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Allosteric signaling and dynamics of the clamshell-like NMDA receptor GluN1 N-terminal domain

Nature Structural & Molecular Biology volume 20, pages 477–485 (2013)Cite this article

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Abstract

N-methyl-D-aspartate receptors (NMDARs), neuronal glutamate-gated ion channels, are obligatory heterotetramers composed of GluN1 and GluN2 subunits. Each subunit contains two extracellular clamshell-like domains with an agonist-binding domain and a distal N-terminal domain (NTD). The GluN2 NTDs form mobile regulatory domains. In contrast, the dynamics of GluN1 NTD and its contribution to NMDAR function remain poorly understood. Here we show that GluN1 NTD is neither static nor functionally silent. Perturbing the conformation of GluN1 NTD affects both receptor gating and pharmacological properties. GluN1 NTD undergoes structural rearrangements that involve hinge bending and large twisting and untwisting motions, allowing for new intra- and intersubunit contacts. GluN1 NTD acts in trans with GluN2 NTD to influence binding of glutamate but, notably, not of GluN1 coagonist glycine. Our work uncovers a dynamic role of GluN1 NTD in controlling NMDAR function through new interdomain allosteric interactions.

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Figure 1: GluN1 NTD hinge mutations affect NMDAR channel activity.
Figure 2: Locking GluN1 NTD in a closed-cleft form downregulates receptor activity.
Figure 3: Impact of GluN1 NTD disulfide trapping on receptor pharmacology.
Figure 4: GluN1 NTD acts in trans and tunes glutamate, but not glycine, sensitivity.
Figure 5: GluN1 NTD undergoes conformational changes during receptor activation.
Figure 6: GluN1 NTD undergoes large conformational changes.

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Acknowledgements

This work was supported by the Fondation pour la Recherche Médicale (“Equipe FRM” grant DEQ20081213996 to P.P.; “bourse FRM” to S.Z.), Université-Pierre-et-Marie-Curie (to S.Z.) and the China Scholarship Council (to S.Z.). We thank M. Gielen for comments on the manuscript.

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Authors and Affiliations

  1. Ecole Normale Supérieure, Institut de Biologie, Paris, France

    Shujia Zhu, David Stroebel, C Andrea Yao & Pierre Paoletti

  2. Institut National de la Santé et de la Recherche Médicale, U1024, Paris, France

    Shujia Zhu, David Stroebel, C Andrea Yao & Pierre Paoletti

  3. Centre National de la Recherche Scientifique, UMR 8197, Paris, France

    Shujia Zhu, David Stroebel, C Andrea Yao & Pierre Paoletti

  4. Shanghai Key Laboratory of Brain Functional Genomics, East China Normal University, Shanghai, China

    Shujia Zhu

  5. Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, Centre National de la Recherche Scientifique, UPR 9080, Paris, France

    Antoine Taly

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Contributions

S.Z. designed and performed experiments, and analyzed data. D.S. designed experiments and analyzed structural data. C.A.Y. performed and analyzed the single-channel recordings. A.T. performed the NMA. P.P. supervised the work and participated in data analysis. S.Z. and P.P. wrote the manuscript.

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Correspondence to Pierre Paoletti.

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Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–6 and Supplementary Tables 1–4 (PDF 2035 kb)

Supplementary Movie 1

Motions observed in mode 9 of the Normal Mode Analysis. The GluN2B NTD is shown in grey and the GluN1 NTD in cyan (upper lobe) and yellow (lower lobe). GluN2B NTD and GluN1 NTD upper lobes were superimposed to highlight the relative motion of GluN1 NTD lower lobe. The GluN1 NTD undergoes almost pure twisting-untwisting motions. The movie illustrates the dihedrals vectors that were used to measure the twist-untwist interlobe motions, then... untwist conformation of the GluN1 NTD. (MOV 15146 kb)

Supplementary Movie 2

Motions observed in mode 8 of the Normal Mode Analysis. The GluN2B NTD is shown in grey and the GluN1 NTD in cyan (upper lobe) and yellow (lower lobe). The GluN1 NTD undergoes a large interlobe twisting-opening and untwisting-closure motion. Note also the rotation movement between the two NTDs at the level of the upper lobe-upper lobe interface. (MOV 11952 kb)

Supplementary Movie 3

Motions observed in mode 12 of the Normal Mode Analysis. The GluN2B NTD is shown in grey and the GluN1 NTD in cyan (upper lobe) and yellow (lower lobe). GluN2B and GluN1 NTD upper lobes were superimposed... (MOV 7692 kb)

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Zhu, S., Stroebel, D., Yao, C. et al. Allosteric signaling and dynamics of the clamshell-like NMDA receptor GluN1 N-terminal domain. Nat Struct Mol Biol 20, 477–485 (2013). https://doi.org/10.1038/nsmb.2522

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