메뉴 건너뛰기




Volumn 47, Issue 2, 2007, Pages 668-675

Analysis of ligand-bound water molecules in high-resolution crystal structures of protein-ligand complexes

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEXATION; CRYSTAL STRUCTURE; CRYSTALLOGRAPHY; IMAGE RESOLUTION; LIGANDS; PROTEINS;

EID: 34247187356     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci6003527     Document Type: Article
Times cited : (147)

References (37)
  • 1
    • 85135598766 scopus 로고    scopus 로고
    • Mancera, R. L. De novo Ligand Design with Explicit Water Molecules: An Application to Bacterial Neuraminidase. J. Comput.-Aided Mol. Des. 2002, 16, 479-499.
    • Mancera, R. L. De novo Ligand Design with Explicit Water Molecules: An Application to Bacterial Neuraminidase. J. Comput.-Aided Mol. Des. 2002, 16, 479-499.
  • 2
    • 0027587199 scopus 로고
    • Structural Analysis of MHC Class I Molecules with Bound Peptide Antigens
    • Wilson, I. A.; Fremont, D. H. Structural Analysis of MHC Class I Molecules with Bound Peptide Antigens. Semin. Immunol. 1993, 5, 75-80.
    • (1993) Semin. Immunol , vol.5 , pp. 75-80
    • Wilson, I.A.1    Fremont, D.H.2
  • 3
    • 0031008974 scopus 로고    scopus 로고
    • Mean Field Analysis of FKBP12 Complexes with FK506 and Rapamycin: Implications for a Role of Crystallographic Water Molecules in Molecular Recognition and Specificity
    • Rejto, P. A.; Verkhivker, G. M. Mean Field Analysis of FKBP12 Complexes with FK506 and Rapamycin: Implications for a Role of Crystallographic Water Molecules in Molecular Recognition and Specificity. Proteins 1997, 28, 313-324.
    • (1997) Proteins , vol.28 , pp. 313-324
    • Rejto, P.A.1    Verkhivker, G.M.2
  • 4
    • 0033550314 scopus 로고    scopus 로고
    • Novel Aromatic Inhibitors of Influenza Virus Neuraminidase Make Selective Interactions with Conserved Residues and Water Molecules in the Active Site
    • Finley, J. B.; Atigadda, V. R.; Duarte, F.; Zhao, J. J.; Brouillette, M. J.; Air, G. M.; Luo, M. Novel Aromatic Inhibitors of Influenza Virus Neuraminidase Make Selective Interactions with Conserved Residues and Water Molecules in the Active Site. J. Mol. Biol. 1999, 293, 1107-1119.
    • (1999) J. Mol. Biol , vol.293 , pp. 1107-1119
    • Finley, J.B.1    Atigadda, V.R.2    Duarte, F.3    Zhao, J.J.4    Brouillette, M.J.5    Air, G.M.6    Luo, M.7
  • 5
    • 0342803187 scopus 로고    scopus 로고
    • Modeling Cyclooxygenase Inhibition. Implication of Active Site Hydration on the Selectivity of Ketoprofen Analogues
    • Palomer, A.; Perez, J. J.; Navea, S.; Llorens, O.; Pascual, J.; Garcia, L.; Mauleon, D. Modeling Cyclooxygenase Inhibition. Implication of Active Site Hydration on the Selectivity of Ketoprofen Analogues. J. Med. Chem. 2000, 43, 2280-2284.
    • (2000) J. Med. Chem , vol.43 , pp. 2280-2284
    • Palomer, A.1    Perez, J.J.2    Navea, S.3    Llorens, O.4    Pascual, J.5    Garcia, L.6    Mauleon, D.7
  • 6
    • 0028856716 scopus 로고
    • Water Molecules Participate in Proteinase-Inhibitor Interactions: Crystal Structure of Leu18, Ala18, and Gly18 Variants of Turkey Ovomucoid Inhibitor Third Domain Complexed with Streptomyces griseus Proteinase B
    • Huang, K.; Lu, W.; Anderson, S.; Laskowski, M.; James, M. N. G. Water Molecules Participate in Proteinase-Inhibitor Interactions: Crystal Structure of Leu18, Ala18, and Gly18 Variants of Turkey Ovomucoid Inhibitor Third Domain Complexed with Streptomyces griseus Proteinase B. Protein Sci. 1995, 4, 1985-1997.
    • (1995) Protein Sci , vol.4 , pp. 1985-1997
    • Huang, K.1    Lu, W.2    Anderson, S.3    Laskowski, M.4    James, M.N.G.5
  • 7
    • 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
  • 8
    • 0028452862 scopus 로고    scopus 로고
    • Tame, J. R.; Murshudov, G. N.; Dodson, E. J.; Neil, T. K.; Dodson, G. G.; Higgins, C. F.; Wilkinson, A. J. The Structural Basis of Sequence-Independent Peptide Binding by OppA Protein. Science 1994, 264, 1578-1581.
    • Tame, J. R.; Murshudov, G. N.; Dodson, E. J.; Neil, T. K.; Dodson, G. G.; Higgins, C. F.; Wilkinson, A. J. The Structural Basis of Sequence-Independent Peptide Binding by OppA Protein. Science 1994, 264, 1578-1581.
  • 9
    • 0024375861 scopus 로고
    • Substrate Specificity and Affinity of a Protein Modulated by Bound Water Molecules
    • Quiocho, F. A.; Wilson, D. K.; Vyas, N. K. Substrate Specificity and Affinity of a Protein Modulated by Bound Water Molecules. Nature 1989, 340, 404-407.
    • (1989) Nature , vol.340 , pp. 404-407
    • Quiocho, F.A.1    Wilson, D.K.2    Vyas, N.K.3
  • 11
    • 0029134561 scopus 로고
    • The Role of Water Molecules in the Structure-Based Design of (5-Hydroxynorvaline)-2-cyclosporin: Synthesis, Biological Activity, and Crystallographic Analysis with Cyclophilin A
    • Mikol, V.; Papageorgiou, C.; Borer, X. The Role of Water Molecules in the Structure-Based Design of (5-Hydroxynorvaline)-2-cyclosporin: Synthesis, Biological Activity, and Crystallographic Analysis with Cyclophilin A. J. Med. Chem. 1995, 58, 3361-3367.
    • (1995) J. Med. Chem , vol.58 , pp. 3361-3367
    • Mikol, V.1    Papageorgiou, C.2    Borer, X.3
  • 12
    • 4143081344 scopus 로고    scopus 로고
    • Intuitive Calculations of Free Energy of Binding for Protein-Ligand Complexes. 3. The Free Energy Contribution of Structural Water Molecules in HIV-1 Protease Complexes
    • Fornabaio, M.; Spyrakis, F.; Mozzarelli, A.; Cozzini, P.; Abraham, D. J.; Kellogg, G. E. Simple, Intuitive Calculations of Free Energy of Binding for Protein-Ligand Complexes. 3. The Free Energy Contribution of Structural Water Molecules in HIV-1 Protease Complexes. J. Med. Chem. 2004, 47, 4507-4516.
    • (2004) J. Med. Chem , vol.47 , pp. 4507-4516
    • Fornabaio, M.1    Spyrakis, F.2    Mozzarelli, A.3    Cozzini, P.4    Abraham, D.J.5    Kellogg, G.6    Simple, E.7
  • 13
    • 0032961895 scopus 로고    scopus 로고
    • The Particle Concept: Placing Discrete Water Molecules during Protein-Ligand Docking Predictions
    • Rarey, M.; Kramer, B.; Lengaure, T. The Particle Concept: Placing Discrete Water Molecules during Protein-Ligand Docking Predictions. Proteins 1999, 34, 17-28.
    • (1999) Proteins , vol.34 , pp. 17-28
    • Rarey, M.1    Kramer, B.2    Lengaure, T.3
  • 14
    • 2942659093 scopus 로고    scopus 로고
    • Standard Free Energy of Releasing a Localized Water Molecule from the Binding Pockets of Proteins: Double-Decoupling Method
    • Hamelberg, D.; McCammon, J. A. Standard Free Energy of Releasing a Localized Water Molecule from the Binding Pockets of Proteins: Double-Decoupling Method. J. Am. Chem. Soc. 2004, 126, 7683-7689.
    • (2004) J. Am. Chem. Soc , vol.126 , pp. 7683-7689
    • Hamelberg, D.1    McCammon, J.A.2
  • 15
    • 33748513468 scopus 로고    scopus 로고
    • Lu, Y.; Yang, C.-Y.; Wang, S. Binding Free Energy Contributions of Interfacial Waters in HIV-1 Protease/Inhibitor Complexes. J. Am. Chem. Soc. 2006, 128, 11830-11839.
    • Lu, Y.; Yang, C.-Y.; Wang, S. Binding Free Energy Contributions of Interfacial Waters in HIV-1 Protease/Inhibitor Complexes. J. Am. Chem. Soc. 2006, 128, 11830-11839.
  • 16
    • 0029450365 scopus 로고
    • Hydration in Drug Design. 1. Multiple Hydrogen-Bonding Features of Water Molecules in Mediating Protein-Ligand Interactions
    • Poornima, C. S.; Dean, P. M. Hydration in Drug Design. 1. Multiple Hydrogen-Bonding Features of Water Molecules in Mediating Protein-Ligand Interactions. J. Comput.-Aided Mol. Des. 1995, 9, 500-512.
    • (1995) J. Comput.-Aided Mol. Des , vol.9 , pp. 500-512
    • Poornima, C.S.1    Dean, P.M.2
  • 17
    • 0029444719 scopus 로고
    • Hydration in Drug Design. 2. Influence of Local Site Surface Shape on Water Binding
    • Poornima, C. S.; Dean, P. M. Hydration in Drug Design. 2. Influence of Local Site Surface Shape on Water Binding. J. Comput. -Aided Mol. Des. 1995, 9, 513-520.
    • (1995) J. Comput. -Aided Mol. Des , vol.9 , pp. 513-520
    • Poornima, C.S.1    Dean, P.M.2
  • 19
    • 0033081137 scopus 로고    scopus 로고
    • How Many Water Molecules Can Be Detected by Protein Crystallography?
    • Carugo, O.; Bordo, D. How Many Water Molecules Can Be Detected by Protein Crystallography? Acta Crystallogr., Sect. D 1999, 55, 479-483.
    • (1999) Acta Crystallogr., Sect. D , vol.55 , pp. 479-483
    • Carugo, O.1    Bordo, D.2
  • 20
    • 2542530042 scopus 로고    scopus 로고
    • The PDBbind Database: Collection of Binding Affinities for Protein-Ligand Complexes with Known Three-Dimensional Structures
    • Wang, R.; Fang, X.; Lu, Y.; Wang, S. The PDBbind Database: Collection of Binding Affinities for Protein-Ligand Complexes with Known Three-Dimensional Structures. J. Med. Chem. 2004, 47, 2977-2980.
    • (2004) J. Med. Chem , vol.47 , pp. 2977-2980
    • Wang, R.1    Fang, X.2    Lu, Y.3    Wang, S.4
  • 22
    • 0024442361 scopus 로고
    • Is γ-chymoTrypsin a Tetrapeptide Acyl-enzyme Adduct of a Chymotrypsin?
    • Dixon, M. M.; Matthews, B. W. Is γ-chymoTrypsin a Tetrapeptide Acyl-enzyme Adduct of a Chymotrypsin? Biochemistry 1989, 28, 7033-7038.
    • (1989) Biochemistry , vol.28 , pp. 7033-7038
    • Dixon, M.M.1    Matthews, B.W.2
  • 23
    • 0020483485 scopus 로고
    • Iron-Sulfur Clusters and Protein Structure of Azotobacter Ferredoxin at 2.0 Å Resolution
    • Ghosh, D.; O'Donnell, S.; Furey, W., Jr.; Robbins, A. H.; Stout, C. D. Iron-Sulfur Clusters and Protein Structure of Azotobacter Ferredoxin at 2.0 Å Resolution. J. Mol. Biol. 1982, 158, 73-109.
    • (1982) J. Mol. Biol , vol.158 , pp. 73-109
    • Ghosh, D.1    O'Donnell, S.2    Furey Jr., W.3    Robbins, A.H.4    Stout, C.D.5
  • 24
    • 0002518563 scopus 로고    scopus 로고
    • Knowledge-Based B-Factor Restraints for the Refinement of Proteins
    • Tronrude, D. E. Knowledge-Based B-Factor Restraints for the Refinement of Proteins. J. Appl. Crystallogr. 1996, 29, 100-104.
    • (1996) J. Appl. Crystallogr , vol.29 , pp. 100-104
    • Tronrude, D.E.1
  • 25
    • 0019075327 scopus 로고
    • Structural Dynamics of Liganded Myoglobin
    • Frauenfelder, H.; Petsko, G. A. Structural Dynamics of Liganded Myoglobin. Biophys. J. 1980, 32, 465-478.
    • (1980) Biophys. J , vol.32 , pp. 465-478
    • Frauenfelder, H.1    Petsko, G.A.2
  • 26
    • 0015222647 scopus 로고
    • The Interpretation of Protein Structures: Estimation of Static Accessibility
    • Lee, B.; Richards, F. M. The Interpretation of Protein Structures: Estimation of Static Accessibility. J. Mol. Biol. 1971, 55, 379-400.
    • (1971) J. Mol. Biol , vol.55 , pp. 379-400
    • Lee, B.1    Richards, F.M.2
  • 27
    • 84927514013 scopus 로고
    • Nouveles Applications des Parameters Continues a la Theorie des Formes Quadratique
    • Voronoi, G. Nouveles Applications des Parameters Continues a la Theorie des Formes Quadratique. J. Reine Angew. Math. 1908, 134, 198-287.
    • (1908) J. Reine Angew. Math , vol.134 , pp. 198-287
    • Voronoi, G.1
  • 28
    • 0036773411 scopus 로고    scopus 로고
    • Quantification of Protein Surfaces, Volumes and Atom-Atom Contacts Using a Constrained Voronoi Procedure
    • McConkey, B. J.; Sobolev, V.; Edelman, M. Quantification of Protein Surfaces, Volumes and Atom-Atom Contacts Using a Constrained Voronoi Procedure. Bioinformatics 2002, 18, 1365-1373.
    • (2002) Bioinformatics , vol.18 , pp. 1365-1373
    • McConkey, B.J.1    Sobolev, V.2    Edelman, M.3
  • 30
    • 0031592453 scopus 로고    scopus 로고
    • Predicting Conserved Water-Mediated and Polar Ligand Interaction in Proteins using a K-Nearest-Neighbors Genetic Algorithm
    • Raymer, M. L.; Sanschagrin, P. C.; Punch, W. F.; Venkataraman, S.; Goodman, E. D.; Kuhn, L. A. Predicting Conserved Water-Mediated and Polar Ligand Interaction in Proteins using a K-Nearest-Neighbors Genetic Algorithm. J. Mol. Biol. 1997, 265, 445-464.
    • (1997) J. Mol. Biol , vol.265 , pp. 445-464
    • Raymer, M.L.1    Sanschagrin, P.C.2    Punch, W.F.3    Venkataraman, S.4    Goodman, E.D.5    Kuhn, L.A.6
  • 31
    • 0027918556 scopus 로고    scopus 로고
    • Levitt, M.; Park, B. H. Water: Now You See It, Now You Don't. Structure 1993, 1, 223-226.
    • Levitt, M.; Park, B. H. Water: Now You See It, Now You Don't. Structure 1993, 1, 223-226.
  • 32
    • 0028095182 scopus 로고
    • Buried Waters and Internal Cavities in Monomeric Proteins
    • Williams, M. A.; Goodfellow, J. M.; Thornton, J. M. Buried Waters and Internal Cavities in Monomeric Proteins. Protein Sci. 1994, 3, 1224-1235.
    • (1994) Protein Sci , vol.3 , pp. 1224-1235
    • Williams, M.A.1    Goodfellow, J.M.2    Thornton, J.M.3
  • 33
    • 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
  • 34
    • 4544316921 scopus 로고    scopus 로고
    • The Polar Hydrophobicity of Fluorinated Compounds
    • Biffinger, J. C.; Kim, H. W.; DiMagno, S. G. The Polar Hydrophobicity of Fluorinated Compounds. ChemBioChem 2004, 5, 622-627.
    • (2004) ChemBioChem , vol.5 , pp. 622-627
    • Biffinger, J.C.1    Kim, H.W.2    DiMagno, S.G.3
  • 35
    • 0028228418 scopus 로고
    • The Entropic Cost of Bound Water in Crystals and Biomolecules
    • Dunitz J. D. The Entropic Cost of Bound Water in Crystals and Biomolecules. Science 1994, 264, 670-671.
    • (1994) Science , vol.264 , pp. 670-671
    • Dunitz, J.D.1
  • 36
    • 0030466444 scopus 로고    scopus 로고
    • 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.1    Just, E.2
  • 37
    • 0037533880 scopus 로고    scopus 로고
    • Thermodynamic Contributions of the Ordered Water Molecule in HIV-1 Protease
    • Li, Z.; Lazaridis, T. Thermodynamic Contributions of the Ordered Water Molecule in HIV-1 Protease. J. Am. Chem. Soc. 2003, 125, 6636-6637.
    • (2003) J. Am. Chem. Soc , vol.125 , pp. 6636-6637
    • Li, Z.1    Lazaridis, T.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.