Structural Mechanism of N-Methyl-D-Aspartate Receptor Type 1 Partial Agonism

PLoS ONE

Volumn 7, Issue 10, 2012, Pages

  Ylilauri, Mikko ^a   Pentikäinen, Olli T ^a  

^a UNIVERSITY OF JYVÄSKYLÄ   (Finland)

Author keywords

[No Author keywords available]

Indexed keywords

N METHYL DEXTRO ASPARTIC ACID RECEPTOR 1;

ARTICLE; CONTROLLED STUDY; CRYSTAL STRUCTURE; ENERGY TRANSFER; FORCE; LIGAND BINDING DOMAIN; MATHEMATICAL ANALYSIS; MOLECULAR DYNAMICS; MOLECULAR MECHANICS; PROTEIN CONFORMATION; PROTEIN DOMAIN; PROTEIN STRUCTURE;

CRYSTALLOGRAPHY; CYCLOSERINE; GLYCINE; LIGANDS; MOLECULAR CONFORMATION; MOLECULAR DYNAMICS SIMULATION; PROTEIN BINDING; PROTEIN STRUCTURE, TERTIARY; RECEPTORS, N-METHYL-D-ASPARTATE;

EID: 84867497048     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0047604     Document Type: Article

References (53)

1. Traynelis SF, Wollmuth LP, McBain CJ, Menniti FS, Vance KM, et al. (2010) Glutamate receptor ion channels: structure, regulation, and function. Pharmacol Rev 62: 405-496.
2. Lisman JE, McIntyre CC, (2001) Synaptic plasticity: a molecular memory switch. Curr Biol 11: R788-91.
3. Nakazawa K, Quirk MC, Chitwood RA, Watanabe M, Yeckel MF, et al. (2002) Requirement for hippocampal CA3 NMDA receptors in associative memory recall. Science 297: 211-218.
4. Citri A, Malenka RC, (2008) Synaptic plasticity: multiple forms, functions, and mechanisms. Neuropsychopharmacology 33: 18-41.
5. Kalia LV, Kalia SK, Salter MW, (2008) NMDA receptors in clinical neurology: excitatory times ahead. Lancet Neurol 7: 742-755.
6. Waxman EA, Lynch DR, (2005) N-methyl-D-aspartate receptor subtypes: multiple roles in excitotoxicity and neurological disease. Neuroscientist 11: 37-49.
7. Sobolevsky AI, Rosconi MP, Gouaux E, (2009) X-ray structure, symmetry and mechanism of an AMPA-subtype glutamate receptor. Nature 462: 745-756.
8. Paoletti P, (2011) Molecular basis of NMDA receptor functional diversity. Eur J Neurosci 33: 1351-1365.
9. Armstrong N, Sun Y, Chen GQ, Gouaux E, (1998) Structure of a glutamate-receptor ligand-binding core in complex with kainate. Nature 395: 913-917.
10. Kuusinen A, Arvola M, Keinänen K, (1995) Molecular dissection of the agonist binding site of an AMPA receptor. EMBO J 14: 6327-6332.
11. Furukawa H, Gouaux E, (2003) Mechanisms of activation, inhibition and specificity: crystal structures of the NMDA receptor NR1 ligand-binding core. EMBO J 22: 2873-2885.
12. Inanobe A, Furukawa H, Gouaux E, (2005) Mechanism of partial agonist action at the NR1 subunit of NMDA receptors. Neuron 47: 71-84.
13. Armstrong N, Gouaux E, (2000) Mechanisms for activation and antagonism of an AMPA-sensitive glutamate receptor: crystal structures of the GluR2 ligand binding core. Neuron 28: 165-181.
14. Mayer ML, (2005) Crystal structures of the GluR5 and GluR6 ligand binding cores: molecular mechanisms underlying kainate receptor selectivity. Neuron 45: 539-552.
15. Furukawa H, Singh SK, Mancusso R, Gouaux E, (2005) Subunit arrangement and function in NMDA receptors. Nature 438: 185-192.
16. Frydenvang K, Lash LL, Naur P, Postila PA, Pickering DS, et al. (2009) Full domain closure of the ligand-binding core of the ionotropic glutamate receptor iGluR5 induced by the high affinity agonist dysiherbaine and the functional antagonist 8,9-dideoxyneodysiherbaine. J Biol Chem 284: 14219-14229.
17. Jin R, Banke TG, Mayer ML, Traynelis SF, Gouaux E, (2003) Structural basis for partial agonist action at ionotropic glutamate receptors. Nat Neurosci 6: 803-810.
18. Rambhadran A, Gonzalez J, Jayaraman V, (2011) Conformational changes at the agonist binding domain of the N-methyl-D-aspartic acid receptor. J Biol Chem 286: 16953-16957.
19. Chen PE, Geballe MT, Katz E, Erreger K, Livesey MR, et al. (2008) Modulation of glycine potency in rat recombinant NMDA receptors containing chimeric NR2A/2D subunits expressed in Xenopus laevis oocytes. J Physiol 586: 227-245.
20. Kussius CL, Popescu GK, (2009) Kinetic basis of partial agonism at NMDA receptors. Nat Neurosci 12: 1114-1120.
21. Ramanoudjame G, Du M, Mankiewicz KA, Jayaraman V, (2006) Allosteric mechanism in AMPA receptors: a FRET-based investigation of conformational changes. Proc Natl Acad Sci U S A 103: 10473-10478.
22. Kaye SL, Sansom MSP, Biggin PC, (2006) Molecular dynamics simulations of the ligand-binding domain of an N-methyl-D-aspartate receptor. J Biol Chem 281: 12736-12742.
23. Postila PA, Swanson GT, Pentikäinen OT, (2010) Exploring kainate receptor pharmacology using molecular dynamics simulations. Neuropharmacology 58: 515-527.
24. Vijayan R, Sahai MA, Czajkowski T, Biggin PC, (2010) A comparative analysis of the role of water in the binding pockets of ionotropic glutamate receptors. Phys Chem Chem Phys 12: 14057-14066.
25. Lash-Van Wyhe LL, Postila PA, Tsubone K, Sasaki M, Pentikäinen OT, et al. (2010) Pharmacological activity of C10-substituted analogs of the high-affinity kainate receptor agonist dysiherbaine. Neuropharmacology 58: 640-649.
26. Pentikäinen U, Settimo L, Johnson MS, Pentikäinen OT, (2006) Subtype selectivity and flexibility of ionotropic glutamate receptors upon antagonist ligand binding. Org Biomol Chem 4: 1058-1070.
27. Lau AY, Roux B, (2007) The free energy landscapes governing conformational changes in a glutamate receptor ligand-binding domain. Structure 15: 1203-1214.
28. Ogden KK, Traynelis SF, (2011) New advances in NMDA receptor pharmacology. Trends Pharmacol Sci 32: 726-733.
29. Priestley T, Marshall GR, Hill RG, Kemp JA, (1998) L-687,414, a low efficacy NMDA receptor glycine site partial agonist in vitro, does not prevent hippocampal LTP in vivo at plasma levels known to be neuroprotective. Br J Pharmacol 124: 1767-1773.
30. Wood PL, Mahmood SA, Moskal JR, (2008) Antinociceptive action of GLYX-13: an N-methyl-D-aspartate receptor glycine site partial agonist. Neuroreport 19: 1059-1061.
31. Urwyler S, Floersheim P, Roy BL, Koller M, (2009) Drug design, in vitro pharmacology, and structure-activity relationships of 3-acylamino-2-aminopropionic acid derivatives, a novel class of partial agonists at the glycine site on the N-methyl-D-aspartate (NMDA) receptor complex. J Med Chem 52: 5093-5107.
32. Moskal JR, Burgdorf J, Kroes RA, Brudzynski SM, Panksepp J, (2011) A novel NMDA receptor glycine-site partial agonist, GLYX-13, has therapeutic potential for the treatment of autism. Neurosci Biobehav Rev 35: 1982-1988.
33. Banke TG, Traynelis SF, (2003) Activation of NR1/NR2B NMDA receptors. Nat Neurosci 6: 144-152.
34. Moretti L, Pentikäinen OT, Settimo L, Johnson MS, (2004) Model structures of the N-methyl-D-aspartate receptor subunit NR1 explain the molecular recognition of agonist and antagonist ligands. J Struct Biol 145: 205-215.
35. Dravid SM, Burger PB, Prakash A, Geballe MT, Yadav R, et al. (2010) Structural determinants of D-cycloserine efficacy at the NR1/NR2C NMDA receptors. J Neurosci 30: 2741-2754.
36. Postila PA, Ylilauri M, Pentikainen OT, (2011) Full and Partial Agonism of Ionotropic Glutamate Receptors Indicated by Molecular Dynamics Simulations. J Chem Inf Model 51: 1037-1047.
37. Talukder I, Wollmuth LP, (2011) Local constraints in either the GluN1 or GluN2 subunit equally impair NMDA receptor pore opening. J Gen Physiol 138: 179-194.
38. Tsui V, Case DA (2000-2001) Theory and applications of the generalized Born solvation model in macromolecular simulations. Biopolymers 56: 275-291.
39. Kollman PA, Massova I, Reyes C, Kuhn B, Huo S, et al. (2000) Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. Acc Chem Res 33: 889-897.
40. Priestley T, Laughton P, Myers J, Le Bourdellés B, Kerby J, et al. (1995) Pharmacological properties of recombinant human N-methyl-D-aspartate receptors comprising NR1a/NR2A and NR1a/NR2B subunit assemblies expressed in permanently transfected mouse fibroblast cells. Mol Pharmacol 48: 841-848.
41. Moriyoshi K, Masu M, Ishii T, Shigemoto R, Mizuno N, et al. (1991) Molecular cloning and characterization of the rat NMDA receptor. Nature 354: 31-37.
42. Lehtonen JV, Still D, Rantanen V, Ekholm J, Björklund D, et al. (2004) BODIL: a molecular modeling environment for structure-function analysis and drug design. J Comput Aided Mol Des 18: 401-419.
43. Petrey D, Xiang Z, Tang CL, Xie L, Gimpelev M, et al. (2003) Using multiple structure alignments, fast model building, and energetic analysis in fold recognition and homology modeling. Proteins 53 (Suppl 6):: 430-435.
44. Bayly CI, Cieplak P, Cornell WD, Kollman PA, (1993) A well-behaved electrostatic potential based method using charge restrains for deriving atomic charges: The RESP model. J Phys Chem 97: 10269.
45. Wang H, Liu Y, Huai Q, Cai J, Zoraghi R, et al. (2006) Multiple conformations of phosphodiesterase-5: implications for enzyme function and drug development. J Biol Chem 281: 21469-21479.
46. Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, et al. (2005) Scalable molecular dynamics with NAMD. J Comput Chem 26: 1781-1802.
47. Feller SE, Zhang Y, Pastor RW, (1995) Constant pressure molecular dynamics simulation: The Langevin piston method. J Chem Phys 103: 4613-4621.
48. Schlick T, Skeel RD, Brunger AT, Kalé LV, Board JAJ, et al. (1999) Algorithmic Challenges in Computational Molecular Biophysics. J Comput Phys 151: 9-48.
49. Darden T, York D, Pedersen L, (1993) Particle mesh Ewald: An W Log(N) method for Ewald sums in large systems. J Chem Phys 98: 10089-10092.
50. Ryckaert J, Ciccotti G, Berendsen HJ, (1977) Numerical Integration of the Cartesian Equations of motion of a system with constraints: Molecular dynamics of n-alkanes. J Comput Phys 23: 327.
51. Case DA, Cheatham TE3, Darden T, Gohlke H, Luo R, et al (2005) The Amber biomolecular simulation programs. J Comput Chem 26: 1668-1688.
52. Kraulis P, (1991) MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures. J Appl Crystallogr 24: 946-950.
53. Merritt EA, Bacon DJ, (1997) Raster3D: photorealistic molecular graphics. Methods Enzymol 277: 505-524.