CoChat
Sign Up
Cited by 82Neuroscience and Neuropharmacology ResearchGenetics and Neurodevelopmental DisordersAmino Acid Enzymes and Metabolism

Disease-associated missense mutations in GluN2B subunit alter NMDA receptor ligand binding and ion channel properties

Open access
Fedele, Laura, Newcombe, Joseph, Topf, Maya, Gibb, Alasdair, Harvey, Robert J., Smart, Trevor G.·2018·Nature Communications
DOI 10.1038/s41467-018-02927-4PMC PMC5840332
Open this paper in CoChat — free accountOpen PDF

Abstract

Genetic and bioinformatic analyses have identified missense mutations in GRIN2B encoding the NMDA receptor GluN2B subunit in autism, intellectual disability, Lennox Gastaut and West Syndromes. Here, we investigated several such mutations using a near-complete, hybrid 3D model of the human NMDAR and studied their consequences with kinetic modelling and electrophysiology. The mutants revealed reductions in glutamate potency; increased receptor desensitisation; and ablation of voltage-dependent Mg 2+block. In addition, we provide new views on Mg 2+and NMDA channel blocker binding sites. We demonstrate that these mutants have significant impact on excitatory transmission in developing neurons, revealing profound changes that could underlie their associated neurological disorders. Of note, the NMDAR channel mutant GluN2B V618G unusually allowed Mg 2+permeation, whereas nearby N615I reduced Ca 2+permeability. By identifying the binding site for an NMDAR antagonist that is used in the clinic to rescue gain-of-function phenotypes, we show that drug binding may be modified by some GluN2B disease-causing mutations.

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1038/s41467-018-02927-4

Cites

3 of 3 references verified0 citation errors · 0 not checkable

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Cites

Flagged first, then by citations

Research works printed but not linked: 66

  1. [2]Cull-Candy S Brickley S Farrant M NMDA receptor subunits: diversity, development and disease Curr. Opin. Neurobiol. 2001 11 327 335 10.1016/S0959-4388(00)00215-4 11399431 · DOI · Paper page
  2. [3]Paoletti P Molecular basis of NMDA receptor functional diversity Eur. J. Neurosci. 2011 33 1351 1365 10.1111/j.1460-9568.2011.07628.x 21395862 · DOI
  3. [5]Allen AS De novo mutations in epileptic encephalopathies Nature 2013 501 217 221 10.1038/nature12439 23934111 PMC3773011 · DOI · Paper page
  4. [6]Lemke JR GRIN2B mutations in West syndrome and intellectual disability with focal epilepsy Ann. Neurol. 2014 75 147 154 10.1002/ana.24073 24272827 PMC4223934 · DOI
  5. [7]Li D GRIN2D recurrent de novo dominant mutation causes a severe epileptic encephalopathy treatable with NMDA receptor channel blockers Am. J. Hum. Genet. 2016 99 802 816 10.1016/j.ajhg.2016.07.013 27616483 PMC5065652 · DOI
  6. [8]Ogden, K. K. et al. Molecular mechanism of disease-associated mutations in the pre-M1 helix of NMDA receptors and potential rescue pharmacology. PLoS Genet. 13, 1–35 (2017). PMC5240934 28095420
  7. [10]Lee CH NMDA receptor structures reveal subunit arrangement and pore architecture Nature 2014 511 191 197 10.1038/nature13548 25008524 PMC4263351 · DOI
  8. [11]Karakas E Furukawa H Crystal structure of a heterotetrameric NMDA receptor ion channel Science 2014 344 992 997 10.1126/science.1251915 24876489 PMC4113085 · DOI
  9. [12]Tajima N Activation of NMDA receptors and the mechanism of inhibition by ifenprodil Nature 2016 534 63 68 10.1038/nature17679 27135925 PMC5136294 · DOI
  10. [13]Zhu S Mechanism of NMDA receptor inhibition and activation Cell 2016 165 704 714 10.1016/j.cell.2016.03.028 27062927 PMC4914038 · DOI
  11. [14]Alsaloum M Kazi R Gan Q Amin J Wollmuth LP A molecular determinant of subtype-specific desensitization in Ionotropic glutamate receptors J. Neurosci. 2016 36 2617 2622 10.1523/JNEUROSCI.2667-15.2016 26937003 PMC4879209 · DOI
  12. [15]Jones KS VanDongen HMA VanDongen AMJ The NMDA receptor M3 segment is a conserved transduction element coupling ligand binding to channel opening J. Neurosci. 2002 22 2044 2053 11896144 PMC6758261
  13. [16]Paoletti P Neyton J Ascher P Glycine-independent and subunit-specific potentiation of NMDA responses by extracellular Mg2+ Neuron 1995 15 1109 1120 10.1016/0896-6273(95)90099-3 7576654 · DOI
  14. [17]Das SR Magnusson KR Changes in expression of splice cassettes of NMDA receptor GluN1 subunits within the frontal lobe and memory in mice during aging Behav. Brain Res. 2011 222 122 133 10.1016/j.bbr.2011.03.045 21443909 PMC3099138 · DOI
  15. [18]Yilmazer ND Korth M Recent progress in treating protein-ligand interactions with quantum mechanical methods Int. J. Mol. Sci. 2016 17 742 10.3390/ijms17050742 PMC4881564 27196893 · DOI
  16. [19]Burnashev N Control by asparagine residues of calcium permeability and magnesium blockade in the NMDA receptor Science 1992 257 1415 1419 10.1126/science.1382314 1382314 · DOI
  17. [20]Wollmuth LP Kuner T Seeburg PH Sakmann B Differential contribution of the NR1- and NR2A-subunits to the selectivity filter of recombinant NMDA receptor channels J. Physiol. 1996 491 779 797 10.1113/jphysiol.1996.sp021257 8815211 PMC1158818 · DOI
  18. [21]Sakurada K Masu M Nakanishi S Alteration of Ca2+ permeability and sensitivity to Mg2+ and channel blockers by a single amino acid substitution in the N-methyl-D-aspartate receptor J. Biol. Chem. 1993 268 410 415 8416947
  19. [22]Williams K The sewhilstlectivity filter of the N-methyl-D-aspartate receptor: a tryptophan residue controls block and permeation of Mg2+ Mol. Pharmacol. 1998 53 933 941 9584221
  20. [23]Mesbahi-Vasey S Veras L Yonkunas M Johnson JW Kurnikova G All atom NMDA receptor transmembrane domain model development and simulations in lipid bilayers and water PLoS ONE 2017 45817 eaal3729 PMC5459333 28582391
  21. [24]Ascher P Nowak L The role of divalent cations in the N-methyl-D-aspartate respondes of mouse central neurones in culture J. Physiol. 1988 399 247 266 10.1113/jphysiol.1988.sp017078 2457089 PMC1191662 · DOI · Paper page
  22. [25]Sobolevsky AI Yelshansky MV The trapping block of NMDA receptor channels in acutely isolated rat hippocampal neurones J. Physiol. 2000 526 493 506 10.1111/j.1469-7793.2000.t01-2-00493.x 10922002 PMC2270033 · DOI
  23. [26]Kotermanski SE Wood JT Johnson JW Memantine binding to a superficial site on NMDA receptors contributes to partial trapping J. Physiol. 2009 587 4589 4603 10.1113/jphysiol.2009.176297 19687120 PMC2768015 · DOI
  24. [27]Huang Z Gibb AJ Mg2 + block properties of triheteromeric GluN1–GluN2B–GluN2D NMDA receptors on neonatal rat substantia nigra pars compacta dopaminergic neurones J. Physiol. 2014 592 2059 2078 10.1113/jphysiol.2013.267864 24614743 PMC4027860 · DOI
  25. [28]Blanpied T Boeckman F Aizenman E Johnson J Trapping channel block of NMDA-activated responses by amantadine and memantine J. Neurophysiol. 1997 77 309 323 10.1152/jn.1997.77.1.309 9120573 · DOI
  26. [29]Qian A Antonov SM Johnson JW Modulation by permeant ions of Mg2+ inhibition of NMDA-activated whole-cell currents in rat cortical neurons J. Physiol. 2002 538 65 77 10.1113/jphysiol.2001.012685 11773317 PMC2290035 · DOI
  27. [30]Kotermanski SE Johnson JW Mg2+ imparts NMDA receptor subtype selectivity to the Alzheimer’s drug memantine J. Neurosci. 2009 29 2774 2779 10.1523/JNEUROSCI.3703-08.2009 19261873 PMC2679254 · DOI · Paper page
  28. [31]Clements JD Westbrook GL Activation kinetics reveal the number of glutamate and glycine binding sites on the N-methyl-D-aspartate receptor Neuron 1991 7 605 613 10.1016/0896-6273(91)90373-8 1681832 · DOI
  29. [33]Moss, G. W. J. & Moczydlowski, E. in Ion Channels: A Practical Approach (ed. Ashley, R. H.) 69–112 (IRL Press, Oxford, 1995).
  30. [34]Mayer ML Westbrook GL Permeation and block of N-methyl-D-aspartic acid receptor channels by divalent cations in mouse cultured central neurones J. Physiol. 1987 394 501 527 10.1113/jphysiol.1987.sp016883 2451020 PMC1191974 · DOI
  31. [35]Ghasemi M Schachter SC The NMDA receptor complex as a therapeutic target in epilepsy: a review Epilepsy Behav. 2011 22 617 640 10.1016/j.yebeh.2011.07.024 22056342 · DOI
  32. [36]Chez MG Memantine as adjunctive therapy in children diagnosed with autistic spectrum disorders: an observation maintenance tolerability J. Child. Neurol. 2007 22 574 579 10.1177/0883073807302611 17690064 · DOI
  33. [37]Pierson TM GRIN2A mutation and early-onset epileptic encephalopathy: personalized therapy with memantine Ann. Clin. Transl. Neurol. 2014 1 190 198 10.1002/acn3.39 24839611 PMC4019449 · DOI
  34. [38]Hansen KB Ogden KK Yuan H Traynelis SF Distinct functional and pharmacological properties of triheteromeric GluN1/GluN2A/GluN2B NMDA receptors Neuron 2014 81 1084 1096 10.1016/j.neuron.2014.01.035 24607230 PMC3957490 · DOI
  35. [39]Cheriyan J Balsara RD Hansen KB Castellino FJ Pharmacology of triheteromeric N-methyl-D-aspartate receptors Neurosci. Lett. 2016 617 240 246 10.1016/j.neulet.2016.02.032 26917100 PMC5312704 · DOI
  36. [40]McKay S Direct pharmacological monitoring of the developmental switch in NMDA receptor subunit composition using TCN213, a GluN2A-selective, glycine-dependent antagonist Br. J. Pharmacol. 2012 166 924 937 10.1111/j.1476-5381.2011.01748.x 22022974 PMC3417419 · DOI
  37. [41]Tovar KR Westbrook GL The incorporation of NMDA receptors with a distinct subunit composition at nascent hippocampal synapses in vitro J. Neurosci. 1999 19 4180 4188 10234045 PMC6782704
  38. [42]Edman S TCN 201 selectively blocks GluN2A-containing NMDARs in a GluN1 co-agonist dependent but non-competitive manner Neuropharmacology 2012 63 441 449 10.1016/j.neuropharm.2012.04.027 22579927 PMC3384000 · DOI
  39. [43]Stocca G Vicini S Increased contribution of NR2A subunit to synaptic NMDA receptors in developing rat cortical neurons J. Physiol. 1998 507 13 24 10.1111/j.1469-7793.1998.013bu.x 9490809 PMC2230772 · DOI
  40. [44]Monyer H Burnashev N Laurie DJ Sakmann B Seeburg PH Developmental and regional expression in the rat brain and functional properties of four NMDA receptors Neuron 1994 12 529 540 10.1016/0896-6273(94)90210-0 7512349 · DOI · Paper page
  41. [45]Jespersen A Tajima N Fernandez-Cuervo G Garnier-Amblard EC Furukawa H Structural insights into competitive antagonism in NMDA receptors Neuron 2014 81 366 378 10.1016/j.neuron.2013.11.033 24462099 PMC3997178 · DOI
  42. [46]Swanger SA Mechanistic insight into nmda receptor dysregulation by rare variants in the GluN2A and GluN2B agonist binding domains Am. J. Hum. Genet. 2016 99 1261 1280 10.1016/j.ajhg.2016.10.002 27839871 PMC5142120 · DOI
  43. [47]Clements J Lester RA Tong G Jahr CE Westbrook GL The time course of glutamate in the synaptic cleft Science 1992 258 1498 1501 10.1126/science.1359647 1359647 · DOI
  44. [48]Wei H Reduced glutamate release in adult BTBR mouse model of autism-spectrum disorder Neurochem. Res. 2016 41 3129 3137 10.1007/s11064-016-2035-5 27538958 · DOI
  45. [49]Duguid IC Smart TG Retrograde activation of presynaptic NMDA receptors enhances GABA release at cerebellar interneuron-Purkinje cell synapses Nat. Neurosci. 2004 7 525 533 10.1038/nn1227 15097992 · DOI
  46. [50]Hattori R Kuchibhotla KV Froemke RC Komiyama T Functions and dysfunctions of neocortical inhibitory neuron subtypes Nat. Neurosci. 2017 20 1199 1208 10.1038/nn.4619 28849791 PMC7082034 · DOI
  47. [51]Pang X Zhou HX Structural modeling for the open state of an NMDA receptor J. Struct. Biol. 2017 200 369 375 10.1016/j.jsb.2017.07.005 28739483 PMC5733723 · DOI
  48. [52]Bar-Shira O Maor R Chechik G Gene expression switching of receptor subunits in human brain development PLoS Comput. Biol. 2015 11 1 21 10.1371/journal.pcbi.1004559 PMC4670163 26636753 · DOI
  49. [53]Platzer K GRIN2B encephalopathy: novel findings on phenotype, variant clustering, functional consequences and treatment aspects J. Med. Genet. 2017 54 460 470 10.1136/jmedgenet-2016-104509 28377535 PMC5656050 · DOI
  50. [54]Limapichat W Yu WY Branigan E Lester HA Dougherty DA Key binding interactions for memantine in the NMDA receptor ACS Chem. Neurosci. 2013 4 255 260 10.1021/cn300180a 23421676 PMC3751542 · DOI
  51. [55]Lü, W., Du, J., Goehring, A. & Gouaux, E. Cryo-EM structures of the triheteromeric NMDA receptor and its allosteric modulation. Science3729, eaal3729 (2017). PMC5568803 28232581
  52. [56]Glasgow NG Siegler Retchless B Johnson JW Molecular bases of NMDA receptor subtype-dependent properties J. Physiol. 2015 593 83 95 10.1113/jphysiol.2014.273763 25556790 PMC4293056 · DOI
  53. [57]Glasgow NG Povysheva NV Azofeifa AM Johnson JW Memantine and ketamine differentially alter NMDA receptor desensitization J. Neurosci. 2017 37 9686 9704 10.1523/JNEUROSCI.1173-17.2017 28877967 PMC5628409 · DOI
  54. [58]Andrej S Blundell TL Comparative protein modelling by satisfaction of spatial restraints J. Mol. Biol. 1993 234 779 815 10.1006/jmbi.1993.1626 8254673 · DOI · Paper page
  55. [59]Shen MY Sali A Statistical potential for assessment and prediction of protein structures Protein Sci. 2006 15 2507 2524 10.1110/ps.062416606 17075131 PMC2242414 · DOI
  56. [60]Studer G Biasini M Schwede T Assessing the local structural quality of transmembrane protein models using statistical potentials (QMEANBrane) Bioinformatics 2014 30 505 511 10.1093/bioinformatics/btu457 PMC4147910 25161240 · DOI
  57. [61]Lomize MA Pogozheva ID Joo H Mosberg HI Lomize AL OPM database and PPM web server: Resources for positioning of proteins in membranes Nucleic Acids Res. 2012 40 370 376 10.1093/nar/gkr703 PMC3245162 21890895 · DOI
  58. [62]Farabella I TEMPy: a Python library for assessment of three-dimensional electron microscopy density fits J. Appl. Crystallogr. 2015 48 1314 1323 10.1107/S1600576715010092 26306092 PMC4520291 · DOI
  59. [63]Mori H Masaki H Yamakura T Mishina M Identification by mutagenesis of a Mg2+-block site of the NMDA receptor channel Nature 1992 358 673 675 10.1038/358673a0 1386653 · DOI
  60. [64]Chai JDa Head-Gordon M Long-range corrected hybrid density functionals with damped atom-atom dispersion corrections J. Chem. Theory Comput. 2013 10 6616 6620 18989472
  61. [65]Barone V Cossi M Quantum calculation of molecular energies and energy gradients in solution by a conductor solvent model J. Phys. Chem. A 1998 102 1995 2001 10.1021/jp9716997 · DOI
  62. [66]Hollmann M Zinc potentiates agonist-induced currents at certain splice variants of the NMDA receptor Neuron 1993 10 943 954 10.1016/0896-6273(93)90209-A 7684237 · DOI
  63. [67]Clarke RJ Johnson JW Voltage-dependent gating of NR1/2B NMDA receptors J. Physiol. 2008 586 5727 5741 10.1113/jphysiol.2008.160622 18936081 PMC2655412 · DOI
  64. [68]Vicini S Functional and pharmacological differences between recombinant N-methyl-D-aspartate receptors J. Neurophysiol. 1998 79 555 566 10.1152/jn.1998.79.2.555 9463421 · DOI
  65. [69]Banke TG Dravid SM Traynelis SF Protons Trap NR1/NR2B NMDA receptors in a nonconducting state J. Neurosci. 2005 25 42 51 10.1523/JNEUROSCI.3154-04.2005 15634765 PMC6725198 · DOI
  66. [70]Antonov SM Johnson JW Permeant ion regulation of N-methyl-D-aspartate receptor channel block by Mg2+ Proc. Natl Acad. Sci. USA 1999 96 14571 14576 10.1073/pnas.96.25.14571 10588746 PMC24477 · DOI

Cited by

Sorted by citations

Authors
Fedele, L., Newcombe, J., Topf, M., Gibb, A., Harvey, R. J., & Smart, T. G.
Affiliations
  • UCL School of Pharmacy (GB)
  • University of London (GB)
  • University College London (GB)
  • University of the Sunshine Coast (AU)
Corresponding author
Harvey, Robert J.
ORCID
Venue
Nature Communications
Publisher
Springer Science and Business Media LLC
Published
2018-03-06
Volume
9
Issue
1
Pages
957-957
ISSN
2041-1723 (ISSN-L)
DOI
10.1038/s41467-018-02927-4
PMC
PMC5840332
OpenAlex
W2805162652
Cited by
82
References
3
Citations by year
2026: 8 · 2025: 6 · 2024: 8 · 2023: 7 · 2022: 11 · 2021: 15 · 2020: 13 · 2019: 13 · 2018: 1
FWCI
4.78
Type
journal article
Language
en
Open access
Licence
Locations
  • Nature Communications (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • BIROn (Birkbeck, University of London) (acceptedVersion)
  • RePEc: Research Papers in Economics (submittedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
  • UCL Discovery (University College London) (submittedVersion)
  • Research Portal (King's College London) (submittedVersion, other-oa)
Funders
Medical Research Council (MR/M013502/1, MR/K005537/1)
Topics
  • Life Sciences › Neuroscience › Cellular and Molecular Neuroscience › Neuroscience and Neuropharmacology Research
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetics and Neurodevelopmental Disorders
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Biochemistry › Amino Acid Enzymes and Metabolism
Keywords
GluN2B, NMDA receptor, missense mutations, NR2B subunit, autism spectrum disorder, intellectual disability, Lennox-Gastaut syndrome, West syndrome, receptor desensitization, Mg2+ block, excitatory synaptic transmission, kinetic modeling, drug binding
MeSH terms
Amino Acid Sequence, Animals, Cell Membrane Permeability, Disease, Glutamates, Humans, Ion Channels, Ligands, Magnesium, Memantine, Models, Molecular, Neurons, Receptors, N-Methyl-D-Aspartate, Rats, Sprague-Dawley, Computational Biology, Excitatory Postsynaptic Potentials, Mutation, Missense, Protein Subunits, HEK293 Cells

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review