Phase-plate cryo-EM structure of a biased agonistbound human GLP-1 receptor-Gs complex

Nature

Volumn 555, Issue 7694, 2018, Pages 121-125

  Liang, Yi Lynn ^a   Khoshouei, Maryam ^b   Glukhova, Alisa ^a   Furness, Sebastian G B ^a   Zhao, Peishen ^a   Clydesdale, Lachlan ^a   Koole, Cassandra ^a   Truong, Tin T ^a   Thal, David M ^a   Lei, Saifei ^c,d   Radjainia, Mazdak ^a,e   Danev, Radostin ^b   Baumeister, Wolfgang ^b   Wang, Ming Wei ^c,d,f   Miller, Laurence J ^a,g   Christopoulos, Arthur ^a   Sexton, Patrick M ^a,f   Wootten, Denise ^a  

^a MONASH UNIVERSITY   (Australia)

^b MAX PLANCK INSTITUTE OF BIOCHEMISTRY   (Germany)

^c UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

^d SHANGHAI INSTITUTE OF MATERIA MEDICA   (China)

^e Thermo Fisher Scientific   (United States)

^f FUDAN UNIVERSITY   (China)

^g MAYO GRADUATE SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

G PROTEIN COUPLED RECEPTOR; GLUCAGON LIKE PEPTIDE 1 RECEPTOR; GUANINE NUCLEOTIDE BINDING PROTEIN; GLP1R PROTEIN, HUMAN; GLUCAGON LIKE PEPTIDE 1; STIMULATORY GUANINE NUCLEOTIDE BINDING PROTEIN;

CELL; CHEMICAL BINDING; DIABETES; PEPTIDE; PROTEIN; RESOLUTION;

AMINO TERMINAL SEQUENCE; ARTICLE; BINDING AFFINITY; BINDING SITE; COMPARATIVE STUDY; COMPLEX FORMATION; CRYOELECTRON MICROSCOPY; HUMAN; IN VIVO STUDY; MEMBRANE POTENTIAL; MOLECULAR DYNAMICS; PHASE PLATE CRYOELECTRON MICROSCOPY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN CONFORMATION; PROTEIN EXPRESSION; PROTEIN INTERACTION; PROTEIN STRUCTURE; AGONISTS; CHEMISTRY; METABOLISM; MOLECULAR MODEL; ULTRASTRUCTURE;

BINDING SITES; CRYOELECTRON MICROSCOPY; GLUCAGON-LIKE PEPTIDE 1; GLUCAGON-LIKE PEPTIDE-1 RECEPTOR; GTP-BINDING PROTEIN ALPHA SUBUNITS, GS; HUMANS; MODELS, MOLECULAR; PROTEIN CONFORMATION;

EID: 85042499588     PISSN: 00280836     EISSN: 14764687     Source Type: Journal    
DOI: 10.1038/nature25773     Document Type: Article

References (44)

1. de Graaf, C. et al. Glucagon-like peptide-1 and its class B G protein-coupled receptors: A long march to therapeutic successes. Pharmacol. Rev. 68, 954-1013 (2016).
2. Zhang, Y. et al. Cryo-EM structure of the activated GLP-1 receptor in complex with a G protein. Nature 546, 248-253 (2017).
3. Hager, M. V., Clydesdale, L., Gellman, S. H., Sexton, P. M. & Wootten, D. Characterization of signal bias at the GLP-1 receptor induced by backbone modification of GLP-1. Biochem. Pharmacol. 136, 99-108 (2017).
4. Koole, C. et al. Allosteric ligands of the glucagon-like peptide 1 receptor (GLP-1R) differentially modulate endogenous and exogenous peptide responses in a pathway-selective manner: Implications for drug screening. Mol. Pharmacol. 78, 456-465 (2010).
5. Wootten, D. et al. Differential activation and modulation of the glucagon-like peptide-1 receptor by small molecule ligands. Mol. Pharmacol. 83, 822-834 (2013).
6. Zhang, H. et al. Autocrine selection of a GLP-1R G-protein biased agonist with potent antidiabetic effects. Nat. Commun. 6, 8918 (2015).
7. Mann, R. et al. Peptide binding at the GLP-1 receptor. Biochem. Soc. Trans. 35, 713-716 (2007).
8. Manandhar, B. & Ahn, J. M. Glucagon-like peptide-1 (GLP-1) analogs: Recent advances, new possibilities, and therapeutic implications. J. Med. Chem. 58, 1020-1037 (2015).
9. Liang, Y. L. et al. Phase-plate cryo-EM structure of a class B GPCR-G-protein complex. Nature 546, 118-123 (2017).
10. Danev, R., Buijsse, B., Khoshouei, M., Plitzko, J. M. & Baumeister, W. Volta potential phase plate for in-focus phase contrast transmission electron microscopy. Proc. Natl Acad. Sci. USA 111, 15635-15640 (2014).
11. Khoshouei, M., Radjainia, M., Baumeister, W. & Danev, R. Cryo-EM structure of haemoglobin at 3.2 Å determined with the Volta phase plate. Nat. Commun. 8, 16099 (2017).
12. Khoshouei, M. et al. Volta phase plate cryo-EM of the small protein complex Prx3. Nat. Commun. 7, 10534 (2016).
13. Siu, F. Y. et al. Structure of the human glucagon class B G-protein-coupled receptor. Nature 499, 444-449 (2013).
14. Hollenstein, K. et al. Structure of class B GPCR corticotropin-releasing factor receptor 1. Nature 499, 438-443 (2013).
15. Jazayeri, A. et al. Crystal structure of the GLP-1 receptor bound to a peptide agonist. Nature 546, 254-258 (2017).
16. Runge, S., Thøgersen, H., Madsen, K., Lau, J. & Rudolph, R. Crystal structure of the ligand-bound glucagon-like peptide-1 receptor extracellular domain. J. Biol. Chem. 283, 11340-11347 (2008).
17. Wootten, D. et al. The extracellular surface of the GLP-1 receptor is a molecular trigger for biased agonism. Cell 165, 1632-1643 (2016).
18. Coopman, K. et al. Residues within the transmembrane domain of the glucagon-like peptide-1 receptor involved in ligand binding and receptor activation: Modelling the ligand-bound receptor. Mol. Endocrinol. 25, 1804-1818 (2011).
19. Dods, R. L. & Donnelly, D. The peptide agonist-binding site of the glucagon-like peptide-1 (GLP-1) receptor based on site-directed mutagenesis and knowledge-based modelling. Biosci. Rep. 36, e00285 (2015).
20. Koole, C. et al. Second extracellular loop of human glucagon-like peptide-1 receptor (GLP-1R) has a critical role in GLP-1 peptide binding and receptor activation. J. Biol. Chem. 287, 3642-3658 (2012).
21. Wootten, D. et al. Key interactions by conserved polar amino acids located at the transmembrane helical boundaries in class B GPCRs modulate activation, effector specificity and biased signalling in the glucagon-like peptide-1 receptor. Biochem. Pharmacol. 118, 68-87 (2016).
22. Yang, D. et al. Structural determinants of binding the seven-transmembrane domain of the glucagon-like peptide-1 receptor (GLP-1R). J. Biol. Chem. 291, 12991-13004 (2016).
23. Moon, M. J. et al. Ligand binding pocket formed by evolutionarily conserved residues in the glucagon-like peptide-1 (GLP-1) receptor core domain. J. Biol. Chem. 290, 5696-5706 (2015).
24. Wootten, D. et al. A hydrogen-bonded polar network in the core of the glucagon-like peptide-1 receptor is a fulcrum for biased agonism: Lessons from class B crystal structures. Mol. Pharmacol. 89, 335-347 (2016).
25. Wootten, D., Simms, J., Miller, L. J., Christopoulos, A. & Sexton, P. M. Polar transmembrane interactions drive formation of ligand-specific and signal pathway-biased family B G protein-coupled receptor conformations. Proc. Natl Acad. Sci. USA 110, 5211-5216 (2013).
26. Furness, S. G. B. et al. Ligand-dependent modulation of G protein conformation alters drug efficacy. Cell 167, 739-749.e11 (2016).
27. Gregorio, G. G. et al. Single-molecule analysis of ligand efficacy in β 2AR-Gprotein activation. Nature 547, 68-73 (2017).
28. Cleator, J. H., Mehta, N. D., Kurtz, D. T. & Hildebrandt, J. D. The N54 mutant of Gα s has a conditional dominant negative phenotype which suppresses hormone-stimulated but not basal cAMP levels. FEBS Lett. 443, 205-208 (1999).
29. Lee, E., Taussig, R. & Gilman, A. G. The G226A mutant of Gsα highlights the requirement for dissociation of G protein subunits. J. Biol. Chem. 267, 1212-1218 (1992).
30. Iiri, T., Bell, S. M., Baranski, T. J., Fujita, T. & Bourne, H. R. A Gsα mutant designed to inhibit receptor signaling through Gs. Proc. Natl Acad. Sci. USA 96, 499-504 (1999).
31. Berlot, C. H. A highly effective dominant negative α s construct containing mutations that affect distinct functions inhibits multiple Gs-coupled receptor signaling pathways. J. Biol. Chem. 277, 21080-21085 (2002).
32. Berlot, C. H. & Bourne, H. R. Identification of effector-activating residues of Gsα . Cell 68, 911-922 (1992).
33. Mastronarde, D. N. Automated electron microscope tomography using robust prediction of specimen movements. J. Struct. Biol. 152, 36-51 (2005).
34. Zheng, S. Q. et al. MotionCor2: Anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Nat. Methods 14, 331-332 (2017).
35. Zhang, K. Gctf: Real-time CTF determination and correction. J. Struct. Biol. 193, 1-12 (2016).
36. Tang, G.et al. EMAN2: An extensible image processing suite for electron microscopy. J. Struct. Biol. 157, 38-46 (2007).
37. Kimanius, D., Forsberg, B. O., Scheres, S. H. & Lindahl, E. Accelerated cryo-EM structure determination with parallelisation using GPUs in RELION-2. eLife 5, e18722 (2016).
38. Emsley, P. & Cowtan, K. Coot: Model-building tools for molecular graphics. Acta Crystallogr. D 60, 2126-2132 (2004).
39. Adams, P. D. et al. PHENIX: A comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D 66, 213-221 (2010).
40. Chen, V. B. et al. MolProbity: All-atom structure validation for macromolecular crystallography. Acta Crystallogr. D 66, 12-21 (2010).
41. Savage, E. E., Wootten, D., Christopoulos, A., Sexton, P. M. & Furness, S. G. A simple method to generate stable cell lines for the analysis of transient protein-protein interactions. Biotechniques 54, 217-221 (2013).
42. Hager, M. V. J., Johnson, L. M., Wootten, D., Sexton, P. M. & Gellman, S. H. β -Arrestin-biased agonists of the GLP-1 receptor from β -amino acid residue incorporation into GLP-1 analogues. J. Am. Chem. Soc. 138, 14970-14979 (2016).
43. Pettersen, E. F. et al. UCSF Chimera-a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605-1612 (2004).
44. Ehlert, F. J. The relationship between muscarinic receptor occupancy and adenylate cyclase inhibition in the rabbit myocardium. Mol. Pharmacol. 28, 410-421 (1985).