메뉴 건너뛰기




Volumn 460, Issue A, 2009, Pages 263-288

Chapter 13 Modeling Small Molecule-Compound Binding to G-Protein-Coupled Receptors

Author keywords

[No Author keywords available]

Indexed keywords

G PROTEIN COUPLED RECEPTOR; LIGAND;

EID: 65549111760     PISSN: 00766879     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0076-6879(09)05213-6     Document Type: Review
Times cited : (23)

References (51)
  • 1
    • 33645523756 scopus 로고    scopus 로고
    • A comparative study of available software for high-accuracy homology modeling: From sequence alignments to structural models
    • Akbar N., Sitkoff D., and Krystek S. A comparative study of available software for high-accuracy homology modeling: From sequence alignments to structural models. Protein Sci. 15 (2006) 808-824
    • (2006) Protein Sci. , vol.15 , pp. 808-824
    • Akbar, N.1    Sitkoff, D.2    Krystek, S.3
  • 3
    • 77957055780 scopus 로고
    • Integrated methods for modeling G-protein coupled receptors
    • Ballesteros J., and Weinstein H. Integrated methods for modeling G-protein coupled receptors. Methods Neurosci. 25 (1995) 366-428
    • (1995) Methods Neurosci. , vol.25 , pp. 366-428
    • Ballesteros, J.1    Weinstein, H.2
  • 5
    • 0038458865 scopus 로고    scopus 로고
    • Modeling the 3D structure of GPCRs: Advances and application to drug discovery
    • Becker O.M., Shacham S., Marantz Y., and Noiman S. Modeling the 3D structure of GPCRs: Advances and application to drug discovery. Curr. Opin. Drug Discov. Dev. 6 (2003) 353-361
    • (2003) Curr. Opin. Drug Discov. Dev. , vol.6 , pp. 353-361
    • Becker, O.M.1    Shacham, S.2    Marantz, Y.3    Noiman, S.4
  • 7
    • 50149116588 scopus 로고    scopus 로고
    • Agonist-induced conformational changes in bovine rhodopsin: Insight into activation of G-protein-coupled receptors
    • Bhattacharya S., Hall S.E., and Vaidehi N. Agonist-induced conformational changes in bovine rhodopsin: Insight into activation of G-protein-coupled receptors. J. Mol. Biol. 382 (2008) 539-555
    • (2008) J. Mol. Biol. , vol.382 , pp. 539-555
    • Bhattacharya, S.1    Hall, S.E.2    Vaidehi, N.3
  • 8
    • 44049086134 scopus 로고    scopus 로고
    • Ligand-stabilized conformational states of human beta(2) adrenergic receptor: Insight into G-protein-coupled receptor activation
    • Bhattacharya S., Hall S.E., Li H., and Vaidehi N. Ligand-stabilized conformational states of human beta(2) adrenergic receptor: Insight into G-protein-coupled receptor activation. Biophys. J. 94 (2008) 2027-2042
    • (2008) Biophys. J. , vol.94 , pp. 2027-2042
    • Bhattacharya, S.1    Hall, S.E.2    Li, H.3    Vaidehi, N.4
  • 9
    • 0037235663 scopus 로고    scopus 로고
    • Protein-based virtual screening of chemical databases. II. Are homology models of G-protein coupled receptors suitable targets?
    • Bissantz C., Bernard P., Hibert M., and Rognan D. Protein-based virtual screening of chemical databases. II. Are homology models of G-protein coupled receptors suitable targets?. Proteins 50 (2003) 5-25
    • (2003) Proteins , vol.50 , pp. 5-25
    • Bissantz, C.1    Bernard, P.2    Hibert, M.3    Rognan, D.4
  • 10
    • 0042511005 scopus 로고    scopus 로고
    • A graph theory algorithm for protein side-chain prediction
    • Canutescu A.A., Shelenkov A.A., Dunbrack Jr. R.L.,. A graph theory algorithm for protein side-chain prediction. Protein Sci. 12 (2003) 2001-2014
    • (2003) Protein Sci. , vol.12 , pp. 2001-2014
    • Canutescu, A.A.1    Shelenkov, A.A.2    Dunbrack Jr., R.L.3
  • 11
    • 16344378642 scopus 로고    scopus 로고
    • Analysis of side-chain rotamers in transmembrane proteins
    • Chamberlain A.K., and Bowie J.U. Analysis of side-chain rotamers in transmembrane proteins. Biophys. J. 87 (2004) 3460-3469
    • (2004) Biophys. J. , vol.87 , pp. 3460-3469
    • Chamberlain, A.K.1    Bowie, J.U.2
  • 13
    • 33846218265 scopus 로고    scopus 로고
    • How a small change in retinal leads to G-protein activation: Initial events suggested by molecular dynamics calculations
    • Crozier P.S., Stevens M.J., and Woolf T.B. How a small change in retinal leads to G-protein activation: Initial events suggested by molecular dynamics calculations. Proteins 66 (2007) 559-574
    • (2007) Proteins , vol.66 , pp. 559-574
    • Crozier, P.S.1    Stevens, M.J.2    Woolf, T.B.3
  • 15
    • 0029907599 scopus 로고    scopus 로고
    • Requirement of rigid-body motion of transmembrane helices for light activation of rhodopsin
    • Farrens D.L., Altenbach C., Yang K., Hubbell W.L., and Khorana H.G. Requirement of rigid-body motion of transmembrane helices for light activation of rhodopsin. Science 274 (1996) 768-770
    • (1996) Science , vol.274 , pp. 768-770
    • Farrens, D.L.1    Altenbach, C.2    Yang, K.3    Hubbell, W.L.4    Khorana, H.G.5
  • 17
    • 0001246294 scopus 로고    scopus 로고
    • Generalized Born model based on a surface integral formulation
    • Ghosh A., Rapp C.S., and Friesner R.A. Generalized Born model based on a surface integral formulation. J. Phys. Chem. B 102 (1998) 10983-10990
    • (1998) J. Phys. Chem. B , vol.102 , pp. 10983-10990
    • Ghosh, A.1    Rapp, C.S.2    Friesner, R.A.3
  • 21
    • 0024520745 scopus 로고
    • Site-directed mutagenesis by overlap extension using the polymerase chain reaction
    • Ho S.N., Hunt H.D., Horton R.M., Pullen J.K., and Pease L.R. Site-directed mutagenesis by overlap extension using the polymerase chain reaction. Gene 77 (1989) 51-59
    • (1989) Gene , vol.77 , pp. 51-59
    • Ho, S.N.1    Hunt, H.D.2    Horton, R.M.3    Pullen, J.K.4    Pease, L.R.5
  • 22
    • 47749099638 scopus 로고    scopus 로고
    • Mechanism of signal propagation upon retinal isomerization: Insights from molecular dynamics simulations of rhodpsin restrained by normal modes
    • Isin B., Schulten K., Tajkhorshid E., and Bahar I. Mechanism of signal propagation upon retinal isomerization: Insights from molecular dynamics simulations of rhodpsin restrained by normal modes. Biophys. J. 95 (2008) 789-803
    • (2008) Biophys. J. , vol.95 , pp. 789-803
    • Isin, B.1    Schulten, K.2    Tajkhorshid, E.3    Bahar, I.4
  • 24
    • 34447633368 scopus 로고    scopus 로고
    • Conformational complexity of G-protein-coupled receptors
    • Kobilka B.K., and Deupi X. Conformational complexity of G-protein-coupled receptors. Trends Pharmacol. Sci. 28 (2007) 397-406
    • (2007) Trends Pharmacol. Sci. , vol.28 , pp. 397-406
    • Kobilka, B.K.1    Deupi, X.2
  • 25
    • 3042798261 scopus 로고    scopus 로고
    • Molecular mechanisms of ligand binding, signaling, and regulation within the superfamily of G-protein-coupled receptors: Molecular modeling and mutagenesis approaches to receptor structure and function
    • Kristiansen K. Molecular mechanisms of ligand binding, signaling, and regulation within the superfamily of G-protein-coupled receptors: Molecular modeling and mutagenesis approaches to receptor structure and function. Pharm. Ther. 103 (2004) 21-80
    • (2004) Pharm. Ther. , vol.103 , pp. 21-80
    • Kristiansen, K.1
  • 26
    • 3242793327 scopus 로고    scopus 로고
    • Historical review: A brief history and personal retrospective of seven-transmembrane receptors
    • Lefkowitz R.J. Historical review: A brief history and personal retrospective of seven-transmembrane receptors. Trends Pharmacol. Sci. 25 (2004) 413-422
    • (2004) Trends Pharmacol. Sci. , vol.25 , pp. 413-422
    • Lefkowitz, R.J.1
  • 28
    • 0028304962 scopus 로고
    • Satisfying hydrogen bonding potential in proteins
    • McDonald I.K., and Thornton J.M. Satisfying hydrogen bonding potential in proteins. J. Mol. Biol. 238 (1994) 777-793
    • (1994) J. Mol. Biol. , vol.238 , pp. 777-793
    • McDonald, I.K.1    Thornton, J.M.2
  • 29
    • 34447626644 scopus 로고    scopus 로고
    • GPCR functional selectivity has therapeutic impact
    • Mailman R.B. GPCR functional selectivity has therapeutic impact. Trends Pharmacol. Sci. 28 (2007) 390-396
    • (2007) Trends Pharmacol. Sci. , vol.28 , pp. 390-396
    • Mailman, R.B.1
  • 31
    • 9144240095 scopus 로고
    • DREIDING-a generic force field for molecular simulations
    • Mayo S.L., Olafson B.D., Goddard III W.A.,. DREIDING-a generic force field for molecular simulations. J. Phys. Chem. 94 (1990) 8897-8909
    • (1990) J. Phys. Chem. , vol.94 , pp. 8897-8909
    • Mayo, S.L.1    Olafson, B.D.2    Goddard III, W.A.3
  • 32
    • 43749109187 scopus 로고    scopus 로고
    • Crystal structure of squid rhodopsin
    • Murakami M., and Kouyama T. Crystal structure of squid rhodopsin. Nature 453 (2008) 363-367
    • (2008) Nature , vol.453 , pp. 363-367
    • Murakami, M.1    Kouyama, T.2
  • 34
    • 4344581120 scopus 로고    scopus 로고
    • The retinal conformation and its environment in rhodopsin in light of a new 2.2 A crystal structure
    • Okada T., Sugihara M., Bondar A.N., Elstner M., Entel P., and Buss V. The retinal conformation and its environment in rhodopsin in light of a new 2.2 A crystal structure. J. Mol. Biol. 342 (2004) 571-583
    • (2004) J. Mol. Biol. , vol.342 , pp. 571-583
    • Okada, T.1    Sugihara, M.2    Bondar, A.N.3    Elstner, M.4    Entel, P.5    Buss, V.6
  • 36
    • 47049130668 scopus 로고    scopus 로고
    • Crystal structure of the ligand-free G-protein-coupled receptor opsin
    • Park J.H., Scheerer P., Hofmann K.P., Choe H.W., and Ernst O.P. Crystal structure of the ligand-free G-protein-coupled receptor opsin. Nature 454 (2008) 183-187
    • (2008) Nature , vol.454 , pp. 183-187
    • Park, J.H.1    Scheerer, P.2    Hofmann, K.P.3    Choe, H.W.4    Ernst, O.P.5
  • 38
    • 33646833091 scopus 로고    scopus 로고
    • Structure selection for protein kinase docking and virtual screening: Homology models or crystal structures?
    • Rockey W.M., and Elcock A.H. Structure selection for protein kinase docking and virtual screening: Homology models or crystal structures?. Curr. Protein Pept. Sci. 7 (2006) 437-457
    • (2006) Curr. Protein Pept. Sci. , vol.7 , pp. 437-457
    • Rockey, W.M.1    Elcock, A.H.2
  • 40
    • 33646526072 scopus 로고    scopus 로고
    • I want a new drug: G-protein-coupled receptors in drug development
    • Schlyer S., and Horuk R. I want a new drug: G-protein-coupled receptors in drug development. Drug Discov. Today. 11 (2006) 481-493
    • (2006) Drug Discov. Today. , vol.11 , pp. 481-493
    • Schlyer, S.1    Horuk, R.2
  • 42
    • 33748276474 scopus 로고    scopus 로고
    • Protein-ligand docking: Current status and future challenges
    • Sousa S.F., Fernandes P.A., and Ramos M.J. Protein-ligand docking: Current status and future challenges. Proteins 65 (2006) 15-26
    • (2006) Proteins , vol.65 , pp. 15-26
    • Sousa, S.F.1    Fernandes, P.A.2    Ramos, M.J.3
  • 43
    • 1942487807 scopus 로고    scopus 로고
    • First principles prediction of the structure and function of G protein-coupled receptors: Validation for bovine rhodopsin
    • Trabanino R., Hall S.E., Vaidehi N., Floriano W., and Goddard W.A. First principles prediction of the structure and function of G protein-coupled receptors: Validation for bovine rhodopsin. Biophys. J. 86 (2004) 1904-1921
    • (2004) Biophys. J. , vol.86 , pp. 1904-1921
    • Trabanino, R.1    Hall, S.E.2    Vaidehi, N.3    Floriano, W.4    Goddard, W.A.5
  • 47
    • 45649083187 scopus 로고    scopus 로고
    • Functional role of the "ionic lock"-an interhelical hydrogen-bond network in family A heptahelical receptors
    • Vogel R., Mahalingam M., Lüdeke S., Huber T., Siebert F., and Sakmar T.P. Functional role of the "ionic lock"-an interhelical hydrogen-bond network in family A heptahelical receptors. J. Mol. Biol. 380 (2008) 648-655
    • (2008) J. Mol. Biol. , vol.380 , pp. 648-655
    • Vogel, R.1    Mahalingam, M.2    Lüdeke, S.3    Huber, T.4    Siebert, F.5    Sakmar, T.P.6
  • 48
    • 0025398721 scopus 로고
    • A molecular modeling and drug design program
    • Vriend G. A molecular modeling and drug design program. J. Mol. Graph 8 (1990) 52-56
    • (1990) J. Mol. Graph , vol.8 , pp. 52-56
    • Vriend, G.1
  • 50
    • 0037079587 scopus 로고    scopus 로고
    • Docking of small ligands to low-resolution and theoretically predicted receptor structures
    • Wojciechowski M., and Skolnick J. Docking of small ligands to low-resolution and theoretically predicted receptor structures. J. Comput. Chem. 23 (2002) 189-197
    • (2002) J. Comput. Chem. , vol.23 , pp. 189-197
    • Wojciechowski, M.1    Skolnick, J.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.