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Volumn 52, Issue 45, 2013, Pages 7943-7950

Functional consequences of the open distal pocket of dehaloperoxidase- hemoglobin observed by time-resolved x-ray crystallography

Author keywords

[No Author keywords available]

Indexed keywords

BI-FUNCTIONAL; CONFORMATIONAL STATE; DISTAL POCKET; DOCKING SITES; OPEN ARCHITECTURE; PEROXIDASE CYCLE; REDUCTION POTENTIAL; TIME-RESOLVED;

EID: 84887599535     PISSN: 00062960     EISSN: 15204995     Source Type: Journal    
DOI: 10.1021/bi401118q     Document Type: Article
Times cited : (4)

References (53)
  • 4
    • 70350705724 scopus 로고    scopus 로고
    • Ligand migration and cavities within scapharca dimeric Hbl: Studies by time-resolved crystallography, Xe binding, and computational analysis
    • Knapp, J. E., Pahl, R., Cohen, J., Nichols, J. C., Schulten, K., Gibson, Q. H., Srajer, V., and Royer, W. E. (2009) Ligand migration and cavities within scapharca dimeric Hbl: Studies by time-resolved crystallography, Xe binding, and computational analysis Structure 17, 1494-1504
    • (2009) Structure , vol.17 , pp. 1494-1504
    • Knapp, J.E.1    Pahl, R.2    Cohen, J.3    Nichols, J.C.4    Schulten, K.5    Gibson, Q.H.6    Srajer, V.7    Royer, W.E.8
  • 5
    • 33646755415 scopus 로고    scopus 로고
    • Allosteric action in real time: Time-resolved crystallographic studies of a cooperative dimeric hemoglobin
    • Knapp, J. E., Pahl, R., Srajer, V., and Royer, W. E. (2006) Allosteric action in real time: Time-resolved crystallographic studies of a cooperative dimeric hemoglobin Proc Natl Acad Sci U.S.A. 103, 7649-7654
    • (2006) Proc Natl Acad Sci U.S.A. , vol.103 , pp. 7649-7654
    • Knapp, J.E.1    Pahl, R.2    Srajer, V.3    Royer, W.E.4
  • 6
    • 0035895937 scopus 로고    scopus 로고
    • Mapping the pathways for O2 entry into and exit from myoglobin
    • Scott, E. E., Gibson, Q. H., and Olson, J. S. (2001) Mapping the pathways for O2 entry into and exit from myoglobin J. Biol. Chem. 276, 5177-5188
    • (2001) J. Biol. Chem. , vol.276 , pp. 5177-5188
    • Scott, E.E.1    Gibson, Q.H.2    Olson, J.S.3
  • 7
    • 34547953953 scopus 로고    scopus 로고
    • Ligand pathways in myoglobin: A review of trp cavity mutations
    • Olson, J. S., Soman, J., and Phillips, G. N. (2007) Ligand pathways in myoglobin: A review of trp cavity mutations IUBMB Life 59, 552-562
    • (2007) IUBMB Life , vol.59 , pp. 552-562
    • Olson, J.S.1    Soman, J.2    Phillips, G.N.3
  • 8
    • 0036040539 scopus 로고    scopus 로고
    • Infrared study of carbon monoxide migration among internal cavities of myoglobin mutant L29W
    • Nienhaus, G. U. and Nienhaus, K. (2002) Infrared study of carbon monoxide migration among internal cavities of myoglobin mutant L29W J. Biol. Phys. 28, 163-172
    • (2002) J. Biol. Phys. , vol.28 , pp. 163-172
    • Nienhaus, G.U.1    Nienhaus, K.2
  • 9
    • 0042242570 scopus 로고    scopus 로고
    • Structural dynamics of myoglobin: Spectroscopic and structural characterization of ligand docking sites in myoglobin mutant L29W
    • Nienhaus, K., Deng, P. C., Kriegl, J. M., and Nienhaus, G. U. (2003) Structural dynamics of myoglobin: Spectroscopic and structural characterization of ligand docking sites in myoglobin mutant L29W Biochemistry 42, 9633-9646
    • (2003) Biochemistry , vol.42 , pp. 9633-9646
    • Nienhaus, K.1    Deng, P.C.2    Kriegl, J.M.3    Nienhaus, G.U.4
  • 10
  • 11
    • 37149055029 scopus 로고    scopus 로고
    • Ligand migration and binding in the dimeric hemoglobin of Scapharca inaequivalvis
    • Nienhaus, K., Knapp, J. E., Palladino, P., Royer, W. E., and Nienhaus, G. U. (2007) Ligand migration and binding in the dimeric hemoglobin of Scapharca inaequivalvis Biochemistry 46, 14018-14031
    • (2007) Biochemistry , vol.46 , pp. 14018-14031
    • Nienhaus, K.1    Knapp, J.E.2    Palladino, P.3    Royer, W.E.4    Nienhaus, G.U.5
  • 13
    • 84875793959 scopus 로고    scopus 로고
    • Structural evidence for stabilization of inhibitor binding by a protein cavity in the dehaloperoxidase-hemoglobin from Amphitrite ornata
    • de Serrano, V. and Franzen, S. (2012) Structural evidence for stabilization of inhibitor binding by a protein cavity in the dehaloperoxidase-hemoglobin from Amphitrite ornata Pept. Sci. 98, 27-35
    • (2012) Pept. Sci. , vol.98 , pp. 27-35
    • De Serrano, V.1    Franzen, S.2
  • 14
    • 0039316844 scopus 로고    scopus 로고
    • An unusual dehalogenating peroxidase from the marine terebellid ploychaete Amphitrite ornata
    • Chen, Y. P., Woodin, S. A., Lincoln, D. E., and Lovell, C. R. (1996) An unusual dehalogenating peroxidase from the marine terebellid ploychaete Amphitrite ornata J. Biol. Chem. 271, 4609-4612
    • (1996) J. Biol. Chem. , vol.271 , pp. 4609-4612
    • Chen, Y.P.1    Woodin, S.A.2    Lincoln, D.E.3    Lovell, C.R.4
  • 16
    • 79959950550 scopus 로고    scopus 로고
    • Reactivity of deoxy- and oxyferrous dehaloperoxidase B from Amphitrite ornata: Identification of compound II and its ferrous-hydroperoxide precursor
    • D'Antonio, J. and Ghiladi, R. A. (2011) Reactivity of deoxy- and oxyferrous dehaloperoxidase B from Amphitrite ornata: Identification of compound II and its ferrous-hydroperoxide precursor Biochemistry 50, 5999-6011
    • (2011) Biochemistry , vol.50 , pp. 5999-6011
    • D'Antonio, J.1    Ghiladi, R.A.2
  • 18
  • 19
    • 77954310525 scopus 로고    scopus 로고
    • An analysis of substrate binding interactions in the heme peroxidase enzymes: A structural perspective
    • Gumiero, A., Murphy, E. J., Metcalfe, C. L., Moody, P. C. E., and Raven, E. L. (2010) An analysis of substrate binding interactions in the heme peroxidase enzymes: A structural perspective Arch. Biochem. Biophys. 500, 13-20
    • (2010) Arch. Biochem. Biophys. , vol.500 , pp. 13-20
    • Gumiero, A.1    Murphy, E.J.2    Metcalfe, C.L.3    Moody, P.C.E.4    Raven, E.L.5
  • 20
    • 4344574384 scopus 로고    scopus 로고
    • Picosecond time-resolved X-ray crystallography: Probing protein function in real time
    • Schotte, F., Soman, J., Olson, J. S., Wulff, M., and Anfinrud, P. A. (2004) Picosecond time-resolved X-ray crystallography: Probing protein function in real time J. Struct. Biol. 147, 235-246
    • (2004) J. Struct. Biol. , vol.147 , pp. 235-246
    • Schotte, F.1    Soman, J.2    Olson, J.S.3    Wulff, M.4    Anfinrud, P.A.5
  • 24
    • 79959541238 scopus 로고    scopus 로고
    • RenZ Research Inc. Westmont, IL.
    • Ren, Z. (2010) Precognition User Guide, RenZ Research Inc., Westmont, IL.
    • (2010) Precognition User Guide
    • Ren, Z.1
  • 27
    • 0035923399 scopus 로고    scopus 로고
    • A molecular movie at 1.8 angstrom resolution displays the photocycle of photoactive yellow protein, a eubacterial blue-light receptor, from nanoseconds to seconds
    • Ren, Z., Perman, B., Srajer, V., Teng, T. Y., Pradervand, C., Bourgeois, D., Schotte, F., Ursby, T., Kort, R., Wulff, M., and Moffat, K. (2001) A molecular movie at 1.8 angstrom resolution displays the photocycle of photoactive yellow protein, a eubacterial blue-light receptor, from nanoseconds to seconds Biochemistry 40, 13788-13801
    • (2001) Biochemistry , vol.40 , pp. 13788-13801
    • Ren, Z.1    Perman, B.2    Srajer, V.3    Teng, T.Y.4    Pradervand, C.5    Bourgeois, D.6    Schotte, F.7    Ursby, T.8    Kort, R.9    Wulff, M.10    Moffat, K.11
  • 30
    • 48749148224 scopus 로고
    • Rattle: A "velocity" version of the shake algorithm for molecular dynamics calculations
    • Andersen, H. C. (1983) Rattle: A "velocity" version of the shake algorithm for molecular dynamics calculations J. Comput. Phys. 52, 24-34
    • (1983) J. Comput. Phys. , vol.52 , pp. 24-34
    • Andersen, H.C.1
  • 31
    • 0035870662 scopus 로고    scopus 로고
    • Multigrid methods for classical molecular dynamics simulations of biomolecules
    • Sagui, C. and Darden, T. (2001) Multigrid methods for classical molecular dynamics simulations of biomolecules J. Chem. Phys. 114, 6578-6591
    • (2001) J. Chem. Phys. , vol.114 , pp. 6578-6591
    • Sagui, C.1    Darden, T.2
  • 32
    • 34748844557 scopus 로고    scopus 로고
    • X-ray crystal structural analysis of the binding site in the ferric and oxyferrous forms of the recombinant heme dehaloperoxidase cloned from Amphitrite ornata
    • de Serrano, V., Chen, Z. X., Davis, M. F., and Franzen, S. (2007) X-ray crystal structural analysis of the binding site in the ferric and oxyferrous forms of the recombinant heme dehaloperoxidase cloned from Amphitrite ornata Acta Crystallogr., Sect. D 63, 1094-1101
    • (2007) Acta Crystallogr., Sect. D , vol.63 , pp. 1094-1101
    • De Serrano, V.1    Chen, Z.X.2    Davis, M.F.3    Franzen, S.4
  • 33
    • 33746349251 scopus 로고    scopus 로고
    • Spectroscopic study of substrate binding to the carbonmonoxy form of dehaloperoxidase from Amphitrite ornata
    • Nienhaus, K., Deng, P., Belyea, J., Franzen, S., and Nienhaus, G. U. (2006) Spectroscopic study of substrate binding to the carbonmonoxy form of dehaloperoxidase from Amphitrite ornata J. Phys. Chem. B 110, 13264-13276
    • (2006) J. Phys. Chem. B , vol.110 , pp. 13264-13276
    • Nienhaus, K.1    Deng, P.2    Belyea, J.3    Franzen, S.4    Nienhaus, G.U.5
  • 34
    • 0035923445 scopus 로고    scopus 로고
    • Protein conformational relaxation and ligand migration in myoglobin: A nanosecond to millisecond molecular movie from time-resolved Laue X-ray diffraction
    • Srajer, V., Ren, Z., Teng, T. Y., Schmidt, M., Ursby, T., Bourgeois, D., Pradervand, C., Schildkamp, W., Wulff, M., and Moffat, K. (2001) Protein conformational relaxation and ligand migration in myoglobin: A nanosecond to millisecond molecular movie from time-resolved Laue X-ray diffraction Biochemistry 40, 13802-13815
    • (2001) Biochemistry , vol.40 , pp. 13802-13815
    • Srajer, V.1    Ren, Z.2    Teng, T.Y.3    Schmidt, M.4    Ursby, T.5    Bourgeois, D.6    Pradervand, C.7    Schildkamp, W.8    Wulff, M.9    Moffat, K.10
  • 35
    • 84875986002 scopus 로고    scopus 로고
    • Structural and kinetic study of an internal substrate binding site in dehaloperoxidase-hemoglobin A from Amphitrite ornata
    • Zhao, J., de Serrano, V., Zhao, J., Le, P., and Franzen, S. (2013) Structural and kinetic study of an internal substrate binding site in dehaloperoxidase-hemoglobin A from Amphitrite ornata Biochemistry 52, 2427-2439
    • (2013) Biochemistry , vol.52 , pp. 2427-2439
    • Zhao, J.1    De Serrano, V.2    Zhao, J.3    Le, P.4    Franzen, S.5
  • 36
    • 0021766921 scopus 로고
    • Cavities in proteins: Structure of a metmyoglobin xenon complex solved to 1.9 Å
    • Tilton, R. F., Jr., Kuntz, I. D., Jr., and Petsko, G. A. (1984) Cavities in proteins: Structure of a metmyoglobin xenon complex solved to 1.9 Å Biochemistry 23, 2849-2857
    • (1984) Biochemistry , vol.23 , pp. 2849-2857
    • Tilton Jr., R.F.1    Kuntz Jr., I.D.2    Petsko, G.A.3
  • 38
    • 0028519126 scopus 로고
    • Photolysis-induced structural changes in single crystals of carbonmonoxy myoglobin at 40 K
    • Teng, T.-Y., Srajer, V., and Moffat, K. (1994) Photolysis-induced structural changes in single crystals of carbonmonoxy myoglobin at 40 K Nat. Struct. Biol. 1, 701-705
    • (1994) Nat. Struct. Biol. , vol.1 , pp. 701-705
    • Teng, T.-Y.1    Srajer, V.2    Moffat, K.3
  • 39
    • 0030821996 scopus 로고    scopus 로고
    • Initial trajectory of carbon monoxide after photodissociation from myoglobin at cryogenic temperatures
    • Teng, T. Y., Srajer, V., and Moffat, K. (1997) Initial trajectory of carbon monoxide after photodissociation from myoglobin at cryogenic temperatures Biochemistry 36, 12087-12100
    • (1997) Biochemistry , vol.36 , pp. 12087-12100
    • Teng, T.Y.1    Srajer, V.2    Moffat, K.3
  • 40
    • 0031054657 scopus 로고    scopus 로고
    • Ultrafast rotation and trapping of carbon monoxide dissociated from myoglobin
    • Lim, M. H., Jackson, T. A., and Anfinrud, P. A. (1997) Ultrafast rotation and trapping of carbon monoxide dissociated from myoglobin Nat. Struct. Biol. 4, 209-214
    • (1997) Nat. Struct. Biol. , vol.4 , pp. 209-214
    • Lim, M.H.1    Jackson, T.A.2    Anfinrud, P.A.3
  • 41
    • 0031880931 scopus 로고    scopus 로고
    • Computer simulations of carbon monoxide photodissociation in myoglobin: Structural interpretation of the B states
    • Meller, J. and Elber, R. (1998) Computer simulations of carbon monoxide photodissociation in myoglobin: Structural interpretation of the B states Biophys. J. 74, 789-802
    • (1998) Biophys. J. , vol.74 , pp. 789-802
    • Meller, J.1    Elber, R.2
  • 42
    • 77951298113 scopus 로고    scopus 로고
    • Ligand diffusion in globins: Simulations versus experiment
    • Elber, R. (2010) Ligand diffusion in globins: simulations versus experiment Curr. Opin. Struct. Biol. 20, 162-167
    • (2010) Curr. Opin. Struct. Biol. , vol.20 , pp. 162-167
    • Elber, R.1
  • 43
    • 48249120004 scopus 로고    scopus 로고
    • Atomic level computational identification of ligand migration pathways between solvent and binding site in myoglobin
    • Ruscio, J. Z., Kumar, D., Shukla, M., Prisant, M. G., Murali, T. M., and Onufriev, A. V. (2008) Atomic level computational identification of ligand migration pathways between solvent and binding site in myoglobin Proc. Natl. Acad. Sci. U.S.A. 105, 9204-9209
    • (2008) Proc. Natl. Acad. Sci. U.S.A. , vol.105 , pp. 9204-9209
    • Ruscio, J.Z.1    Kumar, D.2    Shukla, M.3    Prisant, M.G.4    Murali, T.M.5    Onufriev, A.V.6
  • 44
    • 0035957014 scopus 로고    scopus 로고
    • The role of structure, energy landscape, dynamics, and allostery in the enzymatic function of myoglobin
    • Frauenfelder, H., McMahon, B. H., Austin, R. H., Chu, K., and Groves, J. T. (2001) The role of structure, energy landscape, dynamics, and allostery in the enzymatic function of myoglobin Proc. Natl. Acad. Sci. U.S.A. 98, 2370-2374
    • (2001) Proc. Natl. Acad. Sci. U.S.A. , vol.98 , pp. 2370-2374
    • Frauenfelder, H.1    McMahon, B.H.2    Austin, R.H.3    Chu, K.4    Groves, J.T.5
  • 47
    • 36549007107 scopus 로고    scopus 로고
    • 2 migration pathways are not conserved across proteins of a similar fold
    • 2 migration pathways are not conserved across proteins of a similar fold Biophys. J. 93, 3591-3600
    • (2007) Biophys. J. , vol.93 , pp. 3591-3600
    • Cohen, J.1    Schulten, K.2
  • 50
    • 55249126699 scopus 로고    scopus 로고
    • Determinants of substrate internalization in the distal pocket of dehaloperoxidase hemoglobin of Amphitrite ornata
    • Nienhaus, K., Nickel, E., Davis, M. F., Franzen, S., and Nienhaus, G. U. (2008) Determinants of substrate internalization in the distal pocket of dehaloperoxidase hemoglobin of Amphitrite ornata Biochemistry 47, 12985-12994
    • (2008) Biochemistry , vol.47 , pp. 12985-12994
    • Nienhaus, K.1    Nickel, E.2    Davis, M.F.3    Franzen, S.4    Nienhaus, G.U.5
  • 51
    • 0024974675 scopus 로고
    • Structure of myoglobin-ethyl isocyanide histidine as a swinging door for ligand entry
    • Johnson, K. A., Olson, J. S., and Phillips, G. N., Jr. (1989) Structure of myoglobin-ethyl isocyanide histidine as a swinging door for ligand entry J. Mol. Biol. 207, 459-463
    • (1989) J. Mol. Biol. , vol.207 , pp. 459-463
    • Johnson, K.A.1    Olson, J.S.2    Phillips Jr., G.N.3
  • 52
    • 77953655511 scopus 로고    scopus 로고
    • Straight-chain alkyl isocyanides open the distal histidine gate in crystal structures of myoglobin
    • Smith, R. D., Blouin, G. C., Johnson, K. A., Phillips, G. N., and Olson, J. S. (2010) Straight-chain alkyl isocyanides open the distal histidine gate in crystal structures of myoglobin Biochemistry 49, 4977-4986
    • (2010) Biochemistry , vol.49 , pp. 4977-4986
    • Smith, R.D.1    Blouin, G.C.2    Johnson, K.A.3    Phillips, G.N.4    Olson, J.S.5
  • 53
    • 84856420536 scopus 로고    scopus 로고
    • Thin-layer spectroelectrochemistry of the Fe(III)/Fe(II) redox reaction of dehaloperoxidase-hemoglobin
    • D'Antonio, E. L., Bowden, E. F., and Franzen, S. (2012) Thin-layer spectroelectrochemistry of the Fe(III)/Fe(II) redox reaction of dehaloperoxidase-hemoglobin J. Electroanal. Chem. 668, 37-43
    • (2012) J. Electroanal. Chem. , vol.668 , pp. 37-43
    • D'Antonio, E.L.1    Bowden, E.F.2    Franzen, S.3


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