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Volumn 52, Issue 6, 2009, Pages 1712-1722

Does a fast nuclear magnetic resonance spectroscopy- And X-ray crystallography hybrid approach provide reliable structural information of ligand-protein complexes? A case study of metalloproteinases

Author keywords

[No Author keywords available]

Indexed keywords

CGS 27023A; METALLOPROTEINASE;

EID: 64349111295     PISSN: 00222623     EISSN: None     Source Type: Journal    
DOI: 10.1021/jm801388q     Document Type: Article
Times cited : (7)

References (49)
  • 1
    • 0030791762 scopus 로고    scopus 로고
    • X-ray crystallography and NMR reveal complementary views of structure and dynamics
    • Brunger, A. T. X-ray crystallography and NMR reveal complementary views of structure and dynamics. Nat. Struct. Biol. 1997, 4 (Suppl), 862-865.
    • (1997) Nat. Struct. Biol , vol.4 , Issue.SUPPL. , pp. 862-865
    • Brunger, A.T.1
  • 4
    • 26844492158 scopus 로고    scopus 로고
    • Interpreting NMR Data for beta-Peptides Using Molecular Dynamics Simulations
    • Trzesniak, D.; Glattli, A.; Jaun, B.; Van Gunsteren, W. F. Interpreting NMR Data for beta-Peptides Using Molecular Dynamics Simulations. J. Am. Chem. Soc. 2005, 127, 14320-14329.
    • (2005) J. Am. Chem. Soc , vol.127 , pp. 14320-14329
    • Trzesniak, D.1    Glattli, A.2    Jaun, B.3    Van Gunsteren, W.F.4
  • 5
    • 41149169500 scopus 로고    scopus 로고
    • Comparison of multiple crystal structures with NMR data for engrailed homeodomain
    • Religa, T. L. Comparison of multiple crystal structures with NMR data for engrailed homeodomain. J. Biomol. NMR 2008, 40, 189-202.
    • (2008) J. Biomol. NMR , vol.40 , pp. 189-202
    • Religa, T.L.1
  • 6
    • 33751099086 scopus 로고    scopus 로고
    • Catalytic mechanism of cyclo-philin as observed in molecular dynamics simulations: Pathway prediction and reconcilation of X-ray crystallographic and NMR solution data
    • Trzesniak, D.; Van Gunsteren, W. F. Catalytic mechanism of cyclo-philin as observed in molecular dynamics simulations: pathway prediction and reconcilation of X-ray crystallographic and NMR solution data. Protein Sci. 2006, 15, 2544-2551.
    • (2006) Protein Sci , vol.15 , pp. 2544-2551
    • Trzesniak, D.1    Van Gunsteren, W.F.2
  • 7
    • 0029693351 scopus 로고    scopus 로고
    • Bonvin, A. M.; Brunger, A. T. Do NOE distance contain enough information to assess the relative populations of multiconformer structures. J. Biomol. NMR 1996, 7, 72-76.
    • Bonvin, A. M.; Brunger, A. T. Do NOE distance contain enough information to assess the relative populations of multiconformer structures. J. Biomol. NMR 1996, 7, 72-76.
  • 9
    • 40949113653 scopus 로고    scopus 로고
    • Probing Structure in Invisible Protein States with Anisotropic NMR Chemical Shifts
    • Vallurupalli, P.; Hansen, F.; Kay, L. E. Probing Structure in Invisible Protein States with Anisotropic NMR Chemical Shifts. J. Am. Chem. Soc. 2008, 130, 2734-2735.
    • (2008) J. Am. Chem. Soc , vol.130 , pp. 2734-2735
    • Vallurupalli, P.1    Hansen, F.2    Kay, L.E.3
  • 10
    • 50149085281 scopus 로고    scopus 로고
    • Structures of invisible, excited protein states by relaxation dispersion NMR spectroscopy
    • Vallurupalli, P.; Hansen, F.; Kay, L. E. Structures of invisible, excited protein states by relaxation dispersion NMR spectroscopy. Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 11766-11771.
    • (2008) Proc. Natl. Acad. Sci. U.S.A , vol.105 , pp. 11766-11771
    • Vallurupalli, P.1    Hansen, F.2    Kay, L.E.3
  • 11
    • 39749156063 scopus 로고    scopus 로고
    • Probing Chemical Shifts of Invisible States of Proteins with Relaxation Dispersion NMR Spectroscopy: How Well Can We Do?
    • Hansen, F.; Vallurupalli, P.; Lundstrom, P.; Neudecker, P.; Kay, L. E. Probing Chemical Shifts of Invisible States of Proteins with Relaxation Dispersion NMR Spectroscopy: How Well Can We Do? J. Am. Chem. Soc. 2008, 130, 2667-2675.
    • (2008) J. Am. Chem. Soc , vol.130 , pp. 2667-2675
    • Hansen, F.1    Vallurupalli, P.2    Lundstrom, P.3    Neudecker, P.4    Kay, L.E.5
  • 14
    • 25144490502 scopus 로고    scopus 로고
    • How Large is an alpha-Helix? Studies of the Radii of Gyration of Helical Peptides by Small-Angle X-ray Scattering and Molecular Dynamics
    • Zagrovic, B.; Jayachandran, G.; Millett, I. S.; Doniach, S.; Pande, V. S. How Large is an alpha-Helix? Studies of the Radii of Gyration of Helical Peptides by Small-Angle X-ray Scattering and Molecular Dynamics. J. Mol. Biol. 2005, 353, 232-241.
    • (2005) J. Mol. Biol , vol.353 , pp. 232-241
    • Zagrovic, B.1    Jayachandran, G.2    Millett, I.S.3    Doniach, S.4    Pande, V.S.5
  • 15
    • 35148826056 scopus 로고    scopus 로고
    • The Free Energy Landscapes Governing Conformational Changes in a Glutamate Receptor Ligand-Binding Domain
    • Lau, A. Y.; Roux, B. The Free Energy Landscapes Governing Conformational Changes in a Glutamate Receptor Ligand-Binding Domain. Structure 2007, 15, 1203-1214.
    • (2007) Structure , vol.15 , pp. 1203-1214
    • Lau, A.Y.1    Roux, B.2
  • 16
    • 28144451811 scopus 로고    scopus 로고
    • Combining in Silico Tools and NMR Data to Validate Protein- Ligand Structural Models: Application to Matrix Metalloproteinases
    • Bertini, I.; Fragai, M.; Giachetti, A.; Luchinat, C.; Maletta, M.; Parigi, G.; Yeo, K. J. Combining in Silico Tools and NMR Data to Validate Protein- Ligand Structural Models: Application to Matrix Metalloproteinases. J. Med. Chem. 2005, 48, 7544-7559.
    • (2005) J. Med. Chem , vol.48 , pp. 7544-7559
    • Bertini, I.1    Fragai, M.2    Giachetti, A.3    Luchinat, C.4    Maletta, M.5    Parigi, G.6    Yeo, K.J.7
  • 18
    • 0030829521 scopus 로고    scopus 로고
    • Elastin degradation by matrix metallo-proteinases. Cleavage site specificity and mechanisms of elastolysis
    • Mecham, R. P.; Broekelmann, T. J.; Fliszar, C. J.; Shapiro, S. D.; Welgus, H. G; Senior, R. M. Elastin degradation by matrix metallo-proteinases. Cleavage site specificity and mechanisms of elastolysis. J. Biol. Chem. 1997, 272, 18071-18076.
    • (1997) J. Biol. Chem , vol.272 , pp. 18071-18076
    • Mecham, R.P.1    Broekelmann, T.J.2    Fliszar, C.J.3    Shapiro, S.D.4    Welgus, H.G.5    Senior, R.M.6
  • 19
    • 0029005284 scopus 로고
    • Human macrophage metalloelastase. Genomic organization, chromosomal location, gene linkage, and tissue-specific expression
    • Belaaouaj, A.; Shipley, J. M.; Kobayashi, D. K.; Zimonjic, D. B.; Popescu, N.; Silverman, G. A.; Shapiro, S. D. Human macrophage metalloelastase. Genomic organization, chromosomal location, gene linkage, and tissue-specific expression. J. Biol. Chem. 1995, 270, 14568-14575.
    • (1995) J. Biol. Chem , vol.270 , pp. 14568-14575
    • Belaaouaj, A.1    Shipley, J.M.2    Kobayashi, D.K.3    Zimonjic, D.B.4    Popescu, N.5    Silverman, G.A.6    Shapiro, S.D.7
  • 20
    • 0031898338 scopus 로고    scopus 로고
    • Distinct expression profies of stromelysin-2 (MMP-10), collagenase-3 (MMP-13), macrophage metalloelastase (MMP-12), and tissue inhibitor of metalloproteinases-3 (TIMP-3) in intestinal ulcerations
    • Vaalamo, M.; Karjalainen-Lindsberg, M. L.; Puolakkainen, P.; Kere, J.; Saarialho-Kere, U. Distinct expression profies of stromelysin-2 (MMP-10), collagenase-3 (MMP-13), macrophage metalloelastase (MMP-12), and tissue inhibitor of metalloproteinases-3 (TIMP-3) in intestinal ulcerations. Am. J. Pathol. 1998, 152, 1005-1014.
    • (1998) Am. J. Pathol , vol.152 , pp. 1005-1014
    • Vaalamo, M.1    Karjalainen-Lindsberg, M.L.2    Puolakkainen, P.3    Kere, J.4    Saarialho-Kere, U.5
  • 21
    • 0030823772 scopus 로고    scopus 로고
    • Requirement for macrophage elastase for cigarette smoke-induced emphysema in mice
    • Hautamaki, R. D.; Kobayashi, D. K.; Senior, R. M.; Shapiro, S. D. Requirement for macrophage elastase for cigarette smoke-induced emphysema in mice. Science 1997, 277, 2002-2004.
    • (1997) Science , vol.277 , pp. 2002-2004
    • Hautamaki, R.D.1    Kobayashi, D.K.2    Senior, R.M.3    Shapiro, S.D.4
  • 23
    • 0036892580 scopus 로고    scopus 로고
    • Matrix metalloproteinases and neuroinflammation in multiple sclerosis
    • Rosenberg, G. A. Matrix metalloproteinases and neuroinflammation in multiple sclerosis. Neuroscientist 2002, 8, 586-595.
    • (2002) Neuroscientist , vol.8 , pp. 586-595
    • Rosenberg, G.A.1
  • 24
    • 0037447192 scopus 로고    scopus 로고
    • Understanding inflammation in chronic obstructive pulmonary disease: The process begins
    • Snider, G. L. Understanding inflammation in chronic obstructive pulmonary disease: the process begins. Am. J. Respir. Crit. Care Med 2003, 167, 1045-1046.
    • (2003) Am. J. Respir. Crit. Care Med , vol.167 , pp. 1045-1046
    • Snider, G.L.1
  • 25
    • 5644277560 scopus 로고    scopus 로고
    • Association of increased expression of macrophage elastase (matrix metalloproteinase 12) with rheumatoid arthritis
    • Liu, M.; Sun, H.; Wang, X.; Koike, T.; Mishima, H.; Ikeda, K.; Watanabe, T.; Ochiai, N.; Fan, J. Association of increased expression of macrophage elastase (matrix metalloproteinase 12) with rheumatoid arthritis. Arhritis Rheum. 2004, 50, 3112-3117.
    • (2004) Arhritis Rheum , vol.50 , pp. 3112-3117
    • Liu, M.1    Sun, H.2    Wang, X.3    Koike, T.4    Mishima, H.5    Ikeda, K.6    Watanabe, T.7    Ochiai, N.8    Fan, J.9
  • 26
    • 18544391315 scopus 로고    scopus 로고
    • Expression and high yield production of the catalytic domain of matrix metalloproteinase 12 and of an active mutant with increased solubility
    • Banci, L.; Bertini, I.; Ciulli, A.; Fragai, M.; Luchinat, C.; Terni, B. Expression and high yield production of the catalytic domain of matrix metalloproteinase 12 and of an active mutant with increased solubility. J. Mol. Catal. A: Chem 2003, 204-205, 401-408.
    • (2003) J. Mol. Catal. A: Chem , vol.204-205 , pp. 401-408
    • Banci, L.1    Bertini, I.2    Ciulli, A.3    Fragai, M.4    Luchinat, C.5    Terni, B.6
  • 27
    • 0035965125 scopus 로고    scopus 로고
    • Substrate specificity determinants of human macrophage elastase (MMP-12) based in the 1.1 Å crystal structure
    • Lang, R.; Kocourek, A.; Braun, M.; Tschesche, H.; Huber, R.; Bode, W.; Maskos, K. Substrate specificity determinants of human macrophage elastase (MMP-12) based in the 1.1 Å crystal structure. J. Mol. Biol. 2001, 312, 731-742.
    • (2001) J. Mol. Biol , vol.312 , pp. 731-742
    • Lang, R.1    Kocourek, A.2    Braun, M.3    Tschesche, H.4    Huber, R.5    Bode, W.6    Maskos, K.7
  • 32
    • 0842341771 scopus 로고    scopus 로고
    • Dewar, M. J. S.; Zoebisch, E. G.; Healy, E. F.; Stewart, J. J. P. AM1: a new general purpose quantum mechanical molecular model. J. Am. Chem. Soc. 1985, 107, 3902-3909.
    • Dewar, M. J. S.; Zoebisch, E. G.; Healy, E. F.; Stewart, J. J. P. AM1: a new general purpose quantum mechanical molecular model. J. Am. Chem. Soc. 1985, 107, 3902-3909.
  • 33
    • 49149147973 scopus 로고
    • Iterative Partial Equilization of Orbital Electronegativity-A Rapid Access to Atomic Charges
    • Gasteiger, J.; Marsili, M. Iterative Partial Equilization of Orbital Electronegativity-A Rapid Access to Atomic Charges. Tetrahedron 1980, 36, 3219-3228.
    • (1980) Tetrahedron , vol.36 , pp. 3219-3228
    • Gasteiger, J.1    Marsili, M.2
  • 36
    • 6344260593 scopus 로고
    • An All-Atom Empirical Energy Function for the Simulation of Nucleic Acids
    • MacKerell, A. D., Jr.; Wiorkiwicz-Kuczera, J.; Karplus, M. An All-Atom Empirical Energy Function for the Simulation of Nucleic Acids. J. Am. Chem. Soc. 1995, 117, 11946-11975.
    • (1995) J. Am. Chem. Soc , vol.117 , pp. 11946-11975
    • MacKerell Jr., A.D.1    Wiorkiwicz-Kuczera, J.2    Karplus, M.3
  • 38
    • 0035965133 scopus 로고    scopus 로고
    • Crystal Structure of Human Macrophage Elastase (MMP-12) in Complex with a Hydroxamic Acid Inhibitor
    • Nar, H.; Werle, K.; Bauer, M. M. T.; Dollinger, H.; Jung, B. Crystal Structure of Human Macrophage Elastase (MMP-12) in Complex with a Hydroxamic Acid Inhibitor. J. Mol. Biol. 2001, 312, 743-751.
    • (2001) J. Mol. Biol , vol.312 , pp. 743-751
    • Nar, H.1    Werle, K.2    Bauer, M.M.T.3    Dollinger, H.4    Jung, B.5
  • 39
    • 84889120137 scopus 로고
    • Improved methods for building protein models in electron density maps and the location of errors in these models
    • Jones, T. A.; Zou, J. Y.; Cowan, S. W.; Kjeldgaard, M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Cryfstalloogr. Sect. A: Found Crystallogr. 1991, 47, 110-119.
    • (1991) Acta Cryfstalloogr. Sect. A: Found Crystallogr , vol.47 , pp. 110-119
    • Jones, T.A.1    Zou, J.Y.2    Cowan, S.W.3    Kjeldgaard, M.4
  • 40
    • 0031450585 scopus 로고    scopus 로고
    • Bioactive Conformation of a Potent Stromelysin Inhibitor Determined by X-Nucleus Filtered and Multidimensional NMR Spectroscopy
    • Gonella, N. C.; Li, Y.-C.; Zhang, X.; Paris, C. G. Bioactive Conformation of a Potent Stromelysin Inhibitor Determined by X-Nucleus Filtered and Multidimensional NMR Spectroscopy. Bioorg. Med. Chem. 1997, 5 (12), 2193-2201.
    • (1997) Bioorg. Med. Chem , vol.5 , Issue.12 , pp. 2193-2201
    • Gonella, N.C.1    Li, Y.-C.2    Zhang, X.3    Paris, C.G.4
  • 41
    • 11644261806 scopus 로고    scopus 로고
    • Automated Docking Using a Lamarckian Genetic Algorithm and Empirical Binding Free Energy Function
    • Morris, G. M.; Goodsell, D. S.; Halliday, R. S.; Huey, R.; Hart, W. E.; Below, R. K.; Olson, A. J. Automated Docking Using a Lamarckian Genetic Algorithm and Empirical Binding Free Energy Function. J. Comput. Chem. 1998, 19, 1639-1662.
    • (1998) J. Comput. Chem , vol.19 , pp. 1639-1662
    • Morris, G.M.1    Goodsell, D.S.2    Halliday, R.S.3    Huey, R.4    Hart, W.E.5    Below, R.K.6    Olson, A.J.7
  • 45
    • 34548670257 scopus 로고    scopus 로고
    • Crystal Structures of MMP-9 Complexes with Five Inhibitors: Contribution of the Flexible Arg424 Side Chain to Selectivity
    • Tochowicz, A.; Maskos, K.; Huber, R.; Oltenfreiter, R.; Dive, V.; Yiotakis, A.; Zanda, M.; Bode, W.; Goettig, P. Crystal Structures of MMP-9 Complexes with Five Inhibitors: Contribution of the Flexible Arg424 Side Chain to Selectivity. J. Mol. Biol. 2007, 371, 989-1006.
    • (2007) J. Mol. Biol , vol.371 , pp. 989-1006
    • Tochowicz, A.1    Maskos, K.2    Huber, R.3    Oltenfreiter, R.4    Dive, V.5    Yiotakis, A.6    Zanda, M.7    Bode, W.8    Goettig, P.9
  • 46
    • 20144369218 scopus 로고    scopus 로고
    • Blagg, J. A.; Noe, M. C.; Wolf-Gouveia, L. A.; Reiter, L. A.; Laird, E. R.; Chang, S. P.; Danley, D. E.; Downs, J. T.; Elliott, N. C.; Eskra, J. D.; Griffiths, R. J.; Hardink, J. R.; Haugeto, A. I.; Jones, C. S.; Liras, J. L.; Lopresti-Morrow, L. L.; Mitchell, P. G.; Pandit, J.; Robinson, R. P.; Subramanyam, C.; Vaughn-Bowser, M. L.; Yocum, S. A. Potent pyrimidinetrione- based inhibitors of MMP-13 with enhanced selectivity over MMP-14. Bioorg. Med. Chem. Lett. 2005, 15, 1807-1810.
    • Blagg, J. A.; Noe, M. C.; Wolf-Gouveia, L. A.; Reiter, L. A.; Laird, E. R.; Chang, S. P.; Danley, D. E.; Downs, J. T.; Elliott, N. C.; Eskra, J. D.; Griffiths, R. J.; Hardink, J. R.; Haugeto, A. I.; Jones, C. S.; Liras, J. L.; Lopresti-Morrow, L. L.; Mitchell, P. G.; Pandit, J.; Robinson, R. P.; Subramanyam, C.; Vaughn-Bowser, M. L.; Yocum, S. A. Potent pyrimidinetrione- based inhibitors of MMP-13 with enhanced selectivity over MMP-14. Bioorg. Med. Chem. Lett. 2005, 15, 1807-1810.
  • 49
    • 0029644935 scopus 로고
    • Structure of full-length porcine synovial collagenase reveals a C-terminal domain containing a calcium-linked, four-bladed beta-propeller
    • Li, J.; Brick, P.; O'Hare, M. C.; Skarzynski, T.; Lloyd, L. F.; Curry, V. A.; Clark, I. M.; Bigg, H. F.; Hazleman, B. L.; Cawston, T. E. Structure of full-length porcine synovial collagenase reveals a C-terminal domain containing a calcium-linked, four-bladed beta-propeller. Structure 1995, 3, 541-549.
    • (1995) Structure , vol.3 , pp. 541-549
    • Li, J.1    Brick, P.2    O'Hare, M.C.3    Skarzynski, T.4    Lloyd, L.F.5    Curry, V.A.6    Clark, I.M.7    Bigg, H.F.8    Hazleman, B.L.9    Cawston, T.E.10


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