pp. 3576-3585
    • Bagyinka, C.1    Whitehead, J.P.2    Maroney, M.J.3
  • 26
    • 0030799641 scopus 로고    scopus 로고
    • Nature and electronic structure of the Ni-X dinuclear center of Desulfovibrio gigas hydrogenase. Implications for the enzyme mechanism
    • Dole, F., A. Fournel, V. Magro, E. C. Hatchikian, P. Bertrand, and B. Guigliarelli. 1997. Nature and electronic structure of the Ni-X dinuclear center of Desulfovibrio gigas hydrogenase. Implications for the enzyme mechanism. Biochemistry. 36:7847-7854.
    • (1997) Biochemistry , vol.36 , pp. 7847-7854
    • Dole, F.1    Fournel, A.2    Magro, V.3    Hatchikian, E.C.4    Bertrand, P.5    Guigliarelli, B.6
  • 28
    • 0033549110 scopus 로고    scopus 로고
    • A hybrid density functional theory/molecular mechanics study of nickel-iron hydrogenase: Investigation of the active site redox states
    • Amara, P., A. Volbeda, J. C. Fontecilla-Camps, and M. J. Field. 1999. A hybrid density functional theory/molecular mechanics study of nickel-iron hydrogenase: investigation of the active site redox states. J. Am. Chem. Soc. 121:4468-4477.
    • (1999) J. Am. Chem. Soc. , vol.121 , pp. 4468-4477
    • Amara, P.1    Volbeda, A.2    Fontecilla-Camps, J.C.3    Field, M.J.4
  • 29
    • 4243471427 scopus 로고    scopus 로고
    • Ni-Fe hydrogenases: A density functional theory study of active site models
    • de Gioia, L., P. Fantucci, B. Guigliarelli, and P. Bertrand. 1999. Ni-Fe hydrogenases: a density functional theory study of active site models. Inorg. Chem. 38:2658-2662.
    • (1999) Inorg. Chem. , vol.38 , pp. 2658-2662
    • De Gioia, L.1    Fantucci, P.2    Guigliarelli, B.3    Bertrand, P.4
  • 30
    • 0034851266 scopus 로고    scopus 로고
    • Recent theoretical predictions of the active site for the observed forms in the catalytic cycle of Ni-Fe hydrogenase
    • Fan, H.-J., and M. B. Hall. 2001. Recent theoretical predictions of the active site for the observed forms in the catalytic cycle of Ni-Fe hydrogenase. J. Biol. Inorg. Chem. 6:467-473.
    • (2001) J. Biol. Inorg. Chem. , vol.6 , pp. 467-473
    • Fan, H.-J.1    Hall, M.B.2
  • 31
    • 0035127517 scopus 로고    scopus 로고
    • Modeling the active sites of metalloenzymes. 4. Predictions of the unready states of [NiFe] Desulfovibrio gigas hydrogenase from density functional theory
    • Li, S., and M. B. Hall. 2001. Modeling the active sites of metalloenzymes. 4. Predictions of the unready states of [NiFe] Desulfovibrio gigas hydrogenase from density functional theory. Inorg. Chem. 40:18-24.
    • (2001) Inorg. Chem. , vol.40 , pp. 18-24
    • Li, S.1    Hall, M.B.2
  • 35
    • 0034720767 scopus 로고    scopus 로고
    • Structural examination of the nickel site in Chromatium vinosum hydrogenase: Redox state oscillations and structural changes accompanying reductive activation and CO binding
    • Davidson, G., S. B. Choudhury, Z. Gu, K. Bose, W. Roseboom, S. P. J. Albracht, and M. J. Maroney. 2000. Structural examination of the nickel site in Chromatium vinosum hydrogenase: redox state oscillations and structural changes accompanying reductive activation and CO binding. Biochemistry. 39:7468-7479.
    • (2000) Biochemistry , vol.39 , pp. 7468-7479
    • Davidson, G.1    Choudhury, S.B.2    Gu, Z.3    Bose, K.4    Roseboom, W.5    Albracht, S.P.J.6    Maroney, M.J.7
  • 39
    • 3042524904 scopus 로고
    • A well-behaved electrostatic based method using charge restraints for deriving atomic charges: The RESP model
    • Bayly, C. I., P. Cieplak, W. D. Cornell, and P. A. Kollman. 1993. A well-behaved electrostatic based method using charge restraints for deriving atomic charges: the RESP model. J. Phys. Chem. 97:10269-10280.
    • (1993) J. Phys. Chem. , vol.97 , pp. 10269-10280
    • Bayly, C.I.1    Cieplak, P.2    Cornell, W.D.3    Kollman, P.A.4
  • 41
    • 0042041206 scopus 로고
    • UFF, a full periodic table force field for molecular mechanics and molecular dynamics simulations
    • Rappé, A. K., C. J. Casewit, K. S. Colwell, W. A. Goddard III, and W. M. Skiff. 1992. UFF, a full periodic table force field for molecular mechanics and molecular dynamics simulations. J. Am. Chem. Soc. 114:10024-10035.
    • (1992) J. Am. Chem. Soc. , vol.114 , pp. 10024-10035
    • Rappé, A.K.1    Casewit, C.J.2    Colwell, K.S.3    Goddard III, W.A.4    Skiff, W.M.5
  • 43
    • 0035120969 scopus 로고    scopus 로고
    • Some theoretical and computational aspects of the inclusion of proton isomerism in the protonation equilibrium of proteins
    • Baptista, A. M., and C. M. Soares. 2001. Some theoretical and computational aspects of the inclusion of proton isomerism in the protonation equilibrium of proteins. J. Phys. Chem. B. 105:293-309.
    • (2001) J. Phys. Chem. B , vol.105 , pp. 293-309
    • Baptista, A.M.1    Soares, C.M.2
  • 44
    • 0036359052 scopus 로고    scopus 로고
    • Studies of the reduction and protonation behavior of the tetraheme cytochromes using atomic detail
    • Teixeira, V. H., C. M. Soares, and A. M. Baptista. 2002. Studies of the reduction and protonation behavior of the tetraheme cytochromes using atomic detail. J. Biol. Inorg. Chem. 7:200-216.
    • (2002) J. Biol. Inorg. Chem. , vol.7 , pp. 200-216
    • Teixeira, V.H.1    Soares, C.M.2    Baptista, A.M.3
  • 45
    • 0026612756 scopus 로고
    • a values of ionizable groups in bacteriorhodopsin
    • a values of ionizable groups in bacteriorhodopsin. J. Mol. Biol. 224:473-486.
    • (1992) J. Mol. Biol. , vol.224 , pp. 473-486
    • Bashford, D.1    Gerwert, K.2
  • 46
    • 84957665033 scopus 로고    scopus 로고
    • An object-oriented programming suite for electrostatic effects in biological molecules
    • Y. Ishikawa, R. R. Oldehoeft, J. V. W. Reynders, and M. Tholburn, editors. ISCOPE97, Springer, Berlin
    • Bashford, D. 1997. An object-oriented programming suite for electrostatic effects in biological molecules. In Scientific Computing in Object-Oriented Parallel Environments. Y. Ishikawa, R. R. Oldehoeft, J. V. W. Reynders, and M. Tholburn, editors. ISCOPE97, Springer, Berlin, 233-240.
    • (1997) Scientific Computing in Object-Oriented Parallel Environments , pp. 233-240
    • Bashford, D.1
  • 48
    • 23844500381 scopus 로고    scopus 로고
    • On the use of different dielectric constants for computing individual and pairwise terms in Poisson-Boltzmann studies of protein ionization equilibrium
    • Teixeira, V. H., C. C. Cunha, M. Machuqueiro, A. S. F. Oliveira, B. L. Victor, C. M. Soares, and A. M. Baptista. 2005. On the use of different dielectric constants for computing individual and pairwise terms in Poisson-Boltzmann studies of protein ionization equilibrium. J. Phys. Chem. B. 109:14691-14706.
    • (2005) J. Phys. Chem. B , vol.109 , pp. 14691-14706
    • Teixeira, V.H.1    Cunha, C.C.2    Machuqueiro, M.3    Oliveira, A.S.F.4    Victor, B.L.5    Soares, C.M.6    Baptista, A.M.7
  • 50
    • 0035789518 scopus 로고    scopus 로고
    • GROMACS 3.0: A package for molecular simulation and trajectory analysis
    • Lindahl, E., B. Hess, and D. van der Spoel. 2001. GROMACS 3.0: a package for molecular simulation and trajectory analysis. J. Mol. Model. (Online). 7:306-317.
    • (2001) J. Mol. Model. (Online) , vol.7 , pp. 306-317
    • Lindahl, E.1    Hess, B.2    Van Der Spoel, D.3
  • 54
    • 0028040064 scopus 로고
    • Evaluation of the conformational free energies of loops in proteins
    • Smith, K. C., and B. Honig. 1994. Evaluation of the conformational free energies of loops in proteins. Proteins Struct. Funct. Genet. 18:119-132.
    • (1994) Proteins Struct. Funct. Genet. , vol.18 , pp. 119-132
    • Smith, K.C.1    Honig, B.2
  • 55
    • 2242491482 scopus 로고
    • Consistent dielectric properties of the simple point charge and extended point charge water models at 277 and 300 K
    • Smith, P. E., and W. F. van Gunsteren. 1994. Consistent dielectric properties of the simple point charge and extended point charge water models at 277 and 300 K. J. Chem. Phys. 100:3169-3174.
    • (1994) J. Chem. Phys. , vol.100 , pp. 3169-3174
    • Smith, P.E.1    Van Gunsteren, W.F.2
  • 59
    • 21244441201 scopus 로고    scopus 로고
    • 2-sensing [NiFe] hydrogenase from Ralstonia eutropha H16 is based on limited access of oxygen to the active site
    • 2-sensing [NiFe] hydrogenase from Ralstonia eutropha H16 is based on limited access of oxygen to the active site. J. Biol. Chem. 280:23791-23796.
    • (2005) J. Biol. Chem. , vol.280 , pp. 23791-23796
    • Buhrke, T.1    Lenz, O.2    Krauss, N.3    Friedrich, B.4


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