Predicted 3D structures of olfactory receptors with details of odorant binding to OR1G1

Journal of Computer-Aided Molecular Design

Volumn 28, Issue 12, 2014, Pages 1175-1190

  Kim, Soo Kyung ^a   Goddard, William A ^a  

^a CALIFORNIA INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

G protein coupled receptor; Modeling; Olfactory receptors; Protein structure prediction

Indexed keywords

ACTIVATION ANALYSIS; BINDING ENERGY; BIOLOGICAL MEMBRANES; FORECASTING; ODORS;

3D STRUCTURE; G PROTEIN COUPLED RECEPTORS; LOW ENERGY STRUCTURES; LOWER-ENERGY STRUCTURE; LOWEST ENERGY STRUCTURE; MEMBRANE BILAYERS; MODELING; OLFACTORY RECEPTORS; PROTEIN STRUCTURE PREDICTION; SAMPLING METHOD;

PROTEINS;

BUTYRALDEHYDE; CAMPHOR; G PROTEIN COUPLED RECEPTOR; NONANOL; OR1G1 PROTEIN; UNCLASSIFIED DRUG; 1-NONANOL; FATTY ALCOHOL; LIGAND; OLFACTORY RECEPTOR; OR1G1 PROTEIN, HUMAN; PROTEIN BINDING;

ARTICLE; CONFORMATION; DNA TEMPLATE; ENERGY; ODOR; OLFACTORY RECEPTOR; PROTEIN BINDING; PROTEIN STRUCTURE; AMINO ACID SEQUENCE; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; HUMAN; PROTEIN CONFORMATION; PROTEIN TERTIARY STRUCTURE;

AMINO ACID SEQUENCE; BINDING SITES; FATTY ALCOHOLS; HUMANS; LIGANDS; MODELS, MOLECULAR; ODORS; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN STRUCTURE, TERTIARY; RECEPTORS, ODORANT;

EID: 84918801122     PISSN: 0920654X     EISSN: 15734951     Source Type: Journal    
DOI: 10.1007/s10822-014-9793-4     Document Type: Article

References (58)

1. de March CA, Golebiowski J (2014) A computational microscope focused on the sense of smell. Biochimie. doi: 10.1016/j.biochi.2014.06.006
2. Malnic B, Hirono J, Sato T, Buck LB (1999) Combinatorial receptor codes for odors. Cell 96:713-723
3. Duchamp-Viret P, Duchamp A, Chaput MA (2003) Single olfactory sensory neurons simultaneously integrate the components of an odour mixture. Eur J Neurosci 18:2690-2696
4. Jacquier V, Pick H, Vogel H (2006) Characterization of an extended receptive ligand repertoire of the human olfactory receptor OR17-40 comprising structurallly related compounds. J Neurochem 97:537-544
5. Lai PC, Crasto CJ (2012) Beyond modeling: all-atom olfactory receptor model simulations. Frontiers in Genetics 3:1-10
6. Abrol R, Bray JK, Goddard WA III (2011) Bihelix: towards de novo structure prediction of an ensemble of G-protein coupled receptor conformations. Proteins 80:505-518
7. Charlier L, Topin J, Ronin C, Kim S-K, Goddard WA III, Efremov R, Golebiowski J (2012) How broadly tuned olfactory receptors equally recognize their agonists. Human OR1G1 as a test case. Cell Mol Life Sci 69:4205-4213
8. Sanz G, Schlegel C, Pernollet JC, Briand L (2005) Comparision of odorant specificity of two human olfactory receptors from different phylogenetic classes and evidnece for antagonism. Chem Senses 30:69-80
9. Sanz G, Thomas-Danguin T, Hamdani EH, Poupon CL, Briand L, Pernollet J-C, Guichard E, Tromelin A (2008) Relationships between molecular structure and perceived odor quality of ligands for a human olfactory receptor. Chem Senses 33:639-653
10. Wimley WC, Creamer TP, White SH (1996) Solvation energies of amino acid side chains and backbone in a family of host-guest pentapeptides. Biochem 35:5109-5124
11. Hessa TM-B, Bernsel A, Kim H, Sato Y, Lerch-Bader M, Nilsson I, White SH, von Heijne G (2007) Molecular code for transmembrane-helix recognition by the Sec61 translocon. Nature 450:1026-1030
12. Kam VWT, Goddard WA III (2008) Flat-bottom strategy for improved accuracy in protein side-chain placements. J Chem Theor Comput 4:2160-2169
13. Wu B, Chien EY, Mol CD, Fenalti G, Liu W, Katritch V, Abagyan R, Brooun A, Wells P, Bi FC, Hamel DJ, Kuhn P, Handel TM, Cherezov V, Stevens RC (2010) Structures of the CXCR4 chemokine GPCR with small-molecule and cyclic peptide antagonists. Science 330:1066-1071
14. Gelis L, Wolf S, Hatt H, Neuhaus EM, Gerwert K (2012) Prediction of a ligand-binding niche within a human olfactory receptor by combining site-directed mutagenesis with dynamic homology modeling. Angew Chem Int Ed Engl 51:1274-1278
15. Abaffy T, Malhotra A, Luetje CW (2007) The molecular basis for ligand specificity in a mouse olfactory receptor: a network of functionally important residues. J Biol Chem 282:1216-1224
16. Schmiedeberg K, Shirokova E, Weber HP, Schilling B, Meyerhof W, Krautwurst D (2007) Structural determinants of odorant recognition by the human olfactory receptors OR1A1 and OR1A2. J Struct Biol 159:400-412
17. Vaidehi N, Floriano WB, Trabanino R, Hall SE, Freddolino P, Choi EJ, Zamanakos G, Goddard WA III (2002) Prediction of structure and function of G protein-coupled receptors. Proc Natl Acad Sci USA 99:12622-12627
18. Floriano WB, Vaidehi N, Zamanakos G, Goddard WA III (2004) HierVLS hierarchical docking protocol for virtual ligand screening of large-molecule databases. J Med Chem 47:56-71
19. Floriano WB, Vaidehi N, Goddard WA III, Singer MS, Shepherd GM (2000) Molecular mechanisms underlying differential odor responses of a mouse olfactory receptor. Proc Natl Acad Sci USA 97:10712-10716
20. Hall SE, Floriano WB, Vaidehi N, Goddard WA III (2004) Predicted 3-D structures for mouse I7 and rat I7 olfactory receptors and comparision of predicted odor recognition profiles with experiment. Chem Senses 29:595-616
21. Hummel P, Vaidehi N, Floriano WB, Hall SE, Goddard WA III (2005) Test of the binding threshold hypothesis for olfactory receptors: explanation of the differential binding of ketons to the mouse and human orthologs of olfactory receptor 912-93. Protein Sci 14:703-710
22. Pollastri G, Przybylski D, Rost P, Baldi B (2002) Improving the prediction of protein secondary structure in three and eight classes using recurrent neural networks and profiles. Proteins 47:228-235
23. Cook BL, Steuerwald D, Kaiser L, Graveland-Bikker J, Vanberghem M, Berke AP, Herlihy K, Pick H, Vogel H, Zhang S (2009) Large-scale production and study of a synthetic G protein-coupled receptor: human olfactory receptor 17-4. Proc Natl Acad Sci USA 106(29):11925-11930
24. Warne T, Serrano-Vega MJ, Baker JG, Moukhametzianov R, Edwards PC, Henderson R, Leslie AGW, Tate CG, Schertler GFX (2008) Structure of a β1-adrenergic G-protein coupled receptor. Nature 454:486-491
25. Kruse AC, Hu J, Pan AC, Arlow DH, Rosenbaum DM, Rosemond E, Green HF, Liu T, Chae PS, Dror RO, Shaw DE, Weis WI, Wess J, Kobilka BK (2012) Structure and dynamics of the M3 muscarinic acetylcholine receptor. Nature 482:552-556
26. Haga K, Kruse AC, Asada H, Yurugi-Kobayashi T, Shiroishi M, Zhang C, Weis WI, Okada T, Kobilka BK, Haga T, Kobayashi T (2012) Structure of the human M2 muscarinic acetylcholine receptor bound to an antagonist. Nature 482:547-551
27. Jaakola VP, Griffith MT, Hanson MA, Cherezov V, Chien EY, Lane JR, Ijzerman AP, Stevens RC (2008) The 2.6 angstrom crystal structure of a human A2A adenosine receptor bound to an antagonist. Science 322:1211-1277
28. Chien EY, Liu W, Zhao Q, Katritch V, Han GW, Hanson MA, Shi L, Newman AH, Javitch JA, Cherezov V, Stevens RC (2010) Structure of the human dopamine D3 receptor in complex with a D2/D3 selective antagonist. Science 330:1091-1095
29. Katoh K, Kuma K, Toh H, Miyata T (2005) MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acid Res 33:511-518
30. Pollastri G, McLysaght A (2005) Porter: a new, accurate server for protein secondary structure prediction. Bioinformatics 21:1719-1720
31. Palczewski K, Kumasaka T, Hori T, Behnke CA, Motoshima H (2000) Crystal structure of rhodopsin: a G protein-coupled receptor. Science 289:739-745
32. Teller DC, Okada T, Behnke CA, Palczewski K, Stenkamp RE (2001) Advances in determination of a high-resolution three-dimensional structure of rhodopsin, a model of G-protein-coupled receptors (GPCRs). Biochemical 40:7761-7762
33. Okada T, Fujiyoshi Y, Silow M, Navarro J, Landau EM, Shichida Y (2002) Fundamental role of internal water molecules in rhodopsin revealed by Xray crystallography. Proc Natl Acad Sci USA 99:5982-5987
34. Li J, Edwards PC, Burghammer M, Villa C, Schertler GFX (2004) Structure of bovine rhodopsin in a trigonal crystal form. J Mol Biol 343:1409-1438
35. Okada T, Sugihara M, Bondar AN, Elstner M, Entel P, Buss V (2004) The retinal conformation and its environment in rhodopsin in light of a new 2.2 Å crystal structure. J Mol Biol 342(2):571-583
36. Hanson MA, Roth CB, Jo E, Griffith MT, Scott FL, Reinhart G, Desale H, Clemons B, Cahalan SM, Schuerer SC, Sanna MG, Han GW, Kuhn P, Rosen H, Stevens RC (2012) Crystal structure of a lipid G protein-coupled receptor. Science 335:851-855
37. Wu H, Wacker D, Mileni M, Katritch V, Han G, Vardy E, Liu W, Thompson AA, Huang X-P, Carroll FI, Mascarella SW, Westkaemper RB, Mosier PD, Roth BL, Cherezov V, Stevens RC (2012) Structure of the human k-opioid receptor in complex with JDTic. Nature 485:327-332
38. Mayo SL, Olafson BD, Goddard WA III (1990) DREIDING - a generic force field for molecular simulations. J Phys Chem 94:8897-8909
39. Abrol R, Griffith AR, Bray JK, Goddard WA III (2012) Structure prediction of G protein-coupled receptors and their ensemble of functionally important conformations. Methods Mol Biol 914:237-254
40. Abrol R, Kim SK, Bray JK, Griffith AR, Goddard WA (2011) Characterizing and predicting the functional and conformational diversity of seven-transmembrane proteins. Methods 55:405-414
41. Kim S-K, Li Y, Park C, Abrol R, Goddard WA III (2010) Prediction of the 3D structure for the rat urotensin II receptor and comparison of the antagonist binding sites and binding selectivity between human and rat from atomistic simulations. ChemMedChem 5:1594-1608
42. Bhandarkar M, Brunner R, Chipot C, Dalke A, Dixit S, Grayson P, Gullingsrud J, Gursoy A, Hardy D, Hénin J, Humphrey W, Hurwitz D, Krawetz N, Kumar S, Nelson M, Phillips J, Schinozaki A, Zheng G, Zhu F (2008). NAMD User's Guide (Theoretical Biophysics Group, University of Illinois at Urbana-Champaign and Beckman Institute, Urbana) Version 2.6
43. Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E, Chipot C, Skeel RD, Kale L, Schulten K (2005) Scalable molecular dynamics with NAMD. J Comput Chem 26:1781-1802
44. MacKerell AD, Bashford D, Bellott M, Dunbrack RL, Evanseck JD, Field MJ, Fischer S, Gao J, Guo H, Ha S, Joseph-McCarthy D, Kuchnir L, Kuczera K, Lau FTK, Mattos C, Michnick S, Ngo T, Nguyen DT, Prodhom B, Reiher WE, Roux B, Schlenkrich M, Smith JC, Stote R, Straub J, Watanabe M, Wiorkiewicz-Kuczera J, Yin D, Karplus M (1998) All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B 102:3586-3616
45. Feller SE, Yin D, Pastor RW, MacKerell J, MacKerell AD Jr (1997) Molecular dynamics simulation of unsaturated lipids at low hydration: parametrization and comparison with diffraction studies. Biophys J 73:2269-2279
46. Cho AE, Wendel JA, Vaidehi N, Kekenes-Huskey PM, Floriano WB, Maiti PK, Goddard WA III (2005) The MPSim-dock hierarchical docking algorithm: application to the eight trypsin Inhibitor co-crystals. J Comput Chem 26:48-71
47. Watts KS, Dalal P, Murphy RB, Sherman W, Friesner RA, Shelley JC (2010) ConfGen: a conformational search method for efficient generation of bioactive conformers. J Chem Inf Model 50:534-546
48. Cherezov V, Rosenbaum D, Hanson M, Rasmussen S, Thian FS, Kobilka TS, Choi H, Kuhn P, Weis W, Kobilka B, Stevens R (2007) High-resolution crystal structure of an engineered human beta2-adrenergic G protein-coupled receptor. Science 318:1258-1265
49. Thompson AA, Liu W, Chun E, Katritch V, Wu H, Vardy E, Huang XP, Trapella C, Guerrini R, Calo G, Roth BL, Cherezov V, Stevens RC (2012) Structure of the nociceptin/orphanin FQ receptor in complex with a peptide mimetic. Nature 485:395-399
50. Shimamura T, Shiroishi M, Weyand S, Tsujimoto H, Winter G, Katritch V, Abagyan R, Cherezov V, Liu W, Han GW, Kobayashi T, Stevens RC, Iwata S (2011) Structure of the human histamine H1 receptor complex with doxepin. Nature 475:65-70
51. Manglik A, Kruse AC, Kobilka TS, Thian FS, Mathiesen JM, Sunahara RK, Pardo L, Weis WI, Kobilka BK, Granier S (2012) Crystal structure of the μ-opioid receptor bound to a morphinan antagonist. Nature 485:321-326
52. Granier S, Manglik A, Kruse AC, Kobilka TS, Thian FS, Weis WI, Kobilka BK (2012) Structure of the delta-opioid receptor bound to naltrindole. Nature 485:400-404
53. Peng JY, Vaidehi N, Hall SE, Goddard WA III (2006) The predicted 3D structures of the human M1 muscarinic acetylcholine receptor with agonist or antagonist bound. Chem Med Chem 1:878-890
54. Vaidehi N, Schlyer S, Trabanino RJ, Floriano WB, Abrol R, Sharma S, Kochanny M, Koovakat S, Dunning L, Liang M, Fox JM, de Mendonca FL, Pease JE, Goddard WA III, Horuk R (2006) Predictions of CCR1 chemokine receptor structure and BX 471 antagonist binding followed by experimental validation. J Biol Chem 281:27613-27620
55. Bray JK, Goddard WA III (2008) The structure of human serotonin 2c G-protein-coupled receptor bound to agonists and antagonists. J Mol Graph Model 27:66-81
56. Kim S-K, Li Y, Abrol R, Heo J, Goddard WA III (2011) Predicted structures and dynamics for agonists and antagonists bound to serotonin 5-HT2B and 5-HT2C receptors. J Chem Inf Model 51:420-433
57. Kim S-K, Riley L, Abrol R, Jacobson KA, Goddard WA III (2011) Predicted structures of agonist and antagonist bound complexes of adenosine A3 receptor. Proteins 79:1878-1897
58. Kim S-K, Fristrup P, Abrol R, Goddard WA III (2011) Structure-based prediction of subtype selectivity of histamine H3 receptor selective antagonists in clinical trials. J Chem Inf Model 51:3262-3274