Genetically-encoded molecular probes to study G protein-coupled receptors

Journal of Visualized Experiments

Volumn , Issue 79, 2013, Pages

  Naganathan, Saranga ^a   Grunbeck, Amy ^a   Tian, He ^a   Huber, Thomas ^a   Sakmar, Thomas P ^a  

^a ROCKEFELLER UNIVERSITY   (United States)

Author keywords

Biochemistry; Bioorthogonal labeling; G protein coupled receptor; G protein coupled; Genetics; Issue 79; Protein engineering; Receptors; Signal transduction; Site directed mutagenesis; Targeted epitope tagging; Targeted photocrosslinking; Unnatural amino acid

Indexed keywords

EID: 84886814423     PISSN: 1940087X     EISSN: None     Source Type: Journal    
DOI: 10.3791/50588     Document Type: Article

References (38)

1. Huber, T., Menon, S., & Sakmar, T.P. Structural basis for ligand binding and specificity in adrenergic receptors: Implications for GPCR-targeted drug discovery. Biochemistry. 47, 11013-11023 (2008).
2. Steyaert, J. & Kobilka, B.K. Nanobody stabilization of G protein-coupled receptor conformational states. Current opinion in structural biology. 21, 567-572 (2011).
3. Cherezov, V., et al. High-resolution crystal structure of an engineered human beta2-adrenergic G protein-coupled receptor. Science. 318, 1258-1265 (2007).
4. Wu, B., et al. Structures of the CXCR4 chemokine GPCR with small-molecule and cyclic peptide antagonists. Science. 330, 1066-1071 (2010).
5. Rasmussen, S.G., et al. Crystal structure of the beta2 adrenergic receptor-Gs protein complex. Nature. 477, 549-555 (2011).
6. Chin, J.W., et al. An expanded eukaryotic genetic code. Science. 301, 964-967 (2003).
7. Ye, S., et al. Site-specific incorporation of keto amino acids into functional G protein-coupled receptors using unnatural amino acid mutagenesis. The Journal of biological chemistry. 283, 1525-1533 (2008).
8. Ye, S., Huber, T., Vogel, R., & Sakmar, T.P. FTIR analysis of GPCR activation using azido probes. Nature chemical biology. 5, 397-399 (2009).
9. Ye, S., et al. Tracking G-protein-coupled receptor activation using genetically encoded infrared probes. Nature. 464, 1386-1389 (2010).
10. Singh, A., Thornton, E.R., & Westheimer, F.H. The photolysis of diazoacetylchymotrypsin. The Journal of biological chemistry. 237, 3006-3008 (1962).
11. Nakayama, T.A. & Khorana, H.G. Orientation of retinal in bovine rhodopsin determined by cross-linking using a photoactivatable analog of 11-cis-retinal. The Journal of biological chemistry. 265, 15762-15769 (1990).
12. Chen, Q., Pinon, D.I., Miller, L.J., & Dong, M. Molecular basis of glucagon-like peptide 1 docking to its intact receptor studied with carboxyl-terminal photolabile probes. The Journal of biological chemistry. 284, 34135-34144 (2009).
13. Huang, K.S., Radhakrishnan, R., Bayley, H., & Khorana, H.G. Orientation of retinal in bacteriorhodopsin as studied by cross-linking using a photosensitive analog of retinal. The Journal of biological chemistry. 257, 13616-13623 (1982).
14. Zoffmann, S., Turcatti, G., Galzi, J., Dahl, M., & Chollet, A. Synthesis and characterization of fluorescent and photoactivatable MIP-1alpha ligands and interactions with chemokine receptors CCR1 and CCR5. Journal of medicinal chemistry. 44, 215-222 (2001).
15. Janz, J.M., et al. Direct interaction between an allosteric agonist pepducin and the chemokine receptor CXCR4. Journal of the American Chemical Society. 133, 15878-15881 (2011).
16. Chin, J.W., Martin, A.B., King, D.S., Wang, L., & Schultz, P.G. Addition of a photocrosslinking amino acid to the genetic code of Escherichiacoli. Proceedings of the National Academy of Sciences of the United States of America. 99, 11020-11024 (2002).
17. Hino, N., et al. Protein photo-cross-linking in mammalian cells by site-specific incorporation of a photoreactive amino acid. Nature methods. 2, 201-206 (2005).
18. Grunbeck, A., Huber, T., Sachdev, P., & Sakmar, T.P. Mapping the ligand-binding site on a G protein-coupled receptor (GPCR) using genetically encoded photocrosslinkers. Biochemistry. 50, 3411-3413 (2011).
19. Grunbeck, A. et al. Genetically encoded photo-cross-linkers map the binding site of an allosteric drug on a G protein-coupled receptor. ACS chemical biology. 7, 967-972 (2012).
20. Dunham, T.D. & Farrens, D.L. Conformational changes in rhodopsin. Movement of helix f detected by site-specific chemical labeling and fluorescence spectroscopy. The Journal of biological chemistry. 274, 1683-1690 (1999).
21. Maurel, D., et al. Cell-surface protein-protein interaction analysis with time-resolved FRET and snap-tag technologies: application to GPCR oligomerization. Nature methods. 5, 561-567 (2008).
22. Huber, T. & Sakmar, T.P. Escaping the flatlands: new approaches for studying the dynamic assembly and activation of GPCR signaling complexes. Trends in pharmacological sciences. 32, 410-419 (2011).
23. Saxon, E. & Bertozzi, C.R. Cell surface engineering by a modified Staudinger reaction. Science. 287, 2007-2010 (2000).
24. Kiick, K.L., Saxon, E., Tirrell, D.A., & Bertozzi, C.R. Incorporation of azides into recombinant proteins for chemoselective modification by the Staudinger ligation. Proceedings of the National Academy of Sciences of the United States of America. 99, 19-24 (2002).
25. Agard, N.J., Prescher, J.A., & Bertozzi, C.R. A strain-promoted [3 + 2] azide-alkyne cycloaddition for covalent modification of biomolecules in living systems. Journal of the American Chemical Society. 126, 15046-15047 (2004).
26. Kolb, H.C. & Sharpless, K.B. The growing impact of click chemistry on drug discovery. Drug discovery today. 8, 1128-1137 (2003).
27. Huber, T., Botelho, A.V., Beyer, K., & Brown, M.F. Membrane Model for the G-Protein-Coupled Receptor Rhodopsin: Hydrophobic Interface and Dynamical Structure. Biophys. J. 84, 2078-2100 (2004).
28. Okada, T., et al. The retinal conformation and its environment in rhodopsin in light of a new 2.2 Å crystal structure. J. Mol. Biol. 342, 571-583 (2004).
29. Huber, T., Tian, H., Ye, S., Naganathan, S., Kazmi, M.A., Duarte, T., & Sakmar, T.P. Bioorthogonal labeling of functional G protein-coupled receptors at genetically encoded azido groups. submitted (2013).
30. Naganathan, S., Ye, S., Sakmar, T.P., & Huber, T. Site-specific epitope tagging of GPCRs by bioorthogonal modification of a genetically-encoded unnatural amino acid. Biochemistry, DOI: 10.1021/bi301292h (2013).
31. Molday, R.S. & MacKenzie, D. Monoclonal antibodies to rhodopsin: characterization, cross-reactivity, and application as structural probes. Biochemistry. 22, 653-660 (1983).
32. Gether, U., et al. Agonists induce conformational changes in transmembrane domains III and VI of the beta2 adrenoceptor. The EMBO journal. 16, 6737-6747 (1997).
33. Hubbell, W.L., Altenbach, C., Hubbell, C.M., & Khorana, H.G. Rhodopsin structure, dynamics, and activation: A perspective from crystallography, site-directed spin labeling, sulfhydryl reactivity, and disulfide cross-linking. Advances in Protein Chemistry; Membrane Proteins. 63, 243-290 (2003).
34. Cai, K., Itoh, Y., & Khorana, H.G. Mapping of contact sites in complex formation between transducin and light-activated rhodopsin by covalent crosslinking: use of a photoactivatable reagent. Proceedings of the National Academy of Sciences of the United States of America. 98, 4877-4882 (2001).
35. Dorman, G. & Prestwich, G.D. Benzophenone photophores in biochemistry. Biochemistry. 33, 5661-5673 (1994).
36. Zhang, Z., et al. A new strategy for the site-specific modification of proteins in vivo. Biochemistry. 42, 6735-6746 (2003).
37. Dirksen, A., Hackeng, T.M., & Dawson, P.E. Nucleophilic catalysis of oxime ligation. Angew. Chem. Int. Ed. 45, 7581-7584 (2006).
38. Yanagisawa, T., et al. Multistep engineering of pyrrolysyl-tRNA synthetase to genetically encode N(epsilon)-(o-azidobenzyloxycarbonyl) lysine for site-specific protein modification. Chemistry & biology. 15, 1187-1197 (2008).