The dynamics of agonist-β
Journal
Nature chemistry
ISSN: 1755-4349
Titre abrégé: Nat Chem
Pays: England
ID NLM: 101499734
Informations de publication
Date de publication:
08 2023
08 2023
Historique:
received:
29
06
2021
accepted:
12
05
2023
medline:
4
8
2023
pubmed:
23
6
2023
entrez:
22
6
2023
Statut:
ppublish
Résumé
There is considerable uncertainty about the mechanism by which the β
Identifiants
pubmed: 37349378
doi: 10.1038/s41557-023-01238-6
pii: 10.1038/s41557-023-01238-6
doi:
Substances chimiques
GTP-Binding Protein alpha Subunits, Gs
EC 3.6.5.1
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Langues
eng
Sous-ensembles de citation
IM
Pagination
1127-1137Subventions
Organisme : NHLBI NIH HHS
ID : R01 HL155532
Pays : United States
Organisme : NHLBI NIH HHS
ID : R35 HL150807
Pays : United States
Informations de copyright
© 2023. The Author(s), under exclusive licence to Springer Nature Limited.
Références
Lefkowitz, R. J. Seven transmembrane receptors: something old, something new. Acta Physiol. 190, 9–19 (2007).
Hauser, A. S., Attwood, M. M., Rask-Andersen, M., Schiöth, H. B. & Gloriam, D. E. Trends in GPCR drug discovery: new agents, targets and indications. Nat. Rev. Drug Discov. 16, 829–842 (2017).
pubmed: 29075003
pmcid: 6882681
Overington, J. P., Al-Lazikani, B. & Hopkins, A. L. How many drug targets are there?. Nat. Rev. Drug Discov. 5, 993–996 (2006).
pubmed: 17139284
Fredriksson, R., Lagerström, M. C., Lundin, L.-G. & Schiöth, H. B. The G-protein-coupled receptors in the human genome form five main families. Phylogenetic analysis, paralogon groups and fingerprints. Mol. Pharmacol. 63, 1256–1272 (2003).
pubmed: 12761335
Lefkowitz, R. J. The superfamily of heptahelical receptors. Nat. Cell Biol. 2, E133–E136 (2000).
pubmed: 10878827
Ross, E. M., Maguire, M. E., Sturgill, T. W., Biltonen, R. L. & Gilman, A. G. Relationship between the β-adrenergic receptor and adenylate cyclase. J. Biol. Chem. 252, 5761–5775 (1977).
pubmed: 195960
De Lean, A., Stadel, J. M. & Lefkowitz, R. J. A ternary complex model explains the agonist-specific binding properties of the adenylate cyclase-coupled β-adrenergic receptor. J. Biol. Chem. 255, 7108–7117 (1980).
pubmed: 6248546
MacGregor, D. A., Prielipp, R. C., Butterworth, J. F. IV, James, R. L. & Royster, R. L. Relative efficacy and potency of β-adrenoceptor agonists for generating cAMP in human lymphocytes. Chest 109, 194–200 (1996).
pubmed: 8549185
Clark, A. J. The reaction between acetyl choline and muscle cells. J. Physiol. 61, 530–546 (1926).
pubmed: 16993813
pmcid: 1514867
Karlin, A. On the application of ‘a plausible model’ of allosteric proteins to the receptor for acetylcholine. J. Theor. Biol. 16, 306–320 (1967).
pubmed: 6048545
Nygaard, R. et al. The dynamic process of β2-adrenergic receptor activation. Cell 152, 532–542 (2013).
pubmed: 23374348
pmcid: 3586676
Manglik, A. et al. Structural insights into the dynamic process of β2-adrenergic receptor signaling. Cell 161, 1101–1111 (2015).
pubmed: 25981665
pmcid: 4441853
Rosenbaum, D. M. et al. Structure and function of an irreversible agonist-β2 adrenoceptor complex. Nature 469, 236–240 (2011).
pubmed: 21228876
pmcid: 3074335
Gregorio, G. G. et al. Single-molecule analysis of ligand efficacy in β2 AR–G-protein activation. Nature 547, 68–73 (2017).
pubmed: 28607487
pmcid: 5502743
Lerch, M. T. et al. Viewing rare conformations of the β2 adrenergic receptor with pressure-resolved DEER spectroscopy. Proc. Natl Acad. Sci. USA 117, 31824–31831 (2020).
pubmed: 33257561
pmcid: 7749303
Dror, R. O. et al. Activation mechanism of the β2-adrenergic receptor. Proc. Natl Acad. Sci. USA 108, 18684–18689 (2011).
pubmed: 22031696
pmcid: 3219117
Vilardaga, J.-P., Bünemann, M., Krasel, C., Castro, M. & Lohse, M. J. Measurement of the millisecond activation switch of G protein-coupled receptors in living cells. Nat. Biotechnol. 21, 807–812 (2003).
pubmed: 12808462
Barducci, A., Bussi, G. & Parrinello, M. Well-tempered metadynamics: a smoothly converging and tunable free-energy method. Phys. Rev. Lett. 100, 020603 (2008).
pubmed: 18232845
Cherezov, V. et al. High-resolution crystal structure of an engineered human β2-adrenergic G protein-coupled receptor. Science 318, 1258–1265 (2007).
pubmed: 17962520
pmcid: 2583103
Rasmussen, S. G. et al. Crystal structure of the β2 adrenergic receptor–Gs protein complex. Nature 477, 549–555 (2011).
pubmed: 21772288
pmcid: 3184188
Ballesteros, J. A. & Weinstein, H. in Methods in Neurosciences Vol. 25 (ed Sealfon, S. C.), 366–428 (Elsevier, 1995).
Pándy-Szekeres, G. et al. GPCRdb in 2018: adding GPCR structure models and ligands. Nucleic Acids Res. 46, D440–D446 (2017).
pmcid: 5753179
Kobilka, B. K. G protein coupled receptor structure and activation. Biochim. Biophys. Acta 1768, 794–807 (2007).
pubmed: 17188232
Ballesteros, J. A. et al. Activation of the β2-adrenergic receptor involves disruption of an ionic lock between the cytoplasmic ends of transmembrane segments 3 and 6. J. Biol. Chem. 276, 29171–29177 (2001).
pubmed: 11375997
Yao, X. et al. Coupling ligand structure to specific conformational switches in the β2-adrenoceptor. Nat. Chem. Biol. 2, 417–422 (2006).
pubmed: 16799554
Liu, X. et al. Structural insights into the process of GPCR-G protein complex formation. Cell 177, 1243–1251 (2019).
pubmed: 31080070
pmcid: 6991123
Sprang, S. R. G protein mechanisms: insights from structural analysis. Annu. Rev. Biochem. 66, 639–678 (1997).
pubmed: 9242920
Oldham, W. M. & Hamm, H. E. Heterotrimeric G protein activation by G-protein-coupled receptors. Nat. Rev. Mol. Cell Biol. 9, 60–71 (2008).
pubmed: 18043707
Liu, R. et al. Palmitoylation regulates intracellular trafficking of β2 adrenergic receptor/arrestin/phosphodiesterase 4D complexes in cardiomyocytes. PLoS ONE 7, e42658 (2012).
pubmed: 22912718
pmcid: 3415400
Palczewski, K. et al. Crystal structure of rhodopsin: AG protein-coupled receptor. Science 289, 739–745 (2000).
pubmed: 10926528
Branduardi, D., Bussi, G. & Parrinello, M. Metadynamics with adaptive Gaussians. J. Chem. Theory Comput. 8, 2247–2254 (2012).
pubmed: 26588957
Dror, R. O. et al. Identification of two distinct inactive conformations of the β2-adrenergic receptor reconciles structural and biochemical observations. Proc. Natl Acad. Sci. USA 106, 4689–4694 (2009).
pubmed: 19258456
pmcid: 2650503
Eswar, N., Eramian, D., Webb, B., Shen, M.-Y. & Sali, A. in Structural Proteomics 145–159 (Springer, 2008).
Hilger, D. et al. Structural insights into differences in G protein activation by family A and family B GPCRs. Science 369, eaba3373 (2020).
pubmed: 32732395
pmcid: 7954662
Oldham, W. M., Van Eps, N., Preininger, A. M., Hubbell, W. L. & Hamm, H. E. Mechanism of the receptor-catalyzed activation of heterotrimeric G proteins. Nat. Struct. Mol. Biol. 13, 772–777 (2006).
pubmed: 16892066
Onrust, R. et al. Receptor and βγ binding sites in the α subunit of the retinal G protein transducin. Science 275, 381–384 (1997).
pubmed: 8994033
DeMars, G., Fanelli, F. & Puett, D. The extreme C-terminal region of Gαs differentially couples to the luteinizing hormone and β2-adrenergic receptors. Mol. Endocrinol. 25, 1416–1430 (2011).
pubmed: 21622536
pmcid: 3146252
Markby, D. W., Onrust, R. & Bourne, H. R. Separate GTP binding and GTPase activating domains of a Gα subunit. Science 262, 1895–1901 (1993).
pubmed: 8266082
Carpenter, B., Nehmé, R., Warne, T., Leslie, A. G. & Tate, C. G. Structure of the adenosine A
pubmed: 27462812
pmcid: 4979997
Dror, R. O. et al. Structural basis for nucleotide exchange in heterotrimeric G proteins. Science 348, 1361–1365 (2015).
pubmed: 26089515
pmcid: 4968074
Mafi, A., Kim, S.-K., Chou, K. C., Güthrie, B. & Goddard, W. A. III Predicted structure of fully activated Tas1R3/1R3′ homodimer bound to G protein and natural sugars: structural insights into G protein activation by a Class C sweet taste homodimer with natural sugars. J. Am. Chem. Soc. 143, 16824–16838 (2021).
pubmed: 34585929
Kwon, Y. et al. Dimerization of β2-adrenergic receptor is responsible for the constitutive activity subjected to inverse agonism. Cell Chem. Biol. 29, 1532–1540 (2022).
pubmed: 36167077
Mafi, A., Kim, S.-K. & Goddard, W. A. The atomistic level structure for the activated human κ-opioid receptor bound to the full Gi protein and the MP1104 agonist. Proc. Natl Acad. Sci. USA 117, 5836–5843 (2020).
pubmed: 32127473
pmcid: 7084096
Mafi, A., Kim, S.-K. & Goddard, W. A. Mechanism of β-arrestin recruitment by the μ-opioid G protein-coupled receptor. Proc. Natl Acad. Sci. USA 117, 16346–16355 (2020).
pubmed: 32601232
pmcid: 7368253
Zhang, Y. et al. Cryo-EM structure of the activated GLP-1 receptor in complex with a G protein. Nature 546, 248–253 (2017).
pubmed: 28538729
pmcid: 5587415
Liang, Y.-L. et al. Phase-plate cryo-EM structure of a biased agonist-bound human GLP-1 receptor–Gs complex. Nature 555, 121–125 (2018).
pubmed: 29466332
García-Nafría, J., Lee, Y., Bai, X., Carpenter, B. & Tate, C. G. Cryo-EM structure of the adenosine A2A receptor coupled to an engineered heterotrimeric G protein. eLife 7, e35946 (2018).
pubmed: 29726815
pmcid: 5962338
Hu, Q. & Shokat, K. M. Disease-causing mutations in the G protein Gαs subvert the roles of GDP and GTP. Cell 173, 1254–1264 (2018).
pubmed: 29628140
pmcid: 5959768
Guex, N. & Peitsch, M. C. SWISS-MODEL and the Swiss-Pdb Viewer: an environment for comparative protein modeling. Electrophoresis 18, 2714–2723 (1997).
pubmed: 9504803
Griffith, A. R. DarwinDock and GAG-Dock: Methods and Applications for Small Molecule Docking (California Institute of Technology, 2017).
Mayo, S. L., Olafson, B. D. & Goddard, W. A. DREIDING: a generic force field for molecular simulations. J. Phys. Chem. 94, 8897–8909 (1990).
Tak Kam, V. W. & Goddard, W. A. III Flat-bottom strategy for improved accuracy in protein side-chain placements. J. Chem. Theory Comput. 4, 2160–2169 (2008).
pubmed: 26620487
Ring, A. M. et al. Adrenaline-activated structure of β2-adrenoceptor stabilized by an engineered nanobody. Nature 502, 575–579 (2013).
pubmed: 24056936
pmcid: 3822040
Warne, T. et al. The structural basis for agonist and partial agonist action on a β1-adrenergic receptor. Nature 469, 241–244 (2011).
pubmed: 21228877
pmcid: 3023143
Wacker, D. et al. Conserved binding mode of human β2 adrenergic receptor inverse agonists and antagonist revealed by X-ray crystallography. J. Am. Chem. Soc. 132, 11443–11445 (2010).
pubmed: 20669948
pmcid: 2923663
Needleman, S. B. & Wunsch, C. D. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol. 48, 443–453 (1970).
pubmed: 5420325
Pettersen, E. F. et al. UCSF Chimera—a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612 (2004).
pubmed: 15264254
Raniolo, S. & Limongelli, V. Ligand binding free-energy calculations with funnel metadynamics. Nat. Protoc. 15, 2837–2866 (2020).
pubmed: 32814837
Maier, J. A. et al. ff14SB: improving the accuracy of protein side chain and backbone parameters from ff99SB. J. Chem. Theory Comput. 11, 3696–3713 (2015).
pubmed: 26574453
pmcid: 4821407
Wang, J., Wolf, R. M., Caldwell, J. W., Kollman, P. A. & Case, D. A. Development and testing of a general amber force field. J. Comput. Chem. 25, 1157–1174 (2004).
pubmed: 15116359
da Silva, A. W. S. & Vranken, W. F. ACPYPE-AnteChamber PYthon Parser interfacE. BMC Res. Notes 5, 367 (2012).
Wang, J., Wang, W., Kollman, P. A. & Case, D. A. Automatic atom type and bond type perception in molecular mechanical calculations. J. Mol. Graph. Model. 25, 247–260 (2006).
pubmed: 16458552
Jakalian, A., Jack, D. B. & Bayly, C. I. Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation. J. Comput. Chem. 23, 1623–1641 (2002).
pubmed: 12395429
Dickson, C. J. et al. Lipid14: the amber lipid force field. J. Chem. Theory Comput. 10, 865–879 (2014).
pubmed: 24803855
pmcid: 3985482
Lindorff-Larsen, K. et al. Improved side-chain torsion potentials for the Amber ff99SB protein force field. Proteins 78, 1950–1958 (2010).
pubmed: 20408171
pmcid: 2970904
Meagher, K. L., Redman, L. T. & Carlson, H. A. Development of polyphosphate parameters for use with the AMBER force field. J. Comput. Chem. 24, 1016–1025 (2003).
pubmed: 12759902
Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W. & Klein, M. L. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79, 926–935 (1983).
Khoury, G. A., Thompson, J. P., Smadbeck, J., Kieslich, C. A. & Floudas, C. A. Forcefield_PTM: ab initio charge and AMBER forcefield parameters for frequently occurring post-translational modifications. J. Chem. Theory Comput. 9, 5653–5674 (2013).
pubmed: 24489522
pmcid: 3904396
Bussi, G., Donadio, D. & Parrinello, M. Canonical sampling through velocity rescaling. J. Chem. Phys. 126, 014101 (2007).
pubmed: 17212484
Parrinello, M. & Rahman, A. Polymorphic transitions in single crystals: a new molecular dynamics method. J. Appl. Phys. 52, 7182–7190 (1981).
Essmann, U. et al. A smooth particle mesh Ewald method. J. Chem. Phys. 103, 8577–8593 (1995).
Miyamoto, S. & Kollman, P. A. Settle: an analytical version of the SHAKE and RATTLE algorithm for rigid water models. J. Comput. Chem. 13, 952–962 (1992).
Hess, B. P-LINCS: a parallel linear constraint solver for molecular simulation. J. Chem. Theory Comput. 4, 116–122 (2008).
pubmed: 26619985
Abraham, M. J. et al. GROMACS: high performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX 1, 19–25 (2015).
Pronk, S. et al. GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit. Bioinformatics 29, 845–854 (2013).
pubmed: 23407358
pmcid: 3605599
Tribello, G. A., Bonomi, M., Branduardi, D., Camilloni, C. & Bussi, G. PLUMED 2: new feathers for an old bird. Comput. Phys. Commun. 185, 604–613 (2014).