Induced effects of sodium ions on dopaminergic G-protein coupled receptors

PLoS Computational Biology

Volumn 6, Issue 8, 2010, Pages

  Selent, Jana ^a   Sanz, Ferran ^a   Pastor, Manuel ^a   de Fabritiis, Gianni ^a  

^a UNIVERSITAT POMPEU FABRA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING SITES; METAL IONS; MOLECULAR DYNAMICS; PROTEINS; SIGNAL TRANSDUCTION; SODIUM;

ALLOSTERIC MODULATION; ALLOSTERIC SITE; CLASS A; COMPLEX SIGNAL; CONFORMATIONAL CHANGE; G PROTEIN COUPLED RECEPTORS; HUMAN GENOMES; LIGAND BINDING; SIGNAL TRANSDUCTION PATHWAYS; SODIUM IONS;

MODULATION;

BETA 2 ADRENERGIC RECEPTOR; DOPAMINE 2 RECEPTOR; G PROTEIN COUPLED RECEPTOR; MEMBRANE PROTEIN; SODIUM ION;

ARTICLE; BINDING SITE; CONFORMATIONAL TRANSITION; CONTROLLED STUDY; CRYSTALLIZATION; EXTRACELLULAR SPACE; MOLECULAR DYNAMICS; PROTEIN CONFORMATION; PROTEIN FUNCTION; PROTEIN LOCALIZATION; RECEPTOR AFFINITY; RECEPTOR BINDING; SIGNAL TRANSDUCTION; STRUCTURE ANALYSIS;

EID: 78049415021     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1000884     Document Type: Article

References (39)

1. Cherezov V, Rosenbaum DM, Hanson MA, Rasmussen SG, Thian FS, et al. (2007) High-resolution crystal structure of an engineered human beta2- adrenergic G protein-coupled receptor. Science 318: 1258-1265.
2. Hanson MA, Cherezov V, Griffith MT, Roth CB, Jaakola V, et al. (2008) A specific cholesterol binding site is established by the 2.8 A structure of the human beta2-adrenergic receptor. Structure 16: 897-905.
3. Warne T, Serrano-Vega MJ, Baker JG, Moukhametzianov R, Edwards PC, et al. (2008) Structure of a beta1-adrenergic G-protein-coupled receptor. Nature 454: 486-491.
4. Jaakola V, Griffith MT, Hanson MA, Cherezov V, Chien EYT, et al. (2008) The 2.6 angstrom crystal structure of a human A2A adenosine receptor bound to an antagonist. Science 322: 1211-1217.
5. Palczewski K, Kumasaka T, Hori T, Behnke CA, Motoshima H, et al. (2000) Crystal structure of rhodopsin: A G protein-coupled receptor. Science 289: 739-745.
6. Granier S, Kim S, Fung JJ, Bokoch MP, Parnot C (2009) FRET-based measurement of GPCR conformational changes. Methods Mol Biol 552: 253-268.
7. Hoffmann C, Zürn A, Bünemann M, Lohse MJ (2008) Conformational changes in G-protein-coupled receptors-the quest for functionally selective conformations is open. Br J Pharmacol 153 Suppl 1: 358-366.
8. Ericksen SS, Cummings DF, Weinstein H, Schetz JA (2009) Ligand Selectivity of D2 Dopamine Receptors Is Modulated by Changes in Local Dynamics Produced by Sodium Binding. J Pharmacol Exp Ther 328: 40-54.
9. Schetz JA (2005) Allosteric modulation of dopamine receptors. Mini Rev Med Chem 5: 555-561.
10. Neve KA, Cox BA, Henningsen RA, Spanoyannis A, Neve RL (1991) Pivotal role for aspartate-80 in the regulation of dopamine D2 receptor affinity for drugs and inhibition of adenylyl cyclase. Mol Pharmacol 39: 733-739.
11. Javitch JA, Ballesteros JA, Chen J, Chiappa V, Simpson MM (1999) Electrostatic and aromatic microdomains within the binding-site crevice of the D2 receptor: contributions of the second membrane-spanning segment. Biochemistry 38: 7961-7968.
12. Ceresa B, Limbird L (1994) Mutation of an aspartate residue highly conserved among G-protein- coupled receptors results in nonreciprocal disruption of alpha 2- adrenergic receptor-G-protein interactions. A negative charge at amino acid residue 79 forecasts alpha 2A-adrenergic receptor sensitivity to allosteric modulation by monovalent cations and fully effective receptor/G-protein coupling. J Biol Chem 269: 29557-29564.
13. Neve K (1991) Regulation of dopamine D2 receptors by sodium and pH. Mol Pharmacol 39: 570-578.
14. Ballesteros J, Weinstein H (1995) Integrated methods for the construction of three dimensional models and computational probing of structure function relations in G-protein coupled receptor. Methods Neurosci 25: 366-428.
15. Schetz JA, Sibley DR (2001) The binding-site crevice of the D4 dopamine receptor is coupled to three distinct sites of allosteric modulation. J Pharmacol Exp Ther 296: 359-363.
16. Neve KA, Cumbay MG, Thompson KR, Yang R, Buck DC, et al. (2001) Modeling and Mutational Analysis of a Putative Sodium-Binding Pocket on the Dopamine D2 Receptor. Mol Pharmacol 60: 373-381.
17. Laio A, Parrinello M (2002) Escaping free-energy minima. Proc Natl Acad Sci U S A 99: 12562-12566.
18. Laio A, Gervasio FL (2008) Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science. Rep Prog Phys 71: 126601.
19. Scheerer P, Park JH, Hildebrand PW, Kim YJ, Krauss N, et al. (2008) Crystal structure of opsin in its G-protein-interacting conformation. Nature 455: 497-502.
20. Park JH, Scheerer P, Hofmann KP, Choe H, Ernst OP (2008) Crystal structure of the ligand-free G-protein-coupled receptor opsin. Nature 454: 183-187.
21. Ruprecht JJ, Mielke T, Vogel R, Villa C, Schertler GFX (2004) Electron crystallography reveals the structure of metarhodopsin I. EMBO J 23: 3609-3620.
22. Yao X, Parnot C, Deupi X, Ratnala VRP, Swaminath G, et al. (2006) Coupling ligand structure to specific conformational switches in the beta2-adrenoceptor. Nat Chem Biol 2: 417-422.
23. Swaminath G, Deupi X, Lee TW, Zhu W, Thian FS, et al. (2005) Probing the beta2 adrenoceptor binding site with catechol reveals differences in binding and activation by agonists and partial agonists. J Biol Chem 280: 22165-22171.
24. Mobarec JC, Sanchez R, Filizola M (2009) Modern Homology Modeling of GProtein Coupled Receptors: Which Structural Template to Use? J Med Chem 52: 5207-5216.
25. Forrest LR, Tang CL, Honig B (2006) On the Accuracy of Homology Modeling and Sequence Alignment Methods Applied to Membrane Proteins. Biophys J 91: 508-517.
26. MacKerell, Bashford D, Bellott, Dunbrack, Evanseck JD, et al. (1998) All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins{. J Phys Chem B 102: 3586-3616.
27. Motulsky HJ, Insel PA (1983) Influence of sodium on the alpha 2-adrenergic receptor system of human platelets. Role for intraplatelet sodium in receptor binding. J Biol Chem 258: 3913-3919.
28. Huber T, Menon S, Sakmar TP (2008) Structural Basis for Ligand Binding and Specificity in Adrenergic Receptors: Implications for GPCR-Targeted Drug Discovery{. Biochemistry 47: 11013-11023.
29. Dror RO, Arlow DH, Borhani DW, Jensen MØ, Piana S, et al. (2009) Identification of two distinct inactive conformations of the beta2-adrenergic receptor reconciles structural and biochemical observations. Proc Natl Acad Sci U S A 106: 4689-4694.
30. http://www.vimeo.com/7900216.
31. Bhattacharya S, Hall SE, Vaidehi N (2008) Agonist-induced conformational changes in bovine rhodopsin: insight into activation of G-protein-coupled receptors. J Mol Biol 382: 539-555.
32. Bonomi M, Branduardi D, Bussi G, Camilloni C, Provasi D, et al. (2009) PLUMED: A portable plugin for free-energy calculations with molecular dynamics. Comput Phys Commun 180: 1961-1972.
33. Wilson MH, Highfield HA, Limbird LE (2001) The role of a conserved intertransmembrane domain interface in regulating alpha(2a)-adrenergic receptor conformational stability and cell-surface turnover. Mol Pharmacol 59: 929-938.
34. Selent J, López L, Sanz F, Pastor M (2008) Multi-receptor binding profile of clozapine and olanzapine: a structural study based on the new beta2 adrenergic receptor template. Chem Med Chem 3: 1194-1198.
35. Humphrey W, Dalke A, Schulten K (1996) VMD: visual molecular dynamics. J Mol Graph 14: 33-38, 27-28.
36. Harvey MJ, Giupponi G, De Fabritiis G (2009) ACEMD: Accelerating Biomolecular Dynamics in the Microsecond Time Scale. J Chem Theory Comput 5: 1632-1639.
37. Harvey MJ, De Fabritiis G (2009) An Implementation of the Smooth Particle Mesh Ewald Method on GPU Hardware. J Chem Theory Comput 5: 2371-2377.
38. Buch I, Harvey MJ, Giorgino T, Anderson DP, De Fabritiis G (2010) Highthroughput all-atom molecular dynamics simulations using distributed computing. J Chem Inf and Mod 50: 397-403.
39. Giupponi G, Harvey MJ, De Fabritiis G (2008) The impact of accelerator processors for high-throughput molecular modeling and simulation. Drug Discov Today 13: 1052-1058.