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Structure and Function Studies of GPCRs by Site-Specific Incorporation of Unnatural Amino Acids

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Structure and Function of GPCRs

Part of the book series: Topics in Medicinal Chemistry ((TMC,volume 30))

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Abstract

In the past decade, genetic code expansion technology has emerged as discovery tools in studies of GPCRs for monitoring of dynamic protein conformational changes, for the screening of ligand–protein and protein–protein interactions, and as alternatives to conventional labeling approaches for the site-specific labeling of GPCRs with spectroscopy probes. Interactome mapping among GPCRs, their ligands, and interactive proteins discovered using genetically encoded photo-cross-linking unnatural amino acids (Uaas) display methods that link substrate specificity to binding pockets revealed by static X-ray crystal structures are inaccessible by other methodologies. Fluorescent-based analysis to directly monitor the GPCR conformational changes are beginning to move forward into cell-based assays for high-throughput drug screening platforms. This review details the significant progress in Uaa containing GPCRs discovery platforms, as well as advances in understanding the structure activity relationship of GPCRs in the “post structural biology” era.

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References

  1. Rosenbaum DM, Rasmussen SG, Kobilka BK (2009) The structure and function of G-protein-coupled receptors. Nature 459:356–363

    Article  CAS  Google Scholar 

  2. Shoichet BK, Kobilka BK (2012) Structure-based drug screening for G-protein-coupled receptors. Trends Pharmacol Sci 33:268–272

    Article  CAS  Google Scholar 

  3. Granier S, Kobilka B (2012) A new era of GPCR structural and chemical biology. Nat Chem Biol 8:670–673

    Article  CAS  Google Scholar 

  4. Xiang J et al (2016) Successful strategies to determine high-resolution structures of GPCRs. Trends Pharmacol Sci 37:1055–1069

    Article  CAS  Google Scholar 

  5. Daggett KA, Sakmar TP (2011) Site-specific in vitro and in vivo incorporation of molecular probes to study G-protein-coupled receptors. Curr Opin Chem Biol 15:392–398

    Article  CAS  Google Scholar 

  6. Chin JW (2014) Expanding and reprogramming the genetic code of cells and animals. Annu Rev Biochem 83:379–408

    Article  CAS  Google Scholar 

  7. Neumann-Staubitz P, Neumann H (2016) The use of unnatural amino acids to study and engineer protein function. Curr Opin Struct Biol 38:119–128

    Article  CAS  Google Scholar 

  8. Wang L (2016) Genetically encoding new bioreactivity. New Biotechnol. doi:10.1016/j.nbt.2016.10.003

    Article  Google Scholar 

  9. Grunbeck A, Sakmar TP (2013) Probing G protein-coupled receptor ligand interactions with targeted photoactivatable cross-linkers. Biochemistry 52:8625–8632

    Article  CAS  Google Scholar 

  10. Heckler T, Chang L, Zama Y, Naka T, Hecht S (1984) Preparation of '2,('3)-O-acyl-pCpA derivatives as substrates for T4 RNA ligase-mediated “chemical aminoacylation”. Tetrahedron 40:87–94

    Article  CAS  Google Scholar 

  11. Noren CJ, Anthony-Cahill SJ, Griffith MC, Schultz PG (1989) A general method for site-specific incorporation of unnatural amino acids into proteins. Science 244:182

    Article  CAS  Google Scholar 

  12. Nowak MW et al (1995) Nicotinic receptor-binding site probed with unnatural amino-acid-incorporation in intact-cells. Science 268:439–442

    Article  CAS  Google Scholar 

  13. Yang F et al (2015) Phospho-selective mechanisms of arrestin conformations and functions revealed by unnatural amino acid incorporation and 19F-NMR. Nat Commun 6:8202

    Article  Google Scholar 

  14. Beene DL, Dougherty DA, Lester HA (2003) Unnatural amino acid mutagenesis in mapping ion channel function. Curr Opin Neurobiol 13:264–270

    Article  CAS  Google Scholar 

  15. Wang L, Schultz PG (2001) A general approach for the generation of orthogonal tRNAs. Chem Biol 8:883–890

    Article  CAS  Google Scholar 

  16. Sakamoto K et al (2002) Site-specific incorporation of an unnatural amino acid into proteins in mammalian cells. Nucleic Acids Res 30:4692–4699

    Article  CAS  Google Scholar 

  17. Davis L, Chin JW (2012) Designer proteins: applications of genetic code expansion in cell biology. Nat Rev Mol Cell Biol 13:168–182

    Article  CAS  Google Scholar 

  18. Nikić I et al (2014) Minimal tags for rapid dual-color live-cell labeling and super-resolution microscopy. Angew Chem Int Ed 53:2245–2249

    Article  Google Scholar 

  19. Lang K, Chin JW (2014) Cellular incorporation of unnatural amino acids and bioorthogonal labeling of proteins. Chem Rev 114:4764–4806

    Article  CAS  Google Scholar 

  20. Tian H, Fürstenberg A, Huber T (2017) Labeling and single-molecule methods to monitor G protein-coupled receptor dynamics. Chem Rev 117:186–245

    Article  CAS  Google Scholar 

  21. Ye S et al (2008) Site-specific incorporation of keto amino acids into functional G protein-coupled receptors using unnatural amino acid mutagenesis. J Biol Chem 283:1525–1533

    Article  CAS  Google Scholar 

  22. Huang L-Y et al (2008) Unnatural amino acid replacement in a yeast G protein-coupled receptor in its native environment. Biochemistry 47:5638–5648

    Article  CAS  Google Scholar 

  23. Greiss S, Chin JW (2011) Expanding the genetic code of an animal. J Am Chem Soc 133:14196–14199

    Article  CAS  Google Scholar 

  24. Bianco A, Townsley FM, Greiss S, Lang K, Chin JW (2012) Expanding the genetic code of Drosophila melanogaster. Nat Chem Biol 8:748–750

    Article  CAS  Google Scholar 

  25. Kang JY et al (2013) In vivo expression of a light-activatable potassium channel using unnatural amino acids. Neuron 80:358–370

    Article  CAS  Google Scholar 

  26. Zhu SJ et al (2014) Genetically encoding a light switch in an ionotropic glutamate receptor reveals subunit-specific interfaces. Proc Natl Acad Sci U S A 111:6081–6086

    Article  CAS  Google Scholar 

  27. Ernst RJ et al (2016) Genetic code expansion in the mouse brain. Nat Chem Biol 12:776–778

    Article  CAS  Google Scholar 

  28. Zheng Y, Lewis Jr TL, Igo P, Polleux F, Chatterjee A (2017) Virus-enabled optimization and delivery of the genetic machinery for efficient unnatural amino acid mutagenesis in mammalian cells and tissues. ACS Synth Biol 6:13–18

    Article  CAS  Google Scholar 

  29. Ryu Y, Schultz PG (2006) Efficient incorporation of unnatural amino acids into proteins in Escherichia coli. Nat Methods 3:263–265

    Article  CAS  Google Scholar 

  30. Park H-S et al (2011) Expanding the genetic code of Escherichia coli with phosphoserine. Science 333:1151–1154

    Article  CAS  Google Scholar 

  31. Elsässer SJ, Ernst RJ, Walker OS, Chin JW (2016) Genetic code expansion in stable cell lines enables encoded chromatin modification. Nat Methods 13:158–164

    Article  Google Scholar 

  32. Parrish AR et al (2012) Expanding the genetic code of Caenorhabditis elegans using bacterial aminoacyl-tRNA synthetase/tRNA pairs. ACS Chem Biol 7:1292–1302

    Article  CAS  Google Scholar 

  33. Chen Y et al (2017) Heritable expansion of the genetic code in mouse and zebrafish. Cell Res 27:294–297

    Article  CAS  Google Scholar 

  34. Han S et al (2017) Expanding the genetic code of Mus musculus. Nat Commun 8:14568

    Article  CAS  Google Scholar 

  35. Reiter E, Ahn S, Shukla AK, Lefkowitz RJ (2012) Molecular mechanism of β-arrestin-biased agonism at seven-transmembrane receptors. Annu Rev Pharmacol Toxicol 52:179–197

    Article  CAS  Google Scholar 

  36. Marchese A, Trejo J (2013) Ubiquitin-dependent regulation of G protein-coupled receptor trafficking and signaling. Cell Signal 25:707–716

    Article  CAS  Google Scholar 

  37. Huber T, Naganathan S, Tian H, Ye S, Sakmar TP (2013) Unnatural amino acid mutagenesis of GPCRs using amber codon suppression and bioorthogonal labeling. Methods Enzymol 520:281–305

    Article  CAS  Google Scholar 

  38. Huber T, Sakmar TP (2014) Chemical biology methods for investigating G protein-coupled receptor signaling. Chem Biol 21:1224–1237

    Article  CAS  Google Scholar 

  39. Grunbeck A, Huber T, Sakmar TP (2013) Mapping a ligand binding site using genetically encoded photoactivatable crosslinkers. Methods Enzymol 520:307–322

    Article  CAS  Google Scholar 

  40. Hino N et al (2011) Genetic incorporation of a photo-crosslinkable amino acid reveals novel protein complexes with GRB2 in mammalian cells. J Mol Biol 406:343–353

    Article  CAS  Google Scholar 

  41. Grunbeck A, Huber T, Sachdev P, Sakmar TP (2011) Mapping the ligand-binding site on a G protein-coupled receptor (GPCR) using genetically encoded photocrosslinkers. Biochemistry 50:3411–3413

    Article  CAS  Google Scholar 

  42. Grunbeck A et al (2012) Genetically encoded photo-cross-linkers map the binding site of an allosteric drug on a G protein-coupled receptor. ACS Chem Biol 7:967–972

    Article  CAS  Google Scholar 

  43. Valentin-Hansen L et al (2014) Mapping substance P binding sites on the neurokinin-1 receptor using genetic incorporation of a photoreactive amino acid. J Biol Chem 289:18045–18054

    Article  CAS  Google Scholar 

  44. Coin I et al (2013) Genetically encoded chemical probes in cells reveal the binding path of urocortin-I to CRF class B GPCR. Cell 155:1258–1269

    Article  CAS  Google Scholar 

  45. Xiang Z et al (2013) Adding an unnatural covalent bond to proteins through proximity-enhanced bioreactivity. Nat Methods 10:885–888

    Article  CAS  Google Scholar 

  46. Tan Q et al (2013) Structure of the CCR5 chemokine receptor–HIV entry inhibitor maraviroc complex. Science 341:1387–1390

    Article  CAS  Google Scholar 

  47. Kraetke O et al (2005) Photoaffinity cross-linking of the corticotropin-releasing factor receptor type 1 with photoreactive urocortin analogues. Biochemistry 44:15569–15577

    Article  CAS  Google Scholar 

  48. Sato S et al (2010) Crystallographic study of a site-specifically cross-linked protein complex with a genetically incorporated photoreactive amino acid. Biochemistry 50:250–257

    Article  Google Scholar 

  49. Ray-Saha S, Huber T, Sakmar TP (2014) Antibody epitopes on G protein-coupled receptors mapped with genetically encoded photoactivatable cross-linkers. Biochemistry 53:1302–1310

    Article  CAS  Google Scholar 

  50. Reddington SC et al (2013) Different photochemical events of a genetically encoded phenyl azide define and modulate GFP fluorescence. Angew Chem Int Ed 52:5974–5977

    Article  CAS  Google Scholar 

  51. Sakmar TP, Menon ST, Marin EP, Awad ES (2002) Rhodopsin: insights from recent structural studies. Annu Rev Biophys Biomol Struct 31:443–484

    Article  CAS  Google Scholar 

  52. Ye S, Huber T, Vogel R, Sakmar TP (2009) FTIR analysis of GPCR activation using azido probes. Nat Chem Biol 5:397–399

    Article  CAS  Google Scholar 

  53. Ye S et al (2010) Tracking G-protein-coupled receptor activation using genetically encoded infrared probes. Nature 464:1386–1389

    Article  CAS  Google Scholar 

  54. Park M et al (2015) Bioorthogonal labeling of ghrelin receptor to facilitate studies of ligand-dependent conformational dynamics. Chem Biol 22:1431–1436

    Article  CAS  Google Scholar 

  55. Park M, Tian H, Naganathan S, Sakmar TP, Huber T (2015) Quantitative multi-color detection strategies for bioorthogonally labeled GPCRs. Methods Mol Biol 1335:67–93. G protein-coupled receptors in drug discovery: methods and protocols

    Article  Google Scholar 

  56. Malenka R, Nestler E, Hyman S (2009) Neural and neuroendocrine control of the internal milieu. In: Molecular pharmacology. A foundation for clinical neuroscience, 2nd edn. McGraw-Hill Medical, New York, pp. 265–266

    Google Scholar 

  57. Damian M et al (2015) Ghrelin receptor conformational dynamics regulate the transition from a preassembled to an active receptor: Gq complex. Proc Natl Acad Sci 112:1601–1606

    Article  CAS  Google Scholar 

  58. Turcatti G et al (1996) Probing the structure and function of the tachykinin neurokinin-2 receptor through biosynthetic incorporation of fluorescent amino acids at specific sites. J Biol Chem 271:19991–19998

    Article  CAS  Google Scholar 

  59. Tian H, Sakmar TP, Huber T (2016) A simple method for enhancing the bioorthogonality of cyclooctyne reagent. Chem Commun 52:5451–5454

    Article  CAS  Google Scholar 

  60. Naganathan S, Ye S, Sakmar TP, Huber T (2013) Site-specific epitope tagging of G protein-coupled receptors by bioorthogonal modification of a genetically encoded unnatural amino acid. Biochemistry 52:1028–1036

    Article  CAS  Google Scholar 

  61. Naganathan S, Grunbeck A, Tian H, Huber T, Sakmar TP (2013) Genetically-encoded molecular probes to study G protein-coupled receptors. J Vis Exp e50588

    Google Scholar 

  62. Naganathan S et al (2015) Multiplex detection of functional G protein-coupled receptors harboring site-specifically modified unnatural amino acids. Biochemistry 54:776–786

    Article  CAS  Google Scholar 

  63. Tian H, Sakmar TP, Huber T (2012) Site-specific labeling of genetically encoded azido groups for multicolor, single-molecule fluorescence imaging of GPCRs. Methods Cell Biol 117:267–303

    Article  Google Scholar 

  64. Tian H, Sakmar TP, Huber T (2015) Micelle-enhanced bioorthogonal labeling of genetically encoded azido groups on the lipid-embedded surface of a GPCR. Chembiochem 16:1314–1322

    Article  CAS  Google Scholar 

  65. Tian H et al (2014) Bioorthogonal fluorescent labeling of functional G-protein-coupled receptors. Chembiochem 15:1820–1829

    Article  Google Scholar 

  66. Manglik A, Kobilka B (2014) The role of protein dynamics in GPCR function: insights from the β 2 AR and rhodopsin. Curr Opin Cell Biol 27:136–143

    Article  CAS  Google Scholar 

  67. Pless SA, Ahern CA (2013) Unnatural amino acids as probes of ligand-receptor interactions and their conformational consequences. Annu Rev Pharmacol Toxicol 53:211–229

    Article  CAS  Google Scholar 

  68. Van Arnam EB, Lester HA, Dougherty DA (2011) Dissecting the functions of conserved prolines within transmembrane helices of the D2 dopamine receptor. ACS Chem Biol 6:1063–1068

    Article  Google Scholar 

  69. Krall N, da Cruz FP, Boutureira O, Bernardes GJ (2016) Site-selective protein-modification chemistry for basic biology and drug development. Nat Chem 8:103–113

    Article  CAS  Google Scholar 

  70. Herner A, Lin Q (2016) Photo-triggered click chemistry for biological applications. Top Curr Chem 374:1

    Article  CAS  Google Scholar 

  71. Serfling R, Coin I (2016) Incorporation of unnatural amino acids into proteins expressed in mammalian cells. Methods Enzymol 580:89–107

    Article  CAS  Google Scholar 

  72. Klippenstein V, Plested AJ (2014) Probing the channel gating of a glutamate receptor with a photoactive unnatural amino acid. Biophys J 106:29A

    Article  Google Scholar 

  73. Tian M, Ye S (2016) Allosteric regulation in NMDA receptors revealed by the genetically encoded photo-cross-linkers. Sci Rep 6:34751

    Article  CAS  Google Scholar 

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Acknowledgements

We are grateful for M. Kazmi, T. He, T. Huber, and T.P. Sakmar for their supports and advice. Financial support was provided by the Chinese Scholars Council (CSC fellowship to M.T.), the Agence Nationale de la Recherche of France (ANR-JCJC grant to S.Y.), and the National Natural Science Foundation of China (31528007 to S.Y. and C.Y.).

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Correspondence to Shixin Ye .

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Tian, M., Wang, Q., Yuan, C., Ye, S. (2017). Structure and Function Studies of GPCRs by Site-Specific Incorporation of Unnatural Amino Acids. In: Lebon, G. (eds) Structure and Function of GPCRs. Topics in Medicinal Chemistry, vol 30. Springer, Cham. https://doi.org/10.1007/7355_2017_20

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