Structural basis for a broad but selective ligand spectrum of a mouse olfactory receptor: Mapping the odorant-binding site

Journal of Neuroscience

Volumn 25, Issue 7, 2005, Pages 1806-1815

  Katada, Sayako ^a   Hirokawa, Takatsugu ^b   Oka, Yuki ^a   Suwa, Makiko ^b   Touhara, Kazushige ^a  

^a UNIVERSITY OF TOKYO   (Japan)

^b NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

Author keywords

Computer modeling; G protein coupled receptor; Ligand binding; Mutation; Odorant; Olfactory receptor

Indexed keywords

AMINO ACID; G PROTEIN COUPLED RECEPTOR; LIGAND; ODORANT; RECEPTOR BLOCKING AGENT; UNCLASSIFIED DRUG;

ARTICLE; BINDING AFFINITY; BRAIN MAPPING; CHEMICAL ENVIRONMENT; CHEMICAL STRUCTURE; COMPUTER MODEL; COMPUTER PREDICTION; COMPUTER SIMULATION; HUMAN; HUMAN CELL; HYDROGEN BOND; IONIC INTERACTION; LIGAND BINDING; MOLECULAR EVOLUTION; MOLECULAR INTERACTION; MOLECULAR MODEL; MOLECULAR RECOGNITION; MUTATION; OLFACTORY DISCRIMINATION; OLFACTORY RECEPTOR; POINT MUTATION; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FAMILY; RECEPTOR AFFINITY; RECEPTOR BINDING; RECEPTOR BLOCKING; SITE DIRECTED MUTAGENESIS;

ALLOSTERIC REGULATION; AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; ANIMALS; BINDING SITES; CALCIUM; CELL LINE; COMPUTER SIMULATION; DRUG DESIGN; EUGENOL; HUMANS; HYDROGEN-ION CONCENTRATION; HYDROPHOBICITY; KIDNEY; LIGANDS; MICE; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MULTIGENE FAMILY; MUTAGENESIS, SITE-DIRECTED; MUTATION, MISSENSE; ODORS; POINT MUTATION; PROTEIN BINDING; PROTEIN CONFORMATION; RECEPTORS, G-PROTEIN-COUPLED; RECEPTORS, ODORANT; STRUCTURE-ACTIVITY RELATIONSHIP; SUBSTRATE SPECIFICITY;

EID: 14044270215     PISSN: 02706474     EISSN: None     Source Type: Journal    
DOI: 10.1523/JNEUROSCI.4723-04.2005     Document Type: Article

References (56)

1. Amoore JE (1963) Stereochemical theory of olfaction. Nature 198:271-272.
2. Araneda RC, Kini AD, Firestein S (2000) The molecular receptive range of an odorant receptor. Nat Neurosci 3:1248-1255.
3. Ballesteros JA, Jensen AD, Liapakis G, Rasmussen SG, Shi L, Gether U, Javitch JA (2001) Activation of the beta 2-adrenergic receptor involves disruption of an ionic lock between the cytoplasmic ends of transmembrane segments 3 and 6. J Biol Chem 276:29171-29177.
4. Berkhout TA, Blaney FE, Bridges AM, Cooper DG, Forbes IT, Gribble AD, Groot PH, Hardy A, Ife RJ, Kaur R, Moores KE, Shillito H, Willetts J, Witherington J (2003) CCR2: characterization of the antagonist binding site from a combined receptor modeling/mutagenesis approach. J Med Chem 46:4070-4086.
5. Bockaert J, Pin JP (1999) Molecular tinkering of G protein-coupled receptors: an evolutionary success. EMBO J 18:1723-1729.
6. Buck L, Axel R (1991) A novel multigene family may encode odorant receptors: a molecular basis for odor recognition. Cell 65:175-187.
7. Buck LB (1996) Information coding in the vertebrate olfactory system. Annu Rev Neurosci 19:517-544.
8. Church WB, Jones KA, Kuiper DA, Shine J, Iismaa TP (2002) Molecular modeling and site-directed mutagenesis of human GALR1 galanin receptor defines determinants of receptor subtype specificity. Protein Eng 15:313-323.
9. Feinstein P, Mombaerts P (2004) A contextual model for axonal sorting into glomeruli in the mouse olfactory system. Cell 117:817-831.
10. Firestein S (2001) How the olfactory system makes sense of scents. Nature 413:211-218.
11. Floriano WB, Vaidehi N, Goddard III WA, Singer MS, Shepherd GM (2000) Molecular mechanisms underlying differential odor responses of a mouse olfactory receptor. Proc Natl Acad Sci USA 97:10712-10716.
12. Floriano WB, Vaidehi N, Goddard III WA (2004) Making sense of olfaction through predictions of the 3-D structure and function of olfactory receptors. Chem Senses 29:269-290.
13. Halgren TA (1996a) Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94. J Comput Chem 17:490-512.
14. Halgren TA (1996b) Merck molecular force field. II. MMFF94 van der Waals and electrostatic parameters for intermolecular interactions. J Comput Chem 17:520-552.
15. Halgren TA (1996c) Merck molecular force field. III. Molecular geometries and vibrational parameters for intermolecular interactions. J Comput Chem 17:553-586.
16. Halgren TA (1996d) Merck molecular force field. IV. Conformational energies and geometories for MMFF94. J Comput Chem 17:587-615.
17. Halgren TA (1996e) Merck molecular force field. V. Extension of MMFF94 using experimental data, additional computational data, and empirical rules. J Comput Chem 17:616-641.
18. Hopkins AL, Groom CR (2002) The druggable genome. Nat Rev Drug Discov 1:727-730.
19. Hughes AL, Nei M (1988) Pattern of nucleotide substitution at major histocompatibility complex class I loci reveals overdominant selection. Nature 335:167-170.
20. Javitch JA, Fu D, Liapakis G, Chen J (1997) Constitutive activation of the beta2 adrenergic receptor alters the orientation of its sixth membrane-spanning segment. J Biol Chem 272:18546-18549.
21. Kajiya K, Inaki K, Tanaka M, Haga T, Kataoka H, Touhara K (2001) Molecular bases of odor discrimination: reconstitution of olfactory receptors that recognize overlapping sets of odorants. J Neurosci 21:6018-6025.
22. Katada S, Nakagawa T, Kataoka H, Touhara K (2003) Odorant response assays for a heterologously expressed olfactory receptor. Biochem Biophys Res Commun 305:964-969.
23. Katada S, Tanaka M, Touhara K (2004) Structural determinants for membrane trafficking and G protein selectivity of a mouse olfactory receptor. J Neurochem 90:1453-1463.
24. Kataoka R, Goto J (2002) Post-sequence techniques for protein analysis, Pt 1, analysis of whole proteins. Bioinformatics and drug design. In: Posutoshihkuensu Tanpakushitsu Zikkenn-hou 1 (in Japanese), pp 191-201. Tokyo: Tokyo Kagaku Dojin.
25. Klabunde T, Hessler G (2002) Drug design strategies for targeting G-protein-coupled receptors. Chembiochem 3:928-944.
26. Lancet D (1986) Vertebrate olfactory reception. Annu Rev Neurosci 9:329-355.
27. Lapidot M, Pilpel Y, Gilad Y, Falcovitz A, Sharon D, Haaf T, Lancet D (2001) Mouse-human orthology relationships in an olfactory receptor gene cluster. Genomics 71:296-306.
28. Lee C, Irizarry K (2001) The GeneMine system for genome/proteome annotation and collaborative data mining. IBM Systems J 40:592-603.
29. Levitt M (1992) Accurate modeling of protein conformation by automatic segment matching. J Mol Biol 226:507-533.
30. Man O, Gilad Y, Lancet D (2004) Prediction of the odorant binding site of olfactory receptor proteins by human-mouse comparisons. Protein Sci 13:240-254.
31. Manivet P, Schneider B, Smith JC, Choi DS, Maroteaux L, Kellermann O, Launay JM (2002) The serotonin binding site of human and murine 5-HT2B receptors: molecular modeling and site-directed mutagenesis. J Biol Chem 277:17170-17178.
32. Mombaerts P (2004) Genes and ligands for odorant, vomeronasal and taste receptors. Nat Rev Neurosci 5:263-278.
33. Oka Y, Omura M, Kataoka H, Touhara K (2004a) Olfactory receptor antagonism between odorants. EMBO J 23:120-126.
34. Oka Y, Nakamura A, Watanabe H, Touhara K (2004b) An odorant derivative as an antagonist for an olfactory receptor. Chem Senses 9:815-822.
35. Palczewski K, Kumasaka T, Hori T, Behnke CA, Motoshima H, Fox BA, Le Trong I, Teller DC, Okada T, Stenkamp RE, Yamamoto M, Miyano M (2000) Crystal structure of rhodopsin: a G protein-coupled receptor. Science 289:739-745.
36. Pilpel Y, Lancet D (1999) The variable and conserved interfaces of modeled olfactory receptor proteins. Protein Sci 8:969-977.
37. Rivkees SA, Barbhaiya H, IJzerman AP (1999) Identification of the adenine binding site of the human A1 adenosine receptor. J Biol Chem 274:3617-3621.
38. Saam J, Tajkhorshid E, Hayashi S, Schulten K (2002) Molecular dynamics investigation of primary photoinduced events in the activation of rhodopsin. Biophys J 83:3097-3112.
39. Schertler GF (1998) Structure of rhodopsin. Eye 12:504-510.
40. Shepherd GM (1994) Discrimination of molecular signals by the olfactory receptor neuron. Neuron 13:771-790.
41. Singer MS (2000) Analysis of the molecular basis for octanal interactions in the expressed rat 17 olfactory receptor. Chem Senses 25:155-165.
42. Singer MS, Shepherd GM (1994) Molecular modeling of ligand-receptor interactions in the OR5 olfactory receptor. NeuroReport 5:1297-1300.
43. Singer MS, Oliveira L, Vriend G, Shepherd GM (1995) Potential ligand-binding residues in rat olfactory receptors identified by correlated mutation analysis. Receptors Channels 3:89-95.
44. Singer MS, Weisinger-Lewin Y, Lancet D, Shepherd GM (1996) Positive selection moments identify potential functional residues in human olfactory receptors. Receptors Channels 4:141-147.
45. Spalding TA, Burstein ES (2001) Constitutively active muscarinic receptors. Life Sci 68:2511-2516.
46. Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673-4680.
47. Touhara K (2002) Odor discrimination by G protein-coupled olfactory receptors. Microsc Res Tech 58:135-141.
48. Touhara K, Sengoku S, Inaki K, Tsuboi A, Hirono J, Sato T, Sakano H, Haga T (1999) Functional identification and reconstitution of an odorant receptor in single olfactory neurons. Proc Natl Acad Sci USA 96:4040-4045.
49. Vaidehi N, Floriano WB, Trabanino R, Hall SE, Freddolino P, Choi EJ, Zamanakos G, Goddard WA, 3rd (2002) Prediction of structure and function of G protein-coupled receptors. Proc Natl Acad Sci USA 99:12622-12627.
50. Wallace AC, Laskowski RA, Thornton JM (1995) LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions. Protein Eng 8:127-134.
51. Watson SA (1994) The G-protein linked receptor factsbook. New York: Academic.
52. Wetzel CH, Oles M, Wellerdieck C, Kuczkowiak M, Gisselmann G, Hatt H (1999) Specificity and sensitivity of a human olfactory receptor functionally expressed in human embryonic kidney 293 cells and Xenopus laevis oocytes. J Neurosci 19:7426-7433.
53. Wieland K, Zuurmond HM, Krasel C, Ijzerman AP, Lohse MJ (1996) Involvement of Asn-293 in stereospecific agonist recognition and in activation of the beta 2-adrenergic receptor. Proc Natl Acad Sci USA 93:9276-9281.
54. Zhang X, Firestein S (2002) The olfactory receptor gene superfamily of the mouse. Nat Neurosci 5:124-133.
55. Zhao H, Ivic L, Otaki JM, Hashimoto M, Mikoshiba K, Firestein S (1998) Functional expression of a mammalian odorant receptor. Science 279:237-242.
56. Zheng C, Feinstein P, Bozza T, Rodriguez I, Mombaerts P (2000) Peripheral olfactory projections are differentially affected in mice deficient in a cyclic nucleotide-gated channel subunit. Neuron 26:81-91.