Construction of a sequence motif characteristic of aminergic G protein-coupled receptors

Protein Science

Volumn 12, Issue 7, 2003, Pages 1360-1367

  Huang, Enoch S ^a  

^a PFIZER INC   (United States)

Author keywords

Biogenic amines; Bioinformatics; G protein coupled receptor; Motif discovery; Multiple sequence alignment; Protein ligand interactions

Indexed keywords

AMINE; ASPARTIC ACID; G PROTEIN COUPLED RECEPTOR; HISTAMINE H4 RECEPTOR; MEMBRANE PROTEIN; RHODOPSIN; TRYPTOPHAN;

ADRENERGIC SYSTEM; AMINO ACID SEQUENCE; ARTICLE; BIOINFORMATICS; CALCULATION; LIGAND BINDING; MOLECULAR MODEL; PRIORITY JOURNAL; PROTEIN INTERACTION; SEQUENCE ALIGNMENT;

AMINO ACID SEQUENCE; ASPARTIC ACID; CONSERVED SEQUENCE; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MUTATION; PEPTIDES, CYCLIC; PROTEIN CONFORMATION; RECEPTORS, G-PROTEIN-COUPLED; RECEPTORS, HISTAMINE; RHODOPSIN; SEQUENCE ALIGNMENT; TRYPTOPHAN;

EID: 0038309559     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1110/ps.0305603     Document Type: Article

References (41)

1. Attwood, T.K. 2001. A compendium of specific motifs for diagnosing GPCR subtypes. Trends Pharmacol. Sci. 22: 162-165.
2. Attwood, T.K., Beck, M.E., Bleasby, A.J., and Parry-Smith, D.J. 1994. PRINTS: A database of protein motif fingerprints. Nucleic Acids Res. 22: 3590-3596.
3. Attwood, T.K., Croning, M.D., and Gaulton, A. 2002. Deriving structural and functional insights from a ligand-based hierarchical classification of G protein-coupled receptors. Protein Eng. 15: 7-12.
4. Bairoch, A. and Apweiler, R. 2000. The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res. 28: 45-48.
5. Ballesteros, J.A. and Weinstein, H. 1995. Integrated methods for the construction of three dimensional models and computational probing of structure-function relations in G-protein-coupled receptors. Meth. Neurosci. 25: 366-425.
6. Bateman, A., Birney, E., Cerruti, L., Durbin, R., Etwiller, L., Eddy, S.R., Griffiths-Jones, S., Howe, K.L., Marshall, M., and Sonnhammer, E.L. 2002. The Pfam protein families database. Nucleic Acids Res. 30: 276-280.
7. Befort, K., Zilliox, C., Filliol, D., Yue, S., and Kieffer, B.L. 1999. Constitutive activation of the δ opioid receptor by mutations in transmembrane domains III and VII. J. Biol. Chem. 274:18574-18581.
8. Beukers, M.W., Kristiansen, K., Ijzerman, A.P., and Edvardsen, Ø. 1999. TinyGRAP database: A bioinformatics tool to mine G protein-coupled receptor mutant data. TiPS 20: 475-477.
9. Borowsky, B., Adham, N., Jones, K.A., Raddatz, R., Artymyshyn, R., Ogozalek, K.L., Durkin, M.M., Lakhlani, P.P., Bonini, J.A., Pathirana, S., et al. 2001. Trace amines: Identification of a family of mammalian G protein-coupled receptors. Proc. Natl. Acad. Sci. 98: 8966-8971.
10. Bower, M.J., Cohen, F.E., and Dunbrack Jr., R.L. 1997. Prediction of protein side-chain rotamers from a backbone-dependent rotamer library: a new homology modeling tool. J. Mol. Biol. 267: 268-1282.
11. Brezillon, S., Lannoy, V., Franssen, J.D., Le Poul, E., Dupriez, V., Lucchetti, J., Detheux, M., and Parmentier, M. 2003. Identification of natural ligands for the orphan G protein-coupled receptors GPR7 and GPR8. J. Biol. Chem. 278: 776-783.
12. Donnelly, D., Findlay, J.B., and Blundell, T.L., 1994. The evolution and structure of aminergic G protein-coupled receptors. Receptors Channels 2: 61-78.
13. Eddy, S.R. 1998. Profile hidden Markov models. Bioinformatics 14: 755-763.
14. -. 2001. HMMER: Profile hidden Markov models for biological sequence analysis (http://hmmer.wustl.edu/).
15. Flohr, S., Kurz, M., Kostenis, E., Brkovich, A., Fournier, A., and Klabunde, T. 2002. Identification of nonpeptidic urotensin II receptor antagonists by virtual screening based on a pharmacophore model derived from structure-activity relationships and nuclear magnetic resonance studies on urotensin II. J. Med. Chem. 45: 1799-1805.
16. Fraser, C.M., Wang, C.D., Robinson, D.A., Gocayne, J.D., and Venter, J.C. 1989. Site-directed mutagenesis of m1 muscarinic acetylcholine receptors: Conserved aspartic acids play important roles in receptor function. Mol. Pharmacol. 36: 840-847.
17. Gantz, I., DelValle, J., Wang, L.D., Tashiro, T., Munzert, G., Guo, Y.J., Konda, Y., and Yamada, T. 1992. Molecular basis for the interaction of histamine with the histamine H2 receptor. J. Biol. Chem. 267: 20840-20843.
18. Graul, R.C. and Sadee, W. 2001. Evolutionary relationships among G protein-coupled receptors using a clustered database approach. AAPS PharmSci. 3: E12.
19. Hill, J., Duckworth, M., Murdock, P., Rennie, G., Sabido-David, C., Ames, R.S., Szekeres, P., Wilson, S., Bergsma, D.J., Gloger, I.S., et al. 2001. Molecular cloning and functional characterization of MCH2, a novel human MCH receptor. J. Biol. Chem. 276: 20125-20129.
20. Ho, B.Y., Karschin, A., Branchek, T., Davidson, N., and Lester, H.A. 1992. The role of conserved aspartate and serine residues in ligand binding and in function of the 5-HT1A receptor: A site-directed mutation study. FEBS Lett. 312: 259-262.
21. Johnson, J.M. and Church, G.M. 2000. Predicting ligand-binding function in families of bacterial receptors. Proc. Natl. Acad. Sci. 97: 3965-3970.
22. Johnson, J.M., Mason, K., Moallemi, C., Xi, H., Somaroo, S., and Huang, E.S. 2003. Protein family annotation in a multiple alignment viewer. Bioinformatics 19: 544-545.
23. Joost, P. and Methner, A. 2002. Phylogenetic analysis of 277 human G-protein-coupled receptors as a tool for the prediction of orphan receptor ligands. Genome Biol. 3: 1-16.
24. Karchin, R., Karplus, K., and Haussler, D. 2002. Classifying G-protein-coupled receptors with support vector machines. Bioinformatics 18: 147-159.
25. Kuipers, W., Oliveira, L., Vriend, G., and Ijzerman, A.P. 1997. Identification of class-determining residues in G protein-coupled receptors by sequence analysis. Receptors Channels 5: 159-174.
26. Lapinsh, M., Gutcaits, A., Prusis, P., Post, C., Lundstedt, T., and Wikberg, J.E. 2002. Classification of G-protein coupled receptors by alignment-independent extraction of principal chemical properties of primary amino acid sequences. Protein Sci. 11: 795-805.
27. Lavecchia, A., Greco, G., Novellino, E., Vittorio, F., and Ronsisvalle, G. 2000. Modeling of K-opioid receptor/agonists interactions using pharmacophore-based and docking simulations. J. Med. Chem. 43: 2124-2134.
28. Li, J.G., Chen, C., Yin, J., Rice, K., Zhang, Y., Matecka, D., de Riel, J.K., DesJarlais, R.L., and Liu-Chen, L.Y. 1999. ASP147 in the third transmembrane helix of the rat μ opioid receptor forms ion-pairing with morphine and naltrexone. Life Sci. 65: 175-185.
29. 2 receptor. Eur. J. Pharmacol. 227: 205-214.
30. MacDonald, D., Murgolo, N., Zhang, R., Durkin, J.P., Yao, X., Strader, C.D., and Graziano, M.P. 2000. Molecular characterization of the melanin-concentrating hormone/receptor complex: identification of critical residues involved in binding and activation. Mol. Pharmacol. 58: 217-225.
31. Nehring, R.B., Meyerhof, W., and Richter, D. 1995. Aspartic acid residue 124 in the third transmembrane domain of the somatostatin receptor subtype 3 is essential for somatostatin-14 binding. DNA Cell. Biol. 14:939-944.
32. Oda, T., Morikawa, N., Saito, Y., Masuho, Y., and Matsumoto, S. 2000. Molecular cloning and characterization of a novel type of histamine receptor preferentially expressed in leukocytes. J. Biol. Chem. 275: 36781-36786.
33. Page, K.M., Curtis, C.A., Jones, P.G., and Hulme, E.C. 1995. The functional role of the binding site aspartate in muscarinic acetylcholine receptors, probed by site directed mutagenesis. Eur. J. Pharmacol. 289: 429-437.
34. Palczewski, K., Kumasaka, T., Hori, T., Behnke, C.A., Motoshima, H., Fox, B.A., Le Trong, I., Teller, D.C., Okada, T., Stenkamp, R.E., et al. 2000. Crystal structure of rhodopsin: A G protein-coupled receptor. Science 289: 739-745.
35. Rigoutsos, I., Floratos, A., Ouzounis, C., Gao, Y., and Parida, L. 1999. Dictionary building via unsupervised hierarchical motif discovery in the sequence space of natural proteins. Proteins 37: 264-277.
36. A receptors. Mol. Pharmacol. 52: 259-266.
37. Strnad, J. and Hadcock, J.R. 1995. Identification of a critical aspartate residue in transmembrane domain three necessary for the binding of somatostatin to the somatostatin receptor SSTR2. Biochem. Biophys. Res. Commun. 216: 913-921.
38. Surratt, C.K., Johnson, P.S., Moriwaki, A., Seidleck, B.K., Blaschak, C.J., Wang, J.B., and Uhl, G.R. 1994. m-Opiate receptor: Charged transmembrane domain amino acids are critical for agonist recognition and intrinsic activity. J. Biol. Chem. 269: 20548-20553.
39. Wang, C.D., Buck, M.A., and Fraser, C.M. 1991. Site-directed mutagenesis of α 2A-adrenergic receptors: Identification of amino acids involved in ligand binding and receptor activation by agonists. Mol. Pharmacol. 40: 168-179.
40. Wilson, S., Bergsma, D.J., Chambers, J.K., Muir, A.I., Fantom, K.G., Ellis, C., Murdock, P.R., Herrity, N.C., and Stadel, J.M. 1998. Orphan G-protein-coupled receptors: The next generation of drug targets? Br. J. Pharmacol. 125: 1387-1392.
41. Wise, A., Gearing, K., and Rees, S. 2002. Target validation of G-protein-coupled receptors. Drug Discovery Today 7: 235-246.