Mechanistic insights into allosteric regulation of the A2A adenosine G protein-coupled receptor by physiological cations
Abstract
Cations play key roles in regulating G-protein-coupled receptors (GPCRs), although their mechanisms are poorly understood. Here, 19F NMR is used to delineate the effects of cations on functional states of the adenosine A2A GPCR. While Na+ reinforces an inactive ensemble and a partial-agonist stabilized state, Ca2+ and Mg2+ shift the equilibrium toward active states. Positive allosteric effects of divalent cations are more pronounced with agonist and a G-protein-derived peptide. In cell membranes, divalent cations enhance both the affinity and fraction of the high affinity agonist-bound state. Molecular dynamics simulations suggest high concentrations of divalent cations bridge specific extracellular acidic residues, bringing TM5 and TM6 together at the extracellular surface and allosterically driving open the G-protein-binding cleft as shown by rigidity-transmission allostery theory. Lastly, an understanding of cation allostery should enable the design of allosteric agents and enhance our understanding of GPCR regulation in the cellular milieu.
- Authors:
-
- Univ. of Toronto, Mississauga, ON (Canada); Univ. of Toronto, Toronto, ON (Canada)
- Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
- Kwansei Gakuin Univ., Nishinomiya (Japan)
- Univ. of California San Diego School of Medicine, La Jolla, CA (United States)
- Univ. of Toronto, Toronto, ON (Canada); The Hospital for Sick Children, Toronto, ON (Canada)
- Univ. of Toronto, Toronto, ON (Canada)
- Publication Date:
- Research Org.:
- Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
- Sponsoring Org.:
- USDOE Laboratory Directed Research and Development (LDRD) Program
- OSTI Identifier:
- 1435536
- Report Number(s):
- LA-UR-18-20653
Journal ID: ISSN 2041-1723
- Grant/Contract Number:
- AC52-06NA25396
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Nature Communications
- Additional Journal Information:
- Journal Volume: 9; Journal Issue: 1; Journal ID: ISSN 2041-1723
- Publisher:
- Nature Publishing Group
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; Biological Science
Citation Formats
Ye, Libin, Neale, Chris Andrew, Sljoka, Adnan, Lyda, Brent, Pichugin, Dmitry, Tsuchimura, Nobuyuki, Larda, Sacha T., Pomes, Regis, Garcia, Angel E., Ernst, Oliver P., Sunahara, Roger K., and Prosser, R. Scott. Mechanistic insights into allosteric regulation of the A2A adenosine G protein-coupled receptor by physiological cations. United States: N. p., 2018.
Web. doi:10.1038/s41467-018-03314-9.
Ye, Libin, Neale, Chris Andrew, Sljoka, Adnan, Lyda, Brent, Pichugin, Dmitry, Tsuchimura, Nobuyuki, Larda, Sacha T., Pomes, Regis, Garcia, Angel E., Ernst, Oliver P., Sunahara, Roger K., & Prosser, R. Scott. Mechanistic insights into allosteric regulation of the A2A adenosine G protein-coupled receptor by physiological cations. United States. https://doi.org/10.1038/s41467-018-03314-9
Ye, Libin, Neale, Chris Andrew, Sljoka, Adnan, Lyda, Brent, Pichugin, Dmitry, Tsuchimura, Nobuyuki, Larda, Sacha T., Pomes, Regis, Garcia, Angel E., Ernst, Oliver P., Sunahara, Roger K., and Prosser, R. Scott. Tue .
"Mechanistic insights into allosteric regulation of the A2A adenosine G protein-coupled receptor by physiological cations". United States. https://doi.org/10.1038/s41467-018-03314-9. https://www.osti.gov/servlets/purl/1435536.
@article{osti_1435536,
title = {Mechanistic insights into allosteric regulation of the A2A adenosine G protein-coupled receptor by physiological cations},
author = {Ye, Libin and Neale, Chris Andrew and Sljoka, Adnan and Lyda, Brent and Pichugin, Dmitry and Tsuchimura, Nobuyuki and Larda, Sacha T. and Pomes, Regis and Garcia, Angel E. and Ernst, Oliver P. and Sunahara, Roger K. and Prosser, R. Scott},
abstractNote = {Cations play key roles in regulating G-protein-coupled receptors (GPCRs), although their mechanisms are poorly understood. Here, 19F NMR is used to delineate the effects of cations on functional states of the adenosine A2A GPCR. While Na+ reinforces an inactive ensemble and a partial-agonist stabilized state, Ca2+ and Mg2+ shift the equilibrium toward active states. Positive allosteric effects of divalent cations are more pronounced with agonist and a G-protein-derived peptide. In cell membranes, divalent cations enhance both the affinity and fraction of the high affinity agonist-bound state. Molecular dynamics simulations suggest high concentrations of divalent cations bridge specific extracellular acidic residues, bringing TM5 and TM6 together at the extracellular surface and allosterically driving open the G-protein-binding cleft as shown by rigidity-transmission allostery theory. Lastly, an understanding of cation allostery should enable the design of allosteric agents and enhance our understanding of GPCR regulation in the cellular milieu.},
doi = {10.1038/s41467-018-03314-9},
journal = {Nature Communications},
number = 1,
volume = 9,
place = {United States},
year = {2018},
month = {4}
}
Web of Science
Works referenced in this record:
[19] Integrated methods for the construction of three-dimensional models and computational probing of structure-function relations in G protein-coupled receptors
book, January 1995
- Ballesteros, Juan A.; Weinstein, Harel
- Receptor Molecular Biology, Vol. 25, p. 366-428
The 2.1 Å Resolution Structure of Cyanopindolol-Bound β1-Adrenoceptor Identifies an Intramembrane Na+ Ion that Stabilises the Ligand-Free Receptor
journal, March 2014
- Miller-Gallacher, Jennifer L.; Nehmé, Rony; Warne, Tony
- PLoS ONE, Vol. 9, Issue 3
Delineating a Ca 2+ Binding Pocket within the Venus Flytrap Module of the Human Calcium-sensing Receptor
journal, September 2005
- Silve, Caroline; Petrel, Christophe; Leroy, Christine
- Journal of Biological Chemistry, Vol. 280, Issue 45
High-resolution crystal structure of human protease-activated receptor 1
journal, December 2012
- Zhang, Cheng; Srinivasan, Yoga; Arlow, Daniel H.
- Nature, Vol. 492, Issue 7429
Agonist-bound adenosine A2A receptor structures reveal common features of GPCR activation
journal, May 2011
- Lebon, Guillaume; Warne, Tony; Edwards, Patricia C.
- Nature, Vol. 474, Issue 7352
Improved prediction of protein side-chain conformations with SCWRL4
journal, December 2009
- Krivov, Georgii G.; Shapovalov, Maxim V.; Dunbrack, Roland L.
- Proteins: Structure, Function, and Bioinformatics, Vol. 77, Issue 4
Counting out to the flexibility of molecules
journal, November 2005
- Whiteley, Walter
- Physical Biology, Vol. 2, Issue 4
Novel Allosteric Modulators of G Protein-coupled Receptors
journal, June 2015
- Gentry, Patrick R.; Sexton, Patrick M.; Christopoulos, Arthur
- Journal of Biological Chemistry, Vol. 290, Issue 32
The Role of Ligands on the Equilibria Between Functional States of a G Protein-Coupled Receptor
journal, June 2013
- Kim, Tae Hun; Chung, Ka Young; Manglik, Aashish
- Journal of the American Chemical Society, Vol. 135, Issue 25
Molecular Dynamics Simulations of Phosphatidylcholine Membranes: A Comparative Force Field Study
journal, September 2012
- Piggot, Thomas J.; Piñeiro, Ángel; Khalid, Syma
- Journal of Chemical Theory and Computation, Vol. 8, Issue 11
Endogenous Allosteric Modulators of G Protein–Coupled Receptors
journal, February 2015
- van der Westhuizen, Emma T.; Valant, Celine; Sexton, Patrick M.
- Journal of Pharmacology and Experimental Therapeutics, Vol. 353, Issue 2
Modulation of GPCRs by monovalent cations and anions
journal, November 2014
- Strasser, Andrea; Wittmann, Hans-Joachim; Schneider, Erich H.
- Naunyn-Schmiedeberg's Archives of Pharmacology, Vol. 388, Issue 3
Allosteric Modulation of Family C G-Protein-Coupled Receptors: from Molecular Insights to Therapeutic Perspectives
journal, January 2011
- Urwyler, Stephan
- Pharmacological Reviews, Vol. 63, Issue 1
The role of dimer asymmetry and protomer dynamics in enzyme catalysis
journal, January 2017
- Kim, Tae Hun; Mehrabi, Pedram; Ren, Zhong
- Science, Vol. 355, Issue 6322
P-LINCS: A Parallel Linear Constraint Solver for Molecular Simulation
journal, December 2007
- Hess, Berk
- Journal of Chemical Theory and Computation, Vol. 4, Issue 1
Intracellular Transfer of Na+ in an Active-State G-Protein-Coupled Receptor
journal, January 2018
- Vickery, Owen N.; Carvalheda, Catarina A.; Zaidi, Saheem A.
- Structure, Vol. 26, Issue 1
Comparison of simple potential functions for simulating liquid water
journal, July 1983
- Jorgensen, William L.; Chandrasekhar, Jayaraman; Madura, Jeffry D.
- The Journal of Chemical Physics, Vol. 79, Issue 2
Allosteric modulation of A2A adenosine receptors by amiloride analogues and sodium ions
journal, September 2000
- Gao, Zhan-Guo; Ijzerman, Adriaan P.
- Biochemical Pharmacology, Vol. 60, Issue 5
A Leap-frog Algorithm for Stochastic Dynamics
journal, March 1988
- Van Gunsteren, W. F.; Berendsen, H. J. C.
- Molecular Simulation, Vol. 1, Issue 3
An Algorithm for Two-Dimensional Rigidity Percolation: The Pebble Game
journal, November 1997
- Jacobs, Donald J.; Hendrickson, Bruce
- Journal of Computational Physics, Vol. 137, Issue 2
Structural Insights into the Dynamic Process of β 2 -Adrenergic Receptor Signaling
journal, May 2015
- Manglik, Aashish; Kim, Tae Hun; Masureel, Matthieu
- Cell, Vol. 161, Issue 5
Structural Basis for Allosteric Regulation of GPCRs by Sodium Ions
journal, July 2012
- Liu, W.; Chun, E.; Thompson, A. A.
- Science, Vol. 337, Issue 6091
GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit
journal, February 2013
- Pronk, Sander; Páll, Szilárd; Schulz, Roland
- Bioinformatics, Vol. 29, Issue 7
All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins †
journal, April 1998
- MacKerell, A. D.; Bashford, D.; Bellott, M.
- The Journal of Physical Chemistry B, Vol. 102, Issue 18
Interaction of Mg2+ with the allosteric site of muscarinic M2 receptors
journal, April 1998
- Burgmer, Ulrike; Schulz, U.; Tränkle, Christian
- Naunyn-Schmiedeberg's Archives of Pharmacology, Vol. 357, Issue 4
Differential Effects of Mg 2+ and Other Divalent Cations on the Binding of Tritiated Opioid Ligands
journal, August 1992
- Rodriguez, F. D.; Bardaji, E.; Traynor, J. R.
- Journal of Neurochemistry, Vol. 59, Issue 2
Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types
journal, June 2010
- Klauda, Jeffery B.; Venable, Richard M.; Freites, J. Alfredo
- The Journal of Physical Chemistry B, Vol. 114, Issue 23
Biased Signaling Pathways in 2-Adrenergic Receptor Characterized by 19F-NMR
journal, January 2012
- Liu, J. J.; Horst, R.; Katritch, V.
- Science, Vol. 335, Issue 6072
LAMBADA and InflateGRO2: Efficient Membrane Alignment and Insertion of Membrane Proteins for Molecular Dynamics Simulations
journal, September 2012
- Schmidt, Thomas H.; Kandt, Christian
- Journal of Chemical Information and Modeling, Vol. 52, Issue 10
Differential allosteric modulation by amiloride analogues of agonist and antagonist binding at A1 and A3 adenosine receptors
journal, February 2003
- Gao, Zhan-Guo; Melman, Neli; Erdmann, Andreas
- Biochemical Pharmacology, Vol. 65, Issue 4
CHARMM-GUI Membrane Builder for Mixed Bilayers and Its Application to Yeast Membranes
journal, July 2009
- Jo, Sunhwan; Lim, Joseph B.; Klauda, Jeffery B.
- Biophysical Journal, Vol. 97, Issue 1
Effects of mono- and divalent ions on the binding of the adenosine analogue CGS 21680 to adenosine A2 receptors in rat striatum
journal, December 1992
- Johansson, Björn; Parkinson, Fiona E.; Fredholm, Bertil B.
- Biochemical Pharmacology, Vol. 44, Issue 12
Regulation of agonist binding to A2A adenosine receptors: Effects of guanine nucleotides (GDP[S] and GTP[S]) and Mg2+ ion
journal, December 1993
- Mazzoni, Maria R.; Martini, Claudia; Lucacchini, Antonio
- Biochimica et Biophysica Acta (BBA) - Molecular Cell Research, Vol. 1220, Issue 1
Eukaryotic G protein-coupled receptors as descendants of prokaryotic sodium-translocating rhodopsins
journal, October 2015
- Shalaeva, Daria N.; Galperin, Michael Y.; Mulkidjanian, Armen Y.
- Biology Direct, Vol. 10, Issue 1
Activation and allosteric modulation of a muscarinic acetylcholine receptor
journal, November 2013
- Kruse, Andrew C.; Ring, Aaron M.; Manglik, Aashish
- Nature, Vol. 504, Issue 7478
Isostatic Block and Hole Frameworks
journal, January 2013
- Finbow-Singh, Wendy; Whiteley, Walter
- SIAM Journal on Discrete Mathematics, Vol. 27, Issue 2
CHARMM-GUI: A web-based graphical user interface for CHARMM
journal, March 2008
- Jo, Sunhwan; Kim, Taehoon; Iyer, Vidyashankara G.
- Journal of Computational Chemistry, Vol. 29, Issue 11
Allosteric sodium in class A GPCR signaling
journal, May 2014
- Katritch, Vsevolod; Fenalti, Gustavo; Abola, Enrique E.
- Trends in Biochemical Sciences, Vol. 39, Issue 5
Extending the treatment of backbone energetics in protein force fields: Limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations
journal, August 2004
- Mackerell, Alexander D.; Feig, Michael; Brooks, Charles L.
- Journal of Computational Chemistry, Vol. 25, Issue 11
Particle mesh Ewald: An N ⋅log( N ) method for Ewald sums in large systems
journal, June 1993
- Darden, Tom; York, Darrin; Pedersen, Lee
- The Journal of Chemical Physics, Vol. 98, Issue 12
Molecular dynamics with coupling to an external bath
journal, October 1984
- Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.
- The Journal of Chemical Physics, Vol. 81, Issue 8
Activation of the A2A adenosine G-protein-coupled receptor by conformational selection
journal, May 2016
- Ye, Libin; Van Eps, Ned; Zimmer, Marco
- Nature, Vol. 533, Issue 7602
Evaluating conformational free energies: The colony energy and its application to the problem of loop prediction
journal, May 2002
- Xiang, Z.; Soto, C. S.; Honig, B.
- Proceedings of the National Academy of Sciences, Vol. 99, Issue 11
Identification of a Novel Extracellular Cation-sensing G-protein-coupled Receptor
journal, September 2005
- Pi, Min; Faber, Pieter; Ekema, George
- Journal of Biological Chemistry, Vol. 280, Issue 48
A comparison of chemical shift sensitivity of trifluoromethyl tags: optimizing resolution in 19F NMR studies of proteins
journal, March 2015
- Ye, Libin; Larda, Sacha Thierry; Frank Li, Yi Feng
- Journal of Biomolecular NMR, Vol. 62, Issue 1
Structure of an Agonist-Bound Human A2A Adenosine Receptor
journal, March 2011
- Xu, F.; Wu, H.; Katritch, V.
- Science, Vol. 332, Issue 6027
Algorithms for three-dimensional rigidity analysis and a first-order percolation transition
journal, October 2007
- Chubynsky, M. V.; Thorpe, M. F.
- Physical Review E, Vol. 76, Issue 4
A Gα s Carboxyl-Terminal Peptide Prevents G s Activation by the A 2A Adenosine Receptor
journal, July 2000
- Mazzoni, Maria R.; Taddei, Simone; Giusti, Laura
- Molecular Pharmacology, Vol. 58, Issue 1
Molecular control of δ-opioid receptor signalling
journal, January 2014
- Fenalti, Gustavo; Giguere, Patrick M.; Katritch, Vsevolod
- Nature, Vol. 506, Issue 7487
Kinetics of opiate receptor inactivation by sulfhydryl reagents: evidence for conformational change in presence of sodium ions.
journal, June 1975
- Simon, E. J.; Groth, J.
- Proceedings of the National Academy of Sciences, Vol. 72, Issue 6
Protein flexibility predictions using graph theory
journal, January 2001
- Jacobs, Donald J.; Rader, A. J.; Kuhn, Leslie A.
- Proteins: Structure, Function, and Genetics, Vol. 44, Issue 2
A smooth particle mesh Ewald method
journal, November 1995
- Essmann, Ulrich; Perera, Lalith; Berkowitz, Max L.
- The Journal of Chemical Physics, Vol. 103, Issue 19
Structure of the adenosine A2A receptor bound to an engineered G protein
journal, July 2016
- Carpenter, Byron; Nehmé, Rony; Warne, Tony
- Nature, Vol. 536, Issue 7614
Loop modeling: Sampling, filtering, and scoring
journal, January 2008
- Soto, Cinque S.; Fasnacht, Marc; Zhu, Jiang
- Proteins: Structure, Function, and Bioinformatics, Vol. 70, Issue 3
Implementation of the CHARMM Force Field in GROMACS: Analysis of Protein Stability Effects from Correction Maps, Virtual Interaction Sites, and Water Models
journal, January 2010
- Bjelkmar, Pär; Larsson, Per; Cuendet, Michel A.
- Journal of Chemical Theory and Computation, Vol. 6, Issue 2
VMD: Visual molecular dynamics
journal, February 1996
- Humphrey, William; Dalke, Andrew; Schulten, Klaus
- Journal of Molecular Graphics, Vol. 14, Issue 1
Improving the specificity of organophosphorus hydrolase to acephate by mutagenesis at its binding site: a computational study
journal, May 2021
- Badakhshan, Reza; Mohammadi, Mozafar; Farnoosh, Gholamreza
- Journal of Molecular Modeling, Vol. 27, Issue 6
Human aminolevulinate synthase structure reveals a eukaryotic-specific autoinhibitory loop regulating substrate binding and product release
journal, June 2020
- Bailey, Henry J.; Bezerra, Gustavo A.; Marcero, Jason R.
- Nature Communications, Vol. 11, Issue 1
Mechanism of pore opening in the calcium-activated chloride channel TMEM16A
journal, February 2021
- Lam, Andy K. M.; Dutzler, Raimund
- Nature Communications, Vol. 12, Issue 1
Molecular control of δ-opioid receptor signalling
text, January 2014
- M., Giguere, Patrick; Vsevolod, Katritch,; L., Roth, Bryan
- The University of North Carolina at Chapel Hill University Libraries
Allosteric sodium in class A GPCR signaling
text, January 2014
- Vsevolod, Katritch,; Vadim, Cherezov,; C., Stevens, Raymond
- The University of North Carolina at Chapel Hill University Libraries
Structural Insights into the Dynamic Process of β2-Adrenergic Receptor Signaling
journal, September 2015
- Manglik, Aashish; Kim, Tae Hun; Masureel, Matthieu
- Cell, Vol. 162, Issue 6
Works referencing / citing this record:
Allosteric modulation of G protein‐coupled receptors by amiloride and its derivatives. Perspectives for drug discovery?
journal, March 2020
- Massink, Arnault; Amelia, Tasia; Karamychev, Alex
- Medicinal Research Reviews, Vol. 40, Issue 2
Quantum Mechanical and Molecular Mechanics Modeling of Membrane-Embedded Rhodopsins
journal, September 2019
- Ryazantsev, Mikhail N.; Nikolaev, Dmitrii M.; Struts, Andrey V.
- The Journal of Membrane Biology, Vol. 252, Issue 4-5
Could the presence of sodium ion influence the accuracy and precision of the ligand-posing in the human A2A adenosine receptor orthosteric binding site using a molecular docking approach? Insights from Dockbench
journal, October 2018
- Margiotta, Enrico; Deganutti, Giuseppe; Moro, Stefano
- Journal of Computer-Aided Molecular Design, Vol. 32, Issue 12
GPCR drug discovery: integrating solution NMR data with crystal and cryo-EM structures
journal, November 2018
- Shimada, Ichio; Ueda, Takumi; Kofuku, Yutaka
- Nature Reviews Drug Discovery, Vol. 18, Issue 1
Conformational plasticity of ligand-bound and ternary GPCR complexes studied by 19F NMR of the β1-adrenergic receptor
journal, February 2020
- Frei, J. Niclas; Broadhurst, Richard W.; Bostock, Mark J.
- Nature Communications, Vol. 11, Issue 1
A 2A adenosine receptor functional states characterized by 19 F-NMR
journal, November 2018
- Sušac, Lukas; Eddy, Matthew T.; Didenko, Tatiana
- Proceedings of the National Academy of Sciences, Vol. 115, Issue 50
Ca 2+ allostery in PTH-receptor signaling
journal, February 2019
- White, Alex D.; Fang, Fei; Jean-Alphonse, Frédéric G.
- Proceedings of the National Academy of Sciences, Vol. 116, Issue 8
K-Ras G-domain binding with signaling lipid phosphatidylinositol (4,5)-phosphate (PIP2): membrane association, protein orientation, and function
journal, February 2019
- Cao, Shufen; Chung, Stacey; Kim, SoonJeung
- Journal of Biological Chemistry, Vol. 294, Issue 17
19F NMR as a versatile tool to study membrane protein structure and dynamics
journal, October 2019
- Rose-Sperling, Dania; Tran, Mai Anh; Lauth, Luca M.
- Biological Chemistry, Vol. 400, Issue 10
Simultaneous Ligand and Receptor Tracking through NMR Spectroscopy Enabled by Distinct 19F Labels
journal, July 2019
- Simmons, Jeffrey R.; Murza, Alexandre; Lumsden, Michael D.
- International Journal of Molecular Sciences, Vol. 20, Issue 15
Utilization of Biased G Protein-Coupled Receptor Signaling towards Development of Safer and Personalized Therapeutics
journal, May 2019
- Ilter, Metehan; Mansoor, Samman; Sensoy, Ozge
- Molecules, Vol. 24, Issue 11
Common activation mechanism of class A GPCRs
journal, December 2019
- Zhou, Qingtong; Yang, Dehua; Wu, Meng
- eLife, Vol. 8
Conformational plasticity of ligand-bound and ternary GPCR complexes studied by 19F NMR of the β1-adrenergic receptor.
text, January 2020
- Frei, J. Niclas; Broadhurst, Bill; Bostock, Mark J.
- Apollo - University of Cambridge Repository