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Volumn 51, Issue 3, 2003, Pages 423-433

Structure-based identification of binding sites, native ligands and potential inhibitors for G-protein coupled receptors

Author keywords

Flexible ligand receptor docking; Internal coordinate mechanics; Ligand binding pocket prediction; Orphan G protein coupled receptor; Protein ligand docking; Rational drug design; Seven transmembrane receptor; Virtual ligand screening

Indexed keywords

BACTERIORHODOPSIN; BINDING PROTEIN; CELL SURFACE RECEPTOR; G PROTEIN COUPLED RECEPTOR; MEMBRANE PROTEIN; RETINAL; RHODOPSIN;

EID: 0037963157     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.10362     Document Type: Article
Times cited : (79)

References (52)
  • 1
    • 0036490942 scopus 로고    scopus 로고
    • Allosteric binding sites on cell-surface receptors: Novel targets for drug discovery
    • Christopoulos A. Allosteric binding sites on cell-surface receptors: Novel targets for drug discovery. Nat Rev Drug Disc 2001;1:198-210.
    • (2001) Nat Rev Drug Disc , vol.1 , pp. 198-210
    • Christopoulos, A.1
  • 3
    • 0033118334 scopus 로고    scopus 로고
    • Molecular tinkering of G protein-coupled receptors: An evolutionary success
    • Bockaert J, Pin JP. Molecular tinkering of G protein-coupled receptors: An evolutionary success. EMBO J 1999; 18:1723-1729.
    • (1999) EMBO J , vol.18 , pp. 1723-1729
    • Bockaert, J.1    Pin, J.P.2
  • 5
    • 0030938936 scopus 로고    scopus 로고
    • G-protein-coupled receptors: Molecular mechanisms involved in receptor activation and selectivity of G-protein recognition
    • Wess J. G-protein-coupled receptors: Molecular mechanisms involved in receptor activation and selectivity of G-protein recognition. FASEB J 1997;11:346-354.
    • (1997) FASEB J , vol.11 , pp. 346-354
    • Wess, J.1
  • 6
    • 0031565726 scopus 로고    scopus 로고
    • An alpha-carbon template for the transmembrane helices in the rhodopsin family of G-protein-coupled receptors
    • Baldwin JM, Schertler GFX, Unger VM. An alpha-carbon template for the transmembrane helices in the rhodopsin family of G-protein-coupled receptors. J Mol Biol 1997;272:144-164.
    • (1997) J Mol Biol , vol.272 , pp. 144-164
    • Baldwin, J.M.1    Schertler, G.F.X.2    Unger, V.M.3
  • 7
    • 0027465713 scopus 로고
    • Modeling of transmembrane 7 helix bundles
    • Cronet P, Sander C, Vriend G. Modeling of transmembrane 7 helix bundles. Prot Eng 1993;6:59-664.
    • (1993) Prot Eng , vol.6 , pp. 59-664
    • Cronet, P.1    Sander, C.2    Vriend, G.3
  • 8
    • 4243923763 scopus 로고    scopus 로고
    • Using biophysical and biochemical experimental information to generate 3-D structural models oftransmembrane (TM) domains of helical, integral membrane proteins
    • Herzyk P, Hubbard RE. Using biophysical and biochemical experimental information to generate 3-D structural models oftransmembrane (TM) domains of helical, integral membrane proteins. Biophys J 1998;74:A249-A249.
    • (1998) Biophys J , vol.74
    • Herzyk, P.1    Hubbard, R.E.2
  • 9
    • 0033638881 scopus 로고    scopus 로고
    • Modeling and docking the endothelin G-protein-coupled receptor
    • Orry AJW, Wallace BA. Modeling and docking the endothelin G-protein-coupled receptor. Biophys J 2000;79:3083-3094.
    • (2000) Biophys J , vol.79 , pp. 3083-3094
    • Orry, A.J.W.1    Wallace, B.A.2
  • 10
    • 0030998038 scopus 로고    scopus 로고
    • The transmembrane 7-alpha-bundle ofrhodopsin: Distance geometry calculations with hydrogen bonding constraints
    • Pogozheva ID, Lomize AL, Mosberg HI. The transmembrane 7-alpha-bundle ofrhodopsin: Distance geometry calculations with hydrogen bonding constraints. Biophys J 1997;72:1963-1985.
    • (1997) Biophys J , vol.72 , pp. 1963-1985
    • Pogozheva, I.D.1    Lomize, A.L.2    Mosberg, H.I.3
  • 11
    • 0027436983 scopus 로고
    • Molecular-dynamics of the 5-HT(1a) receptor and ligands
    • Sylte I, Edvardsen O, Dahl SG. Molecular-dynamics of the 5-HT(1a) receptor and ligands. Prot Eng 1993;6:691-700.
    • (1993) Prot Eng , vol.6 , pp. 691-700
    • Sylte, I.1    Edvardsen, O.2    Dahl, S.G.3
  • 14
    • 0025292355 scopus 로고
    • Model for the structure of bacteriorhodopsin based on high-resolution electron cryomicroscopy
    • Henderson R, Baldwin JM, Ceska TA, Zemlin F, Beckmann E, Downing KH. Model for the structure of bacteriorhodopsin based on high-resolution electron cryomicroscopy. J Mol Biol 1990;213: 899-929.
    • (1990) J Mol Biol , vol.213 , pp. 899-929
    • Henderson, R.1    Baldwin, J.M.2    Ceska, T.A.3    Zemlin, F.4    Beckmann, E.5    Downing, K.H.6
  • 16
    • 4243301061 scopus 로고
    • 3-Dimensional structure of bovine rhodopsin at 9-angstrom-resolution
    • Unger VM, Schertler GFX. 3-Dimensional structure of bovine rhodopsin at 9-angstrom-resolution. Biophys J 1994;66:A46-A46.
    • (1994) Biophys J , vol.66
    • Unger, V.M.1    Schertler, G.F.X.2
  • 17
    • 0028962270 scopus 로고
    • Low-resolution structure of bovine rhodopsin determined by electron cryomicroscopy
    • Unger VM, Schertler GFX. Low-resolution structure of bovine rhodopsin determined by electron cryomicroscopy. Biophys J 1995;68:1776-1786.
    • (1995) Biophys J , vol.68 , pp. 1776-1786
    • Unger, V.M.1    Schertler, G.F.X.2
  • 19
    • 0032546920 scopus 로고    scopus 로고
    • Proton transfer pathways in bacteriorhodopsin at 2.3 angstrom resolution
    • Luecke H, Richter HT, Lanyi JK. Proton transfer pathways in bacteriorhodopsin at 2.3 angstrom resolution. Science 1998;280: 1934-1937.
    • (1998) Science , vol.280 , pp. 1934-1937
    • Luecke, H.1    Richter, H.T.2    Lanyi, J.K.3
  • 21
    • 0034614621 scopus 로고    scopus 로고
    • Sphingosine 1-phosphate-induced cell proliferation, survival, and related signaling events mediated by G protein-coupled receptors EDG3 and EDG5
    • An SZ, Zheng YH, Bleu T. Sphingosine 1-phosphate-induced cell proliferation, survival, and related signaling events mediated by G protein-coupled receptors EDG3 and EDG5. J Biol Chem 2000;275:288-296.
    • (2000) J Biol Chem , vol.275 , pp. 288-296
    • An, S.Z.1    Zheng, Y.H.2    Bleu, T.3
  • 22
    • 0033600173 scopus 로고    scopus 로고
    • EDG3 is a functional receptor specific for sphingosine 1-phosphate and sphingosylphosphoryleholine with signaling characteristics distinct from EDG1 and AGR16
    • Okamoto H, Takuwa N, Yatomi Y, Gonda K, Shigematsu H, Takuwa Y. EDG3 is a functional receptor specific for sphingosine 1-phosphate and sphingosylphosphoryleholine with signaling characteristics distinct from EDG1 and AGR16. Biochem Biophys Res Comm 1999;260:203-208.
    • (1999) Biochem Biophys Res Comm , vol.260 , pp. 203-208
    • Okamoto, H.1    Takuwa, N.2    Yatomi, Y.3    Gonda, K.4    Shigematsu, H.5    Takuwa, Y.6
  • 23
    • 0034661482 scopus 로고    scopus 로고
    • Sphingosine 1-phosphate signalling in mammalian cells
    • Pyne S, Pyne NJ. Sphingosine 1-phosphate signalling in mammalian cells. Biochem J 2000;349:385-402.
    • (2000) Biochem J , vol.349 , pp. 385-402
    • Pyne, S.1    Pyne, N.J.2
  • 27
    • 0032860406 scopus 로고    scopus 로고
    • The difference between the CB1 and CB2 cannabinoid receptors at position 5.46 is crucial for the selectivity of WIN55212-2 for CB2
    • Song ZH, Slowey CA, Hurst DP, Reggio PH. The difference between the CB1 and CB2 cannabinoid receptors at position 5.46 is crucial for the selectivity of WIN55212-2 for CB2. Mol Pharm 1999;56:834-840.
    • (1999) Mol Pharm , vol.56 , pp. 834-840
    • Song, Z.H.1    Slowey, C.A.2    Hurst, D.P.3    Reggio, P.H.4
  • 28
    • 0032861629 scopus 로고    scopus 로고
    • Molecular modeling of the dopamine D-2 and serotonin 5-HT1A receptor binding modes of the enantiomers of 5-OMe-BPAT
    • Homan EJ, Wikstrom HV, Grol CJ. Molecular modeling of the dopamine D-2 and serotonin 5-HT1A receptor binding modes of the enantiomers of 5-OMe-BPAT. Bioorg Med Chem 1999;7:1805-1820.
    • (1999) Bioorg Med Chem , vol.7 , pp. 1805-1820
    • Homan, E.J.1    Wikstrom, H.V.2    Grol, C.J.3
  • 30
    • 0029043501 scopus 로고
    • Site-directed mutagenesis identifies residues involved in ligand recognition in the human a(2a) adenosine receptor
    • Kim JH, Wess J, Vanrhee AM, Schoneberg T, Jacobson KA. Site-directed mutagenesis identifies residues involved in ligand recognition in the human a(2a) adenosine receptor. J Biol Chem 1995;270:13987-13997.
    • (1995) J Biol Chem , vol.270 , pp. 13987-13997
    • Kim, J.H.1    Wess, J.2    Vanrhee, A.M.3    Schoneberg, T.4    Jacobson, K.A.5
  • 31
    • 0025667804 scopus 로고
    • 3-Dimensional modeling of G-protein-linked receptors
    • Findlay J, Eliopoulos E. 3-Dimensional modeling of G-protein-linked receptors. TIPS 1990; 11:492-499.
    • (1990) TIPS , vol.11 , pp. 492-499
    • Findlay, J.1    Eliopoulos, E.2
  • 32
    • 0025881062 scopus 로고
    • 3-Dimensional models of neurotransmitter G-binding protein-coupled receptors
    • Hibert MF, Trumppkallmeyer S, Bruinvels A, Hoflack J. 3-Dimensional models of neurotransmitter G-binding protein-coupled receptors. Mol Pharm 1991;40:8-15.
    • (1991) Mol Pharm , vol.40 , pp. 8-15
    • Hibert, M.F.1    Trumppkallmeyer, S.2    Bruinvels, A.3    Hoflack, J.4
  • 33
    • 0028773638 scopus 로고
    • Molecular modeling of adenosine receptors - The ligand-binding site on the rat adenosine a(2a) receptor
    • Ijzerman AP, Vanderwenden EM, Vangalen PJM, Jacobson KA. Molecular modeling of adenosine receptors - the ligand-binding site on the rat adenosine a(2a) receptor. Eur J Pharm Mol 1994;268:95-104.
    • (1994) Eur J Pharm Mol , vol.268 , pp. 95-104
    • Ijzerman, A.P.1    Vanderwenden, E.M.2    Vangalen, P.J.M.3    Jacobson, K.A.4
  • 34
    • 0028359361 scopus 로고
    • Modeling of G-protein coupled receptors with bacteriorhodopsin as a template - A novel approach based on interaction energy differences
    • Roper D, Jacoby E, Kruger P, Engels M, Grotzinger J, Wollmer A, Strassburger W. Modeling of G-protein coupled receptors with bacteriorhodopsin as a template - a novel approach based on interaction energy differences. J Rec Res 1994;14:167-186.
    • (1994) J Rec Res , vol.14 , pp. 167-186
    • Roper, D.1    Jacoby, E.2    Kruger, P.3    Engels, M.4    Grotzinger, J.5    Wollmer, A.6    Strassburger, W.7
  • 35
    • 0038217206 scopus 로고    scopus 로고
    • San Diego, CA: Molsoft LLC
    • ICM, version 2.8. San Diego, CA: Molsoft LLC; 2001.
    • (2001) ICM, Version 2.8
  • 37
    • 3042782458 scopus 로고    scopus 로고
    • In silico discovery of novel retinoic acid receptor agonist structures
    • Schapira M, Raaka BM, Samuels HH, Abagyan R. In silico discovery of novel retinoic acid receptor agonist structures. BMC Struc Biol 2001;1:1.
    • (2001) BMC Struc Biol , vol.1 , pp. 1
    • Schapira, M.1    Raaka, B.M.2    Samuels, H.H.3    Abagyan, R.4
  • 40
    • 0001731773 scopus 로고
    • Energy parameters in polypeptides: Ten improved geometrical parameters and nonbonded interactions for use in the ECEPP/3 algorithm, with application to proline-containing peptides
    • Nemethy G, Gibson KD, Palmer KA, Yoon CN, Paterlini G, Zagari A, Rumsey S, Scheraga HA. Energy parameters in polypeptides: Ten improved geometrical parameters and nonbonded interactions for use in the ECEPP/3 algorithm, with application to proline-containing peptides. J Phys Chem 1992;96:6472-6484.
    • (1992) J Phys Chem , vol.96 , pp. 6472-6484
    • Nemethy, G.1    Gibson, K.D.2    Palmer, K.A.3    Yoon, C.N.4    Paterlini, G.5    Zagari, A.6    Rumsey, S.7    Scheraga, H.A.8
  • 41
    • 0001560313 scopus 로고
    • Merck molecular force field I-V
    • Halgren T. Merck molecular force field I-V. J Comp Chem 1995;17:490-641.
    • (1995) J Comp Chem , vol.17 , pp. 490-641
    • Halgren, T.1
  • 43
    • 0032946494 scopus 로고    scopus 로고
    • LIGAND database for enzymes, compounds and reactions
    • Goto S, Nishioka T, Kanehisa M. LIGAND database for enzymes, compounds and reactions. Nucleic Acids Res 1999;27:377-379.
    • (1999) Nucleic Acids Res , vol.27 , pp. 377-379
    • Goto, S.1    Nishioka, T.2    Kanehisa, M.3
  • 44
    • 0036081122 scopus 로고    scopus 로고
    • LIGAND: Database of chemical compounds and reactions in biological pathways
    • Goto S, Okuno Y, Hattori M, Nishioka T, Kanehisa M. LIGAND: Database of chemical compounds and reactions in biological pathways. Nucleic Acids Res 2002;30:402-404.
    • (2002) Nucleic Acids Res , vol.30 , pp. 402-404
    • Goto, S.1    Okuno, Y.2    Hattori, M.3    Nishioka, T.4    Kanehisa, M.5
  • 46
    • 84986522918 scopus 로고
    • ICM - A new method for protein modeling and design: Applications to docking and structure prediction from the distorted native conformation
    • Abagyan R, Totrov M, Kuznetsov D. ICM - a new method for protein modeling and design: Applications to docking and structure prediction from the distorted native conformation. J Comp Chem 1994;15:488-506.
    • (1994) J Comp Chem , vol.15 , pp. 488-506
    • Abagyan, R.1    Totrov, M.2    Kuznetsov, D.3
  • 47
    • 0027955787 scopus 로고
    • Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins
    • Abagyan R, Totrov M. Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins. J Mol Biol 1994;235:983-1002.
    • (1994) J Mol Biol , vol.235 , pp. 983-1002
    • Abagyan, R.1    Totrov, M.2
  • 49
    • 0000504484 scopus 로고    scopus 로고
    • Ab initio folding of peptides by the optimal-bias Monte Carlo minimization procedure
    • Abagyan RA, Totrov M. Ab initio folding of peptides by the optimal-bias Monte Carlo minimization procedure. J Comp Phys 1999;151:402-421.
    • (1999) J Comp Phys , vol.151 , pp. 402-421
    • Abagyan, R.A.1    Totrov, M.2
  • 50
    • 0026681839 scopus 로고
    • Optimal protocol and trajectory visualization for conformational searches of peptides and proteins
    • Abagyan R, Argos P. Optimal protocol and trajectory visualization for conformational searches of peptides and proteins. J Mol Biol 1992;225:519-532.
    • (1992) J Mol Biol , vol.225 , pp. 519-532
    • Abagyan, R.1    Argos, P.2
  • 51
    • 0023430366 scopus 로고
    • Monte Carlo minimization approach to the multiple-minima problem in protein folding
    • Li ZQ, Scheraga HA. Monte Carlo minimization approach to the multiple-minima problem in protein folding. Proc Natl Acad Sci U S A 1987;84:6611-6615.
    • (1987) Proc Natl Acad Sci U S A , vol.84 , pp. 6611-6615
    • Li, Z.Q.1    Scheraga, H.A.2
  • 52
    • 0037157153 scopus 로고    scopus 로고
    • Computational drug design accommodating receptor flexibility: The relaxed complex scheme
    • Lin JH, Perryman AL, Schames JR, McCammon JA. Computational drug design accommodating receptor flexibility: The relaxed complex scheme. J Am Chem Soc 2002;124:5632-5633.
    • (2002) J Am Chem Soc , vol.124 , pp. 5632-5633
    • Lin, J.H.1    Perryman, A.L.2    Schames, J.R.3    McCammon, J.A.4


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