메뉴 건너뛰기




Volumn 42, Issue 10, 1999, Pages 1778-1788

The role of waters in docking strategies with incremental flexibility for carbohydrate derivatives: Heat-labile enterotoxin, a multivalent test case

Author keywords

[No Author keywords available]

Indexed keywords

4 NITROPHENYLGALACTOSIDE; CARBOHYDRATE DERIVATIVE; ENTEROTOXIN; GALACTOSE; LACTOSE;

EID: 0033587105     PISSN: 00222623     EISSN: None     Source Type: Journal    
DOI: 10.1021/jm980472c     Document Type: Article
Times cited : (64)

References (44)
  • 1
    • 0001845266 scopus 로고
    • The epidemiology of cholera and enterotoxigenic E. coli diarrheal disease
    • Developments of Vaccines and Drugs Against Diarrhea, Stockholm, Holmgren, J., Lindberg, A., Möllby, R., Studentlitteratur: Lund
    • Black, R. E. The epidemiology of cholera and enterotoxigenic E. coli diarrheal disease. In Developments of Vaccines and Drugs Against Diarrhea, 11th Nobel Conference, Stockholm, 1985; Holmgren, J., Lindberg, A., Möllby, R., Eds.; Studentlitteratur: Lund, 1986; pp 23-32.
    • (1985) 11th Nobel Conference , pp. 23-32
    • Black, R.E.1
  • 4
    • 0015838424 scopus 로고
    • Interaction of vibrio cholerae enterotoxin with cell membranes
    • Cuatrecasas, P. Interaction of Vibrio cholerae enterotoxin with cell membranes. Biochemistry 1973, 12, 3547-3558.
    • (1973) Biochemistry , vol.12 , pp. 3547-3558
    • Cuatrecasas, P.1
  • 5
    • 0347349553 scopus 로고
    • Mechanism of cholera toxin action: Covalent modification of the guanyl nucleotide-binding protein of the adenylate cyclase system
    • Cassel, D.; Pfeuffer, T. Mechanism of cholera toxin action: Covalent modification of the guanyl nucleotide-binding protein of the adenylate cyclase system. Proc. Natl. Acad. Sci. U.S.A. 1978, 75, 2669-2673.
    • (1978) Proc. Natl. Acad. Sci. U.S.A. , vol.75 , pp. 2669-2673
    • Cassel, D.1    Pfeuffer, T.2
  • 6
    • 0028935644 scopus 로고
    • Identification of errors among database sequence entries and comparison of correct amino acid sequences for the heat-labile enterotoxins of Escherichia coli and Vibrio cholerae
    • Domenighini, M.; Pizza, M.; Jobling, M. G,; Holmes, R. K.; Rappuoli, R. Identification of errors among database sequence entries and comparison of correct amino acid sequences for the heat-labile enterotoxins of Escherichia coli and Vibrio cholerae. Mol. Microbiol. 1995, 15, 1165-1167.
    • (1995) Mol. Microbiol. , vol.15 , pp. 1165-1167
    • Domenighini, M.1    Pizza, M.2    Jobling, M.G.3    Holmes, R.K.4    Rappuoli, R.5
  • 7
    • 0028123001 scopus 로고
    • Galactose-binding site in Escherichia coli heat-labile enterotoxin (LT) and cholera toxin (CT)
    • Merritt, E. A.; Sixma, T. K.; Kalk, K. H.; Van Zanten, B. A. M.; Hol, W. G. J. Galactose-binding site in Escherichia coli heat-labile enterotoxin (LT) and cholera toxin (CT). Mol. Microbiol. 1994, 13, 745-753.
    • (1994) Mol. Microbiol. , vol.13 , pp. 745-753
    • Merritt, E.A.1    Sixma, T.K.2    Kalk, K.H.3    Van Zanten, B.A.M.4    Hol, W.G.J.5
  • 8
    • 0027174854 scopus 로고
    • Refined structure of Escherichia coli heat-labile enterotoxin, a close relative of choleratoxin
    • Sixma, T. K.; Kalk, K. H.; Van Zanten, B. A. M.; Hol, W. G. J. Refined structure of Escherichia coli heat-labile enterotoxin, a close relative of choleratoxin. J. Mol. Biol. 1993, 230, 890-918.
    • (1993) J. Mol. Biol. , vol.230 , pp. 890-918
    • Sixma, T.K.1    Kalk, K.H.2    Van Zanten, B.A.M.3    Hol, W.G.J.4
  • 9
  • 10
    • 0030011313 scopus 로고    scopus 로고
    • Tumor marker disaccharide D-Gal-β1,3-GalNAc complexed to heat-labile enterotoxin from Escherichia coli
    • Van den Akker, F.; Steensma, E.; Hol, W. G. J. Tumor marker disaccharide D-Gal-β1,3-GalNAc complexed to heat-labile enterotoxin from Escherichia coli. Protein Sci. 1996, 5, 1184-1188.
    • (1996) Protein Sci. , vol.5 , pp. 1184-1188
    • Van Den Akker, F.1    Steensma, E.2    Hol, W.G.J.3
  • 14
    • 0024351848 scopus 로고
    • 1, and nonlipid oligosaccharide polyvalent ligands
    • 1, and nonlipid oligosaccharide polyvalent ligands. J. Biol. Chem. 1989, 264, 13233-13237.
    • (1989) J. Biol. Chem. , vol.264 , pp. 13233-13237
    • Schengrund, C.L.1    Ringler, N.J.2
  • 15
    • 0024392687 scopus 로고
    • Binding specificities of heat-labile enterotoxins isolated from porcine and human enterotoxygenic Escherichia coli for different gangliosides
    • Sugii, S.; Tsuji, T. Binding specificities of heat-labile enterotoxins isolated from porcine and human enterotoxygenic Escherichia coli for different gangliosides. Can. J. Microbiol. 1989, 35, 670-673.
    • (1989) Can. J. Microbiol. , vol.35 , pp. 670-673
    • Sugii, S.1    Tsuji, T.2
  • 16
    • 0033522424 scopus 로고    scopus 로고
    • Structure-based exploration of the ganglioside GM1 binding sites of E. coli heat-labile enterotoxin and cholera toxin for the discovery of receptor antagonists
    • Minke, W. E.; Roach, C.; Hol, W. G. J.; Verlinde, C. L. M. J. Structure-based exploration of the ganglioside GM1 binding sites of E. coli heat-labile enterotoxin and cholera toxin for the discovery of receptor antagonists. Biochemistry 1999, 38, 5684-5692.
    • (1999) Biochemistry , vol.38 , pp. 5684-5692
    • Minke, W.E.1    Roach, C.2    Hol, W.G.J.3    Verlinde, C.L.M.J.4
  • 17
    • 0028773887 scopus 로고
    • Structure-based drug design: Progress, results and challenges
    • Verlinde, C. L. M. J.; Hol, W. G. J. Structure-based drug design: progress, results and challenges. Structure 1994, 2, 577-587.
    • (1994) Structure , vol.2 , pp. 577-587
    • Verlinde, C.L.M.J.1    Hol, W.G.J.2
  • 19
    • 0029705324 scopus 로고    scopus 로고
    • Docking of flexible ligands. Applications of AUTODOCK
    • Goodsell, D. S.; Morris, G. M.; Olson, A. J. Docking of flexible ligands. Applications of AUTODOCK. J. Mol. Recognit. 1996, 9, 1-5.
    • (1996) J. Mol. Recognit. , vol.9 , pp. 1-5
    • Goodsell, D.S.1    Morris, G.M.2    Olson, A.J.3
  • 20
    • 0344020339 scopus 로고
    • Multiple-start Monte Carlo docking of flexible ligands
    • Merz, K. M., Jr., Le Grand, S. M., Eds.; Birkhäuser: Boston
    • Hart, T. N.; Read, R. J. Multiple-start Monte Carlo docking of flexible ligands. In The protein folding problem and tertiary structure prediction; Merz, K. M., Jr., Le Grand, S. M., Eds.; Birkhäuser: Boston, 1994; pp 71-108.
    • (1994) The Protein Folding Problem and Tertiary Structure Prediction , pp. 71-108
    • Hart, T.N.1    Read, R.J.2
  • 21
    • 0029294584 scopus 로고
    • Molecular recognition of the inhibitor AG-1343 by HIV-1 protease: Conformationally flexible docking by evolutionary programming
    • Gehlhaar, D. K; Verkhivker, G. M.; Rejto, P. A.; Herman, C. J.; Fogel, D. B.; Fogel, L. J.; Freer, S. T. Molecular recognition of the inhibitor AG-1343 by HIV-1 protease: conformationally flexible docking by evolutionary programming. Chem. Biol. 1995, 2, 317-324.
    • (1995) Chem. Biol. , vol.2 , pp. 317-324
    • Gehlhaar, D.K.1    Verkhivker, G.M.2    Rejto, P.A.3    Herman, C.J.4    Fogel, D.B.5    Fogel, L.J.6    Freer, S.T.7
  • 22
    • 43949148576 scopus 로고
    • A genetic algorithm based method for docking flexible molecules
    • Judson, R. S.; Jaeger E. P.; Treasurywala A. M. A genetic algorithm based method for docking flexible molecules. J. Mol. Struct. 1994, 308, 191-206.
    • (1994) J. Mol. Struct. , vol.308 , pp. 191-206
    • Judson, R.S.1    Jaeger, E.P.2    Treasurywala, A.M.3
  • 24
    • 0030599010 scopus 로고    scopus 로고
    • A fast flexible docking method using an incremental construction algorithm
    • Rarey, M.; Kramer, B.; Lengauer, T.; Klebe, G. A fast flexible docking method using an incremental construction algorithm. J. Mol. Biol. 1996, 261, 470-489.
    • (1996) J. Mol. Biol. , vol.261 , pp. 470-489
    • Rarey, M.1    Kramer, B.2    Lengauer, T.3    Klebe, G.4
  • 25
    • 0030154893 scopus 로고    scopus 로고
    • Hammerhead: Fast, fully automated docking of flexible ligands to protein binding sites
    • Welch, W.; Ruppert, J.; Jain, A. N. Hammerhead: fast, fully automated docking of flexible ligands to protein binding sites. Chem. Biol. 1996, 3, 449-462.
    • (1996) Chem. Biol. , vol.3 , pp. 449-462
    • Welch, W.1    Ruppert, J.2    Jain, A.N.3
  • 26
    • 0031552362 scopus 로고    scopus 로고
    • Development and validation of a genetic algorithm for flexible docking
    • Jones, G.; Willett, P.; Glen, R. C.; Leach, A. R.; Taylor, R. Development and validation of a genetic algorithm for flexible docking. J. Mol. Biol. 1997, 267, 727-748.
    • (1997) J. Mol. Biol. , vol.267 , pp. 727-748
    • Jones, G.1    Willett, P.2    Glen, R.C.3    Leach, A.R.4    Taylor, R.5
  • 27
    • 0028158936 scopus 로고
    • Ligand docking to proteins with discrete side-chain flexibility
    • Leach, A. R. Ligand docking to proteins with discrete side-chain flexibility. J. Mol. Biol. 1994, 235, 345-356.
    • (1994) J. Mol. Biol. , vol.235 , pp. 345-356
    • Leach, A.R.1
  • 29
    • 0000287302 scopus 로고
    • Structure and function of E. colt heat-labile enterotoxin and cholera toxin B pentamer
    • Moss, J., Iglewski, B., Vaughan, M., Tu, A. T., Eds.; Marcel Dekker Inc.
    • Hol, W. G. J.; Sixma, T. K.; Merritt, E. A. Structure and function of E. colt heat-labile enterotoxin and cholera toxin B pentamer. In Bacterial toxins and virulence factors in disease. Handbook of natural toxins, Volume 8; Moss, J., Iglewski, B., Vaughan, M., Tu, A. T., Eds.; Marcel Dekker Inc., 1995; pp 185-223.
    • (1995) Bacterial Toxins and Virulence Factors in Disease. Handbook of Natural Toxins , vol.8 , pp. 185-223
    • Hol, W.G.J.1    Sixma, T.K.2    Merritt, E.A.3
  • 31
    • 0027185516 scopus 로고
    • Automated docking in crystallography: Analysis of the substrates of aconitase
    • Goodsell, D. S.; Lauble, H.; Stout, C. D.; Olson, A. J. Automated docking in crystallography: Analysis of the substrates of aconitase. Proteins 1993, 17, 1-10.
    • (1993) Proteins , vol.17 , pp. 1-10
    • Goodsell, D.S.1    Lauble, H.2    Stout, C.D.3    Olson, A.J.4
  • 32
    • 0031573456 scopus 로고    scopus 로고
    • Structural foundation for the design of receptor antagonists targeting Escherichia coli heat-labile enterotoxin
    • Merritt, E. A.; Sarfaty, S.; Feil, I. K.; Hol, W. G. J. Structural foundation for the design of receptor antagonists targeting Escherichia coli heat-labile enterotoxin. Structure 1997, 5, 1485-1499.
    • (1997) Structure , vol.5 , pp. 1485-1499
    • Merritt, E.A.1    Sarfaty, S.2    Feil, I.K.3    Hol, W.G.J.4
  • 33
    • 0026244229 scopus 로고
    • MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures
    • Kraulis, P. J. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr. 1991, 24, 946-950.
    • (1991) J. Appl. Crystallogr. , vol.24 , pp. 946-950
    • Kraulis, P.J.1
  • 34
    • 0006626819 scopus 로고
    • Crystal structure and solid-state NMR analysis of lactulose
    • Jeffrey, G. A.; Wood, R. A.; Pfeffer, P. E.; Hicks, K. B, Crystal structure and solid-state NMR analysis of lactulose. J. Am. Chem. Soc. 1983, 705, 2128-2133.
    • (1983) J. Am. Chem. Soc. , vol.705 , pp. 2128-2133
    • Jeffrey, G.A.1    Wood, R.A.2    Pfeffer, P.E.3    Hicks, K.B.4
  • 36
    • 0021871375 scopus 로고
    • A computational procedure for determining energetically favorable binding sites on biologically important macromolecules
    • Goodford, P. J. A computational procedure for determining energetically favorable binding sites on biologically important macromolecules. J. Med. Chem. 1985, 28, 849-857.
    • (1985) J. Med. Chem. , vol.28 , pp. 849-857
    • Goodford, P.J.1
  • 37
    • 0027510004 scopus 로고
    • Further development of hydrogen bond functions for use in determining energetically favorable binding sites on molecules of known structure. 2. Ligand probe groups with the ability to form more than two hydrogen bonds
    • Wade, R. C.; Goodford, P. J. Further development of hydrogen bond functions for use in determining energetically favorable binding sites on molecules of known structure. 2. Ligand probe groups with the ability to form more than two hydrogen bonds. J. Med. Chem. 1993, 36, 148-156.
    • (1993) J. Med. Chem. , vol.36 , pp. 148-156
    • Wade, R.C.1    Goodford, P.J.2
  • 39
    • 0025050372 scopus 로고
    • A molecular mechanical force field for the conformational analysis of oligosaccharides: Comparison of theoretical and crystal structures of Manα1-3Manβ1-4GlcNAc
    • Homans, S. W. A molecular mechanical force field for the conformational analysis of oligosaccharides: comparison of theoretical and crystal structures of Manα1-3Manβ1-4GlcNAc. Biochemistry 1990, 29, 9110-9118.
    • (1990) Biochemistry , vol.29 , pp. 9110-9118
    • Homans, S.W.1
  • 40
    • 3342936878 scopus 로고
    • An SCF solvation model for the hydrophobic effect and absolute free energies of aqueous solvation
    • Cramer, C. J.; Truhlar, D. G. An SCF solvation model for the hydrophobic effect and absolute free energies of aqueous solvation. Science 1992, 256, 213-217.
    • (1992) Science , vol.256 , pp. 213-217
    • Cramer, C.J.1    Truhlar, D.G.2
  • 41
    • 0031181346 scopus 로고    scopus 로고
    • QXP: Powerful, rapid algorithms for structure-based design
    • McMartin, C.; Bohacek, R. S. QXP: powerful, rapid algorithms for structure-based design. J. Comput. Aided Mol. Des. 1997, 11, 333-344.
    • (1997) J. Comput. Aided Mol. Des. , vol.11 , pp. 333-344
    • McMartin, C.1    Bohacek, R.S.2
  • 42
    • 11644261806 scopus 로고    scopus 로고
    • Automated docking using a lamarckian genetic algorithm and an empirical binding free energy function
    • Morris, G. M.; Goodsell, D. S.; Halliday, R S.; Huey, R; Hart, W. E.; Belew, R. K.; Olson, A. J. Automated docking using a Lamarckian genetic algorithm and an 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    Belew, R.K.6    Olson, A.J.7
  • 43
    • 0000872589 scopus 로고    scopus 로고
    • Hydrogen-bond acceptor properties of nitro-O atoms: A combined crystallographic database and ab initio molecular orbital study
    • Allen, F. H.; Baalham, C. A.; Lommerse, J. P. M.; Raithby, P. R.; Sparr, E. Hydrogen-bond acceptor properties of nitro-O atoms: A combined crystallographic database and ab initio molecular orbital study. Acta Crystallogr. 1997, 553, 1017-1024.
    • (1997) Acta Crystallogr. , vol.553 , pp. 1017-1024
    • Allen, F.H.1    Baalham, C.A.2    Lommerse, J.P.M.3    Raithby, P.R.4    Sparr, E.5
  • 44
    • 0004151408 scopus 로고
    • ACS Monograph 117; American Chemical Society: Washington, DC
    • Burkert, U.; Allinger, N. L. Molecular Mechanics; ACS Monograph 117; American Chemical Society: Washington, DC, 1982.
    • (1982) Molecular Mechanics
    • Burkert, U.1    Allinger, N.L.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.