Skip to main content
PMC home page
Biophysical Journal logoLink to Biophysical Journal
. 1999 Oct;77(4):1914–1926. doi: 10.1016/S0006-3495(99)77033-5

Intersegment hydrogen bonds as possible structural determinants of the N/Q/R site in glutamate receptors.

D B Tikhonov 1, B S Zhorov 1, L G Magazanik 1
PMCID: PMC1300473  PMID: 10512812

Abstract

Specific electrophysiological and pharmacological properties of ionic channels in NMDA, AMPA, and kainate subtypes of ionotropic glutamate receptors (GluRs) are determined by the Asn (N), Gln (Q), and Arg (R) residues located at homologous positions of the pore-lining M2 segments (the N/Q/R site). Presumably, the N/Q/R site is located at the apex of the reentrant membrane loop and forms the narrowest constriction of the pore. Although the shorter Asn residues are expected to protrude in the pore to a lesser extent than the longer Gln residues, the effective dimension of the NMDA channel (corresponding to the size of the largest permeant organic cation) is, surprisingly, smaller than that of the AMPA channel. To explain this paradox, we propose that the N/Q/R residues form macrocyclic structures (rings) stabilized by H-bonds between a NH(2) group in the side chain of a given M2 segment and a C==O group of the main chain in the adjacent M2 segment. Using Monte Carlo minimization, we have explored conformational properties of the rings. In the Asn, but not in the Gln ring, the side-chain oxygens protruding into the pore may facilitate ion permeation and accept H-bonds from the blocking drugs. In this way, the model explains different electrophysiological and pharmacological properties of NMDA and non-NMDA GluR channels. The ring of H-bonded polar residues at the pore narrowing resembles the ring of four Thr(75) residues observed in the crystallographic structure of the KcsA K(+) channel.

Full Text

The Full Text of this article is available as a PDF (689.4 KB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Antonov S. M., Johnson J. W., Lukomskaya N. Y., Potapyeva N. N., Gmiro V. E., Magazanik L. G. Novel adamantane derivatives act as blockers of open ligand-gated channels and as anticonvulsants. Mol Pharmacol. 1995 Mar;47(3):558–567. [PubMed] [Google Scholar]
  2. Bennett J. A., Dingledine R. Topology profile for a glutamate receptor: three transmembrane domains and a channel-lining reentrant membrane loop. Neuron. 1995 Feb;14(2):373–384. doi: 10.1016/0896-6273(95)90293-7. [DOI] [PubMed] [Google Scholar]
  3. Blaschke M., Keller B. U., Rivosecchi R., Hollmann M., Heinemann S., Konnerth A. A single amino acid determines the subunit-specific spider toxin block of alpha-amino-3-hydroxy-5-methylisoxazole-4-propionate/kainate receptor channels. Proc Natl Acad Sci U S A. 1993 Jul 15;90(14):6528–6532. doi: 10.1073/pnas.90.14.6528. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Brackley P. T., Bell D. R., Choi S. K., Nakanishi K., Usherwood P. N. Selective antagonism of native and cloned kainate and NMDA receptors by polyamine-containing toxins. J Pharmacol Exp Ther. 1993 Sep;266(3):1573–1580. [PubMed] [Google Scholar]
  5. Brovtsyna N. B., Tikhonov D. B., Gorbunova O. B., Gmiro V. E., Serduk S. E., Lukomskaya N. Y., Magazanik L. G., Zhorov B. S. Architecture of the neuronal nicotinic acetylcholine receptor ion channel at the binding site of bis-ammonium blockers. J Membr Biol. 1996 Jul;152(1):77–87. doi: 10.1007/s002329900087. [DOI] [PubMed] [Google Scholar]
  6. Burnashev N., Monyer H., Seeburg P. H., Sakmann B. Divalent ion permeability of AMPA receptor channels is dominated by the edited form of a single subunit. Neuron. 1992 Jan;8(1):189–198. doi: 10.1016/0896-6273(92)90120-3. [DOI] [PubMed] [Google Scholar]
  7. Burnashev N., Schoepfer R., Monyer H., Ruppersberg J. P., Günther W., Seeburg P. H., Sakmann B. Control by asparagine residues of calcium permeability and magnesium blockade in the NMDA receptor. Science. 1992 Sep 4;257(5075):1415–1419. doi: 10.1126/science.1382314. [DOI] [PubMed] [Google Scholar]
  8. Burnashev N., Villarroel A., Sakmann B. Dimensions and ion selectivity of recombinant AMPA and kainate receptor channels and their dependence on Q/R site residues. J Physiol. 1996 Oct 1;496(Pt 1):165–173. doi: 10.1113/jphysiol.1996.sp021674. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Burnashev N., Zhou Z., Neher E., Sakmann B. Fractional calcium currents through recombinant GluR channels of the NMDA, AMPA and kainate receptor subtypes. J Physiol. 1995 Jun 1;485(Pt 2):403–418. doi: 10.1113/jphysiol.1995.sp020738. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Campos-Ortega J. A. Numb diverts notch pathway off the tramtrack. Neuron. 1996 Jul;17(1):1–4. doi: 10.1016/s0896-6273(00)80274-3. [DOI] [PubMed] [Google Scholar]
  11. Dingledine R., Hume R. I., Heinemann S. F. Structural determinants of barium permeation and rectification in non-NMDA glutamate receptor channels. J Neurosci. 1992 Oct;12(10):4080–4087. doi: 10.1523/JNEUROSCI.12-10-04080.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Doyle D. A., Morais Cabral J., Pfuetzner R. A., Kuo A., Gulbis J. M., Cohen S. L., Chait B. T., MacKinnon R. The structure of the potassium channel: molecular basis of K+ conduction and selectivity. Science. 1998 Apr 3;280(5360):69–77. doi: 10.1126/science.280.5360.69. [DOI] [PubMed] [Google Scholar]
  13. Ferrer-Montiel A. V., Merino J. M., Planells-Cases R., Sun W., Montal M. Structural determinants of the blocker binding site in glutamate and NMDA receptor channels. Neuropharmacology. 1998;37(2):139–147. doi: 10.1016/s0028-3908(98)00007-0. [DOI] [PubMed] [Google Scholar]
  14. Ferrer-Montiel A. V., Montal M. Pentameric subunit stoichiometry of a neuronal glutamate receptor. Proc Natl Acad Sci U S A. 1996 Apr 2;93(7):2741–2744. doi: 10.1073/pnas.93.7.2741. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Ferrer-Montiel A. V., Sun W., Montal M. A single tryptophan on M2 of glutamate receptor channels confers high permeability to divalent cations. Biophys J. 1996 Aug;71(2):749–758. doi: 10.1016/S0006-3495(96)79274-3. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Ferrer-Montiel A. V., Sun W., Montal M. Molecular design of the N-methyl-D-aspartate receptor binding site for phencyclidine and dizolcipine. Proc Natl Acad Sci U S A. 1995 Aug 15;92(17):8021–8025. doi: 10.1073/pnas.92.17.8021. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Galzi J. L., Changeux J. P. Neuronal nicotinic receptors: molecular organization and regulations. Neuropharmacology. 1995 Jun;34(6):563–582. doi: 10.1016/0028-3908(95)00034-4. [DOI] [PubMed] [Google Scholar]
  18. Geiger J. R., Melcher T., Koh D. S., Sakmann B., Seeburg P. H., Jonas P., Monyer H. Relative abundance of subunit mRNAs determines gating and Ca2+ permeability of AMPA receptors in principal neurons and interneurons in rat CNS. Neuron. 1995 Jul;15(1):193–204. doi: 10.1016/0896-6273(95)90076-4. [DOI] [PubMed] [Google Scholar]
  19. Herlitze S., Raditsch M., Ruppersberg J. P., Jahn W., Monyer H., Schoepfer R., Witzemann V. Argiotoxin detects molecular differences in AMPA receptor channels. Neuron. 1993 Jun;10(6):1131–1140. doi: 10.1016/0896-6273(93)90061-u. [DOI] [PubMed] [Google Scholar]
  20. Hollmann M., Heinemann S. Cloned glutamate receptors. Annu Rev Neurosci. 1994;17:31–108. doi: 10.1146/annurev.ne.17.030194.000335. [DOI] [PubMed] [Google Scholar]
  21. Hollmann M., Maron C., Heinemann S. N-glycosylation site tagging suggests a three transmembrane domain topology for the glutamate receptor GluR1. Neuron. 1994 Dec;13(6):1331–1343. doi: 10.1016/0896-6273(94)90419-7. [DOI] [PubMed] [Google Scholar]
  22. Kashiwagi K., Pahk A. J., Masuko T., Igarashi K., Williams K. Block and modulation of N-methyl-D-aspartate receptors by polyamines and protons: role of amino acid residues in the transmembrane and pore-forming regions of NR1 and NR2 subunits. Mol Pharmacol. 1997 Oct;52(4):701–713. doi: 10.1124/mol.52.4.701. [DOI] [PubMed] [Google Scholar]
  23. Keinänen K., Wisden W., Sommer B., Werner P., Herb A., Verdoorn T. A., Sakmann B., Seeburg P. H. A family of AMPA-selective glutamate receptors. Science. 1990 Aug 3;249(4968):556–560. doi: 10.1126/science.2166337. [DOI] [PubMed] [Google Scholar]
  24. Koh D. S., Geiger J. R., Jonas P., Sakmann B. Ca(2+)-permeable AMPA and NMDA receptor channels in basket cells of rat hippocampal dentate gyrus. J Physiol. 1995 Jun 1;485(Pt 2):383–402. doi: 10.1113/jphysiol.1995.sp020737. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Koradi R., Billeter M., Wüthrich K. MOLMOL: a program for display and analysis of macromolecular structures. J Mol Graph. 1996 Feb;14(1):51-5, 29-32. doi: 10.1016/0263-7855(96)00009-4. [DOI] [PubMed] [Google Scholar]
  26. Köhler M., Burnashev N., Sakmann B., Seeburg P. H. Determinants of Ca2+ permeability in both TM1 and TM2 of high affinity kainate receptor channels: diversity by RNA editing. Neuron. 1993 Mar;10(3):491–500. doi: 10.1016/0896-6273(93)90336-p. [DOI] [PubMed] [Google Scholar]
  27. Laube B., Kuhse J., Betz H. Evidence for a tetrameric structure of recombinant NMDA receptors. J Neurosci. 1998 Apr 15;18(8):2954–2961. doi: 10.1523/JNEUROSCI.18-08-02954.1998. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Lyle T. A., Magill C. A., Britcher S. F., Denny G. H., Thompson W. J., Murphy J. S., Knight A. R., Kemp J. A., Marshall G. R., Middlemiss D. N. Structure and activity of hydrogenated derivatives of (+)-5-methyl-10,11-dihydro-5H-dibenzo[a,d]cyclohepten-5,10-imine (MK-801). J Med Chem. 1990 Mar;33(3):1047–1052. doi: 10.1021/jm00165a026. [DOI] [PubMed] [Google Scholar]
  29. Magazanik L. G., Buldakova S. L., Samoilova M. V., Gmiro V. E., Mellor I. R., Usherwood P. N. Block of open channels of recombinant AMPA receptors and native AMPA/kainate receptors by adamantane derivatives. J Physiol. 1997 Dec 15;505(Pt 3):655–663. doi: 10.1111/j.1469-7793.1997.655ba.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Manallack D. T., Wong M. G., Costa M., Andrews P. R., Beart P. M. Receptor site topographies for phencyclidine-like and sigma drugs: predictions from quantitative conformational, electrostatic potential, and radioreceptor analyses. Mol Pharmacol. 1988 Dec;34(6):863–879. [PubMed] [Google Scholar]
  31. Mano I., Teichberg V. I. A tetrameric subunit stoichiometry for a glutamate receptor-channel complex. Neuroreport. 1998 Jan 26;9(2):327–331. doi: 10.1097/00001756-199801260-00027. [DOI] [PubMed] [Google Scholar]
  32. Mayer M. L., Westbrook G. L. Permeation and block of N-methyl-D-aspartic acid receptor channels by divalent cations in mouse cultured central neurones. J Physiol. 1987 Dec;394:501–527. doi: 10.1113/jphysiol.1987.sp016883. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Mori H., Masaki H., Yamakura T., Mishina M. Identification by mutagenesis of a Mg(2+)-block site of the NMDA receptor channel. Nature. 1992 Aug 20;358(6388):673–675. doi: 10.1038/358673a0. [DOI] [PubMed] [Google Scholar]
  34. Rosenmund C., Stern-Bach Y., Stevens C. F. The tetrameric structure of a glutamate receptor channel. Science. 1998 Jun 5;280(5369):1596–1599. doi: 10.1126/science.280.5369.1596. [DOI] [PubMed] [Google Scholar]
  35. Ruppersberg J. P., Mosbacher J., Günther W., Schoepfer R., Fakler B. Studying block in cloned N-methyl-D-aspartate (NMDA) receptors. Biochem Pharmacol. 1993 Dec 3;46(11):1877–1885. doi: 10.1016/0006-2952(93)90627-9. [DOI] [PubMed] [Google Scholar]
  36. Sankararamakrishnan R., Sansom M. S. Water-mediated conformational transitions in nicotinic receptor M2 helix bundles: a molecular dynamics study. FEBS Lett. 1995 Dec 27;377(3):377–382. doi: 10.1016/0014-5793(95)01376-8. [DOI] [PubMed] [Google Scholar]
  37. Seeburg P. H. The TiPS/TINS lecture: the molecular biology of mammalian glutamate receptor channels. Trends Pharmacol Sci. 1993 Aug;14(8):297–303. doi: 10.1016/0165-6147(93)90047-N. [DOI] [PubMed] [Google Scholar]
  38. Sussman J. L., Harel M., Silman I. Three-dimensional structure of acetylcholinesterase and of its complexes with anticholinesterase drugs. Chem Biol Interact. 1993 Jun;87(1-3):187–197. doi: 10.1016/0009-2797(93)90042-w. [DOI] [PubMed] [Google Scholar]
  39. Sutcliffe M. J., Wo Z. G., Oswald R. E. Three-dimensional models of non-NMDA glutamate receptors. Biophys J. 1996 Apr;70(4):1575–1589. doi: 10.1016/S0006-3495(96)79724-2. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Swanson G. T., Feldmeyer D., Kaneda M., Cull-Candy S. G. Effect of RNA editing and subunit co-assembly single-channel properties of recombinant kainate receptors. J Physiol. 1996 Apr 1;492(Pt 1):129–142. doi: 10.1113/jphysiol.1996.sp021295. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Swanson G. T., Kamboj S. K., Cull-Candy S. G. Single-channel properties of recombinant AMPA receptors depend on RNA editing, splice variation, and subunit composition. J Neurosci. 1997 Jan 1;17(1):58–69. doi: 10.1523/JNEUROSCI.17-01-00058.1997. [DOI] [PMC free article] [PubMed] [Google Scholar]
  42. Tikhonov D. B., Zhorov B. S. Kinked-helices model of the nicotinic acetylcholine receptor ion channel and its complexes with blockers: simulation by the Monte Carlo minimization method. Biophys J. 1998 Jan;74(1):242–255. doi: 10.1016/S0006-3495(98)77783-5. [DOI] [PMC free article] [PubMed] [Google Scholar]
  43. Unwin N. Acetylcholine receptor channel imaged in the open state. Nature. 1995 Jan 5;373(6509):37–43. doi: 10.1038/373037a0. [DOI] [PubMed] [Google Scholar]
  44. Villarroel A., Burnashev N., Sakmann B. Dimensions of the narrow portion of a recombinant NMDA receptor channel. Biophys J. 1995 Mar;68(3):866–875. doi: 10.1016/S0006-3495(95)80263-8. [DOI] [PMC free article] [PubMed] [Google Scholar]
  45. Washburn M. S., Dingledine R. Block of alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors by polyamines and polyamine toxins. J Pharmacol Exp Ther. 1996 Aug;278(2):669–678. [PubMed] [Google Scholar]
  46. Washburn M. S., Numberger M., Zhang S., Dingledine R. Differential dependence on GluR2 expression of three characteristic features of AMPA receptors. J Neurosci. 1997 Dec 15;17(24):9393–9406. doi: 10.1523/JNEUROSCI.17-24-09393.1997. [DOI] [PMC free article] [PubMed] [Google Scholar]
  47. Wenthold R. J., Yokotani N., Doi K., Wada K. Immunochemical characterization of the non-NMDA glutamate receptor using subunit-specific antibodies. Evidence for a hetero-oligomeric structure in rat brain. J Biol Chem. 1992 Jan 5;267(1):501–507. [PubMed] [Google Scholar]
  48. Westbrook G. L. Glutamate receptor update. Curr Opin Neurobiol. 1994 Jun;4(3):337–346. doi: 10.1016/0959-4388(94)90094-9. [DOI] [PubMed] [Google Scholar]
  49. Williams K., Pahk A. J., Kashiwagi K., Masuko T., Nguyen N. D., Igarashi K. The selectivity filter of the N-methyl-D-aspartate receptor: a tryptophan residue controls block and permeation of Mg2+. Mol Pharmacol. 1998 May;53(5):933–941. [PubMed] [Google Scholar]
  50. Wo Z. G., Oswald R. E. Transmembrane topology of two kainate receptor subunits revealed by N-glycosylation. Proc Natl Acad Sci U S A. 1994 Jul 19;91(15):7154–7158. doi: 10.1073/pnas.91.15.7154. [DOI] [PMC free article] [PubMed] [Google Scholar]
  51. Wollmuth L. P., Kuner T., Sakmann B. Adjacent asparagines in the NR2-subunit of the NMDA receptor channel control the voltage-dependent block by extracellular Mg2+. J Physiol. 1998 Jan 1;506(Pt 1):13–32. doi: 10.1111/j.1469-7793.1998.013bx.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  52. Wollmuth L. P., Kuner T., Seeburg P. H., Sakmann B. Differential contribution of the NR1- and NR2A-subunits to the selectivity filter of recombinant NMDA receptor channels. J Physiol. 1996 Mar 15;491(Pt 3):779–797. doi: 10.1113/jphysiol.1996.sp021257. [DOI] [PMC free article] [PubMed] [Google Scholar]
  53. Wollmuth L. P., Sakmann B. Different mechanisms of Ca2+ transport in NMDA and Ca2+-permeable AMPA glutamate receptor channels. J Gen Physiol. 1998 Nov;112(5):623–636. doi: 10.1085/jgp.112.5.623. [DOI] [PMC free article] [PubMed] [Google Scholar]
  54. Wood M. W., VanDongen H. M., VanDongen A. M. Structural conservation of ion conduction pathways in K channels and glutamate receptors. Proc Natl Acad Sci U S A. 1995 May 23;92(11):4882–4886. doi: 10.1073/pnas.92.11.4882. [DOI] [PMC free article] [PubMed] [Google Scholar]
  55. Wu T. Y., Liu C. I., Chang Y. C. A study of the oligomeric state of the alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid-preferring glutamate receptors in the synaptic junctions of porcine brain. Biochem J. 1996 Nov 1;319(Pt 3):731–739. doi: 10.1042/bj3190731. [DOI] [PMC free article] [PubMed] [Google Scholar]
  56. Wyllie D. J., Béhé P., Nassar M., Schoepfer R., Colquhoun D. Single-channel currents from recombinant NMDA NR1a/NR2D receptors expressed in Xenopus oocytes. Proc Biol Sci. 1996 Aug 22;263(1373):1079–1086. doi: 10.1098/rspb.1996.0159. [DOI] [PubMed] [Google Scholar]
  57. Zarei M. M., Dani J. A. Structural basis for explaining open-channel blockade of the NMDA receptor. J Neurosci. 1995 Feb;15(2):1446–1454. doi: 10.1523/JNEUROSCI.15-02-01446.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  58. Zhorov B. S., Ananthanarayanan V. S. Structural model of a synthetic Ca2+ channel with bound Ca2+ ions and dihydropyridine ligand. Biophys J. 1996 Jan;70(1):22–37. doi: 10.1016/S0006-3495(96)79561-9. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Biophysical Journal are provided here courtesy of The Biophysical Society

RESOURCES