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Volumn 45, Issue 22, 2002, Pages 4828-4837

Comparative Binding Energy (COMBINE) analysis of OppA-peptide complexes to relate structure to binding thermodynamics

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; BACTERIAL ENZYME; BACTERIAL PROTEIN; OLIGOPEPTIDE; PERMEASE; PROTEIN OPPA; RECEPTOR; UNCLASSIFIED DRUG; WATER;

EID: 0037168045     PISSN: 00222623     EISSN: None     Source Type: Journal    
DOI: 10.1021/jm020900l     Document Type: Article
Times cited : (50)

References (35)
  • 1
    • 0023038504 scopus 로고
    • Binding specificity of the periplasmic Oligopeptide-binding protein from Escherichia coli
    • Guyer, C. A.; Morgan, D. G.; Staros, J. V. Binding specificity of the periplasmic Oligopeptide-binding protein from Escherichia coli. J. Bacteriol. 1986, 168, 775-779.
    • (1986) J. Bacteriol. , vol.168 , pp. 775-779
    • Guyer, C.A.1    Morgan, D.G.2    Staros, J.V.3
  • 2
    • 0023636673 scopus 로고
    • Uptake of cell-wall peptides by Salmonella typhimurium and Escherichia coli
    • Goodell, E. W.; Higgins, C. F. Uptake of cell-wall peptides by Salmonella typhimurium and Escherichia coli. J. Bacteriol. 1987, 169, 3861-3865.
    • (1987) J. Bacteriol. , vol.169 , pp. 3861-3865
    • Goodell, E.W.1    Higgins, C.F.2
  • 4
    • 0031470826 scopus 로고    scopus 로고
    • Genomic sequence of a Lyme disease spirochaete, Borrelia Burgdorferi
    • Fraser, C. M.; Casjens, S.; Huang, W. M.; Sutton, G. G.; et al. Genomic sequence of a Lyme disease spirochaete, Borrelia Burgdorferi. Nature 1997, 390, 580-586.
    • (1997) Nature , vol.390 , pp. 580-586
    • Fraser, C.M.1    Casjens, S.2    Huang, W.M.3    Sutton, G.G.4
  • 5
    • 0032811591 scopus 로고    scopus 로고
    • Crystallographic and calorimetric analysis of peptide binding to OppA protein
    • Sleigh, S. H.; Seavers, P. R.; Wilkinson, A. J.; Ladbury, J. E.; Tame, J. R. H. Crystallographic and Calorimetric Analysis of Peptide Binding to OppA Protein. J. Mol. Biol. 1999, 291, 393- 415.
    • (1999) J. Mol. Biol. , vol.291 , pp. 393-415
    • Sleigh, S.H.1    Seavers, P.R.2    Wilkinson, A.J.3    Ladbury, J.E.4    Tame, J.R.H.5
  • 6
    • 0032806924 scopus 로고    scopus 로고
    • Relating structure to thermodynamics: The crystal structures and binding affinity of eight OppA-peptide complexes
    • Davies, T. G.; Hubbard, R. E.; Tame, J. R. H. Relating structure to thermodynamics: the crystal structures and binding affinity of eight OppA-peptide complexes. Protein Sci. 1999, 8, 1432-1444.
    • (1999) Protein Sci. , vol.8 , pp. 1432-1444
    • Davies, T.G.1    Hubbard, R.E.2    Tame, J.R.H.3
  • 7
    • 0030855775 scopus 로고    scopus 로고
    • Peptide binding in OppA, the crystal structures of the periplasmic oligopeptide binding protein in the unliganded form and in complex with lysyllysine
    • Sleigh, S. H.; Tame, J. R. H.; Dodson, E. J.; Wilkinson, A. J. Peptide binding in OppA, the crystal structures of the periplasmic oligopeptide binding protein in the unliganded form and in complex with lysyllysine. Biochemistry 1997, 36, 9747-9758.
    • (1997) Biochemistry , vol.36 , pp. 9747-9758
    • Sleigh, S.H.1    Tame, J.R.H.2    Dodson, E.J.3    Wilkinson, A.J.4
  • 8
    • 0029646113 scopus 로고
    • The crystal structures of the oligopeptide-binding protein OppA complexed with tripeptide and tetrapeptide ligands
    • Tame, J. R. H.; Dodson, E. J.; Murshudov, G.; Higgins, C. F.; Wilkinson, A. J. The crystal structures of the oligopeptide-binding protein OppA complexed with tripeptide and tetrapeptide ligands. Structure 1995, 3, 1395-1406.
    • (1995) Structure , vol.3 , pp. 1395-1406
    • Tame, J.R.H.1    Dodson, E.J.2    Murshudov, G.3    Higgins, C.F.4    Wilkinson, A.J.5
  • 9
    • 0030471364 scopus 로고    scopus 로고
    • The role of water in sequence-independent ligand binding by an oligopeptide transporter protein
    • Tame, J. R. H.; Sleigh, S. H.; Wilkinson, A. J.; Ladbury, J. E. The role of water in sequence-independent ligand binding by an oligopeptide transporter protein. Nat. Struct. Biol. 1996, 3, 998-1001.
    • (1996) Nat. Struct. Biol. , vol.3 , pp. 998-1001
    • Tame, J.R.H.1    Sleigh, S.H.2    Wilkinson, A.J.3    Ladbury, J.E.4
  • 10
    • 0030466444 scopus 로고    scopus 로고
    • Just add water! The effect of water on the specificity of protein-ligand binding sites and its potential application to drug design
    • Ladbury J. E. Just add water! The effect of water on the specificity of protein-ligand binding sites and its potential application to drug design. Chem. Biol. 1996, 3, 973-980.
    • (1996) Chem. Biol. , vol.3 , pp. 973-980
    • Ladbury, J.E.1
  • 11
    • 0034635345 scopus 로고    scopus 로고
    • Specificity and interactions of the protein OppA: Partitioning solvent binding effects using mass spectrometry
    • Rostom, A. A.; Tame, J. R. H.; Ladbury, J. E.; Robinson, C. V. Specificity and interactions of the protein OppA: partitioning solvent binding effects using mass spectrometry. J. Mol. Biol. 2000, 296, 269-279.
    • (2000) J. Mol. Biol. , vol.296 , pp. 269-279
    • Rostom, A.A.1    Tame, J.R.H.2    Ladbury, J.E.3    Robinson, C.V.4
  • 12
    • 0028454828 scopus 로고
    • The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure
    • Bohm, H. J. The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure. J. Comput.-Aided Mol. Des. 1994, 12, 243-256.
    • (1994) J. Comput.-Aided Mol. Des. , vol.12 , pp. 243-256
    • Bohm, H.J.1
  • 13
    • 0033545622 scopus 로고    scopus 로고
    • A general and fast scoring function for protein-ligand interactions: A simplified potential approach
    • Muegge, I.; Martin, Y. C. A general and fast scoring function for protein-ligand interactions: a simplified potential approach. J. Med. Chem. 1999, 42, 791-804.
    • (1999) J. Med. Chem. , vol.42 , pp. 791-804
    • Muegge, I.1    Martin, Y.C.2
  • 14
    • 7044239742 scopus 로고
    • Free energy calculations: Applications to chemical and biochemical phenomena
    • Kollman, P. Free energy calculations: Applications to chemical and biochemical phenomena. Chem. Rev. 1993, 93, 2395-2417.
    • (1993) Chem. Rev. , vol.93 , pp. 2395-2417
    • Kollman, P.1
  • 15
    • 0031012579 scopus 로고    scopus 로고
    • Enzyme-inhibitor association thermodynamics: Explicit and continuum solvent studies
    • Resat, H.; Marrone, T. J.; McCammon, J. A. Enzyme-inhibitor association thermodynamics: explicit and continuum solvent studies. Biophys. J. 1997, 72, 522-532.
    • (1997) Biophys. J. , vol.72 , pp. 522-532
    • Resat, H.1    Marrone, T.J.2    McCammon, J.A.3
  • 16
    • 0035846166 scopus 로고    scopus 로고
    • Are free energy calculations useful in practice? A comparison with rapid scoring functions for the p38 MAP kinase protein system
    • Pearlman, D. A.; Charifson, P. S. Are free energy calculations useful in practice? A comparison with rapid scoring functions for the p38 MAP kinase protein system. J. Med. Chem. 2001, 44, 3417-3423.
    • (2001) J. Med. Chem. , vol.44 , pp. 3417-3423
    • Pearlman, D.A.1    Charifson, P.S.2
  • 17
    • 0029000922 scopus 로고
    • Prediction of drug binding affinities by comparative binding energy analysis
    • Ortiz, A. R.; Pisabarro, M. T.; Gago, F.; Wade, R. C. Prediction of Drug Binding Affinities by Comparative Binding Energy Analysis. J. Med. Chem. 1995, 38, 2681-2691.
    • (1995) J. Med. Chem. , vol.38 , pp. 2681-2691
    • Ortiz, A.R.1    Pisabarro, M.T.2    Gago, F.3    Wade, R.C.4
  • 18
    • 0011063965 scopus 로고    scopus 로고
    • Derivation of QSARs using 3D structural models of protein-ligand complexes by COMBINE analysis
    • Holtje, H.-D., Sippl, W., Eds.; Prous Science S. A.: Barcelona
    • Wade, R. C. Derivation of QSARs using 3D structural models of protein-ligand complexes by COMBINE analysis. In Rational Approaches to Drug Design: 13th European Symposium on Quantitative Structure-Activity Relationships; Holtje, H.-D., Sippl, W., Eds.; Prous Science S. A.: Barcelona, 2001; pp 23-28.
    • (2001) Rational Approaches to Drug Design: 13th European Symposium on Quantitative Structure-Activity Relationships , pp. 23-28
    • Wade, R.C.1
  • 19
    • 0030892498 scopus 로고    scopus 로고
    • Reliability of comparative molecular field analysis models: Effects of data scaling and variable selection using a set of human synovial fluid phospholipase A2 inhibitors
    • Ortiz, A. R.; Pastor, M.; Palomer, A.; Cruciani, G.; Gago, F.; Wade, R. C. Reliability of comparative molecular field analysis models: effects of data scaling and variable selection using a set of human synovial fluid phospholipase A2 inhibitors. J. Med. Chem. 1997, 40, 1136-1148.
    • (1997) J. Med. Chem. , vol.40 , pp. 1136-1148
    • Ortiz, A.R.1    Pastor, M.2    Palomer, A.3    Cruciani, G.4    Gago, F.5    Wade, R.C.6
  • 20
    • 0032510317 scopus 로고    scopus 로고
    • Comparative binding energy analysis of HIV-1 protease inhibitors: Incorporation of solvent effects and validation as a powerful tool in receptor-based drug design
    • Perez, C.; Pastor, M.; Ortiz, A. R.; Gago, F. Comparative binding energy analysis of HIV-1 protease inhibitors: incorporation of solvent effects and validation as a powerful tool in receptor-based drug design. J. Med. Chem. 1998, 41, 836-852.
    • (1998) J. Med. Chem. , vol.41 , pp. 836-852
    • Perez, C.1    Pastor, M.2    Ortiz, A.R.3    Gago, F.4
  • 21
    • 0002759123 scopus 로고    scopus 로고
    • Comparative binding energy (COMBINE) analysis on a series of glycogen phosphorylase inhibitors: Comparison with GRID/GOLPE models
    • Gundertofte, K., Jorgensen, F. S., Eds.; Kluwer: New York
    • Pastor, M.; Gago, F.; Cruciani, G. Comparative binding energy (COMBINE) analysis on a series of glycogen phosphorylase inhibitors: comparison with GRID/GOLPE models. In Molecular Modeling and Prediction of Bioactivity; Gundertofte, K., Jorgensen, F. S., Eds.; Kluwer: New York, 2000; pp 329-330.
    • (2000) Molecular Modeling and Prediction of Bioactivity , pp. 329-330
    • Pastor, M.1    Gago, F.2    Cruciani, G.3
  • 22
    • 0035866695 scopus 로고    scopus 로고
    • Comparative binding energy (COMBINE) analysis of influenza neuraminidase-inhibitor complexes
    • Wang, T.; Wade, R. C. Comparative binding energy (COMBINE) analysis of influenza neuraminidase-inhibitor complexes. J. Med. Chem. 2001, 44, 961-971.
    • (2001) J. Med. Chem. , vol.44 , pp. 961-971
    • Wang, T.1    Wade, R.C.2
  • 23
    • 0034050042 scopus 로고    scopus 로고
    • 3D-QSAR methods on the basis of ligand receptor complexes. Application of COMBINE and GRID/GOLPE methodologies to a series of CYP1A2 Ligands
    • Lozano, J. J.; Pastor, M.; Cruciani, G.; Gaedt, K.; Centeno, N. B.; Gago, F.; Sanz, F. 3D-QSAR methods on the basis of ligand receptor complexes. Application of COMBINE and GRID/GOLPE methodologies to a series of CYP1A2 Ligands. J. Comput.-Aided Mol. Des. 2000, 14, 341-353.
    • (2000) J. Comput.-Aided Mol. Des. , vol.14 , pp. 341-353
    • Lozano, J.J.1    Pastor, M.2    Cruciani, G.3    Gaedt, K.4    Centeno, N.B.5    Gago, F.6    Sanz, F.7
  • 24
    • 0035979364 scopus 로고    scopus 로고
    • Comparative Binding Energy (COMBINE) analysis of the substrate specificity of haloalkane dehalogenase from xanthobacter autotrophicus GJ10
    • Kmunicek, J.; Luengo, S.; Gago, F.; Ortiz, A. R.; Wade, R. C.; Damborsky, J. Comparative Binding Energy (COMBINE) analysis of the substrate specificity of haloalkane dehalogenase from xanthobacter autotrophicus GJ10. Biochemistry 2001, 40, 8905-8917.
    • (2001) Biochemistry , vol.40 , pp. 8905-8917
    • Kmunicek, J.1    Luengo, S.2    Gago, F.3    Ortiz, A.R.4    Wade, R.C.5    Damborsky, J.6
  • 25
    • 0034069171 scopus 로고    scopus 로고
    • Nuclear receptor-DNA binding specificity: A COMBINE and Free-Wilson QSAR analysis
    • Tomic, S.; Nilsson, L.; Wade, R. C. Nuclear receptor-DNA binding specificity: A COMBINE and Free-Wilson QSAR analysis. J. Med. Chem. 2000, 43, 1780-1792.
    • (2000) J. Med. Chem. , vol.43 , pp. 1780-1792
    • Tomic, S.1    Nilsson, L.2    Wade, R.C.3
  • 26
    • 0025398721 scopus 로고
    • WHAT IF: A molecular modelling and drug design program
    • Vriend, G. WHAT IF: a molecular modelling and drug design program. J. Mol. Graph. 1990, 8, 52-56.
    • (1990) J. Mol. Graph. , vol.8 , pp. 52-56
    • Vriend, G.1
  • 27
    • 0030442990 scopus 로고    scopus 로고
    • Positioning hydrogen atoms by optimizing hydrogen bond networks in protein structures
    • Hooft, R. W. W.; Sander, C.; Vriend, G. Positioning hydrogen atoms by optimizing hydrogen bond networks in protein structures. Proteins 1996, 26, 363-376.
    • (1996) Proteins , vol.26 , pp. 363-376
    • Hooft, R.W.W.1    Sander, C.2    Vriend, G.3
  • 29
    • 0004150411 scopus 로고    scopus 로고
    • Molecular Simulations Inc.: San Diego, CA
    • InsightII, version 2000; Molecular Simulations Inc.: San Diego, CA.
    • (2000) InsightII, version 2000
  • 32
    • 0027310371 scopus 로고
    • Generating optimal linear PLS estimations (GOLPE): An advanced chemometric tool for handling 3D-QSAR problems
    • Baroni, M.; Costantino, G.; Cruciani, G.; Riganelli, D.; Valigi, R.; Clementi, S. Generating optimal linear PLS estimations (GOLPE): an advanced chemometric tool for handling 3D-QSAR problems. Quant. Struct.-Act. Relat. 1993, 12, 9-20.
    • (1993) Quant. Struct.-Act. Relat. , vol.12 , pp. 9-20
    • Baroni, M.1    Costantino, G.2    Cruciani, G.3    Riganelli, D.4    Valigi, R.5    Clementi, S.6
  • 33
    • 0034601808 scopus 로고    scopus 로고
    • Thermodynamic basis of resistance to HIV-1 protease inhibition: Calorimetric analysis of the V82F/I84V active site resistant mutant
    • Todd, M. J.; Luque, I.; Valazquez-Campoy, A.; Freire, E. Thermodynamic basis of resistance to HIV-1 protease inhibition: calorimetric analysis of the V82F/I84V active site resistant mutant. Biochemistry 2000, 39, 11876-11883.
    • (2000) Biochemistry , vol.39 , pp. 11876-11883
    • Todd, M.J.1    Luque, I.2    Valazquez-Campoy, A.3    Freire, E.4
  • 34
    • 0026573247 scopus 로고
    • In human malaria protective antibodies are directed mainly against the Lys-Glu ion pair within the Lys-Glu-Lys motif of the synthetic vaccine SPf66
    • Molano, A.; Segura, C.; Guzman, F.; Lozada, D.; Patarroyo, M. E. In human malaria protective antibodies are directed mainly against the Lys-Glu ion pair within the Lys-Glu-Lys motif of the synthetic vaccine SPf66. Parasite Immunol. 1992, 14, 111-124.
    • (1992) Parasite Immunol. , vol.14 , pp. 111-124
    • Molano, A.1    Segura, C.2    Guzman, F.3    Lozada, D.4    Patarroyo, M.E.5
  • 35
    • 0026696688 scopus 로고
    • Binding of an antiviral agent to a sensitive and a resistant human rhinovirus. Computer simulation studies with sampling of amino acid side-chain conformations. 1. Mapping the rotamers of residue 188 of viral protein 1
    • Wade, R. C.; McCammon, J. A. Binding of an antiviral agent to a sensitive and a resistant human rhinovirus. Computer simulation studies with sampling of amino acid side-chain conformations. 1. Mapping the rotamers of residue 188 of viral protein 1. J. Mol. Biol. 1992, 225, 679-696.
    • (1992) J. Mol. Biol. , vol.225 , pp. 679-696
    • Wade, R.C.1    McCammon, J.A.2


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