Dynamics and allosteric potential of the AMPA receptor N-terminal domain

By Madhav Sukumaran, Maxim Rossmann, Indira Shrivastava, Anindita Dutta, Ivet Bahar, and Ingo H Greger

Published in The EMBO Journal 30(5): 972-82 on March 2, 2011.
PMID: 21317871. PMCID: PMC3049213. Link to Pubmed page.

Core Facility: Computational Modeling

GluA2 and GluA3 NTDs differ structurally. (A) Left: Topology of an iGluR subunit. The NTD segment is denoted as a green curve and the transmembrane segments as grey columns. Right: Structure of the bipartite GluA2 NTD dimer (PDB 3HSY). The two chains/protomers are coloured green and cyan. Upper and lower lobes (UL, LL) are denoted and their respective interprotomer interfaces are circled. Secondary structural elements contributing to the LL interface are labelled. (B) Structure of the GluA3 NTD (dimer I), with the two protomers coloured red and blue. The UL dimer interface analogous to GluA2 is circled, and the LL interface is shown by a box and an arrow indicating the increased space between the LLs, compared with GluA2. Segments homologous to the GluA2 LL interface segments (from A) are labelled. (C) Lower lobe packing markedly differs between GluA2 and GluA3 NTDs. The lower lobe interface of GluA2 (green) and GluA3 (red) are shown after aligning common secondary structure segments. Note the significantly closer packing of the GluA2 LL interface. Also shown are arginines from GluA3 that project into the interface; this unfavourable electrostatic interaction may contribute to the increased interlobe distance. (D) Sequence conservation in the NTD LL of the AMPA and kainate subfamilies. Different background colours indicate different conservation patterns; for example, conserved sites (columns) within a subfamily are coloured red. Residues that project across the interface are denoted with asterisks (*). Note the markedly higher conservation of the LL interface within the kainate subfamily.


Glutamate-gated ion channels (ionotropic glutamate receptors, iGluRs) sense the extracellular milieu via an extensive extracellular portion, comprised of two clamshell-shaped segments. The distal, N-terminal domain (NTD) has allosteric potential in NMDA-type iGluRs, which has not been ascribed to the analogous domain in AMPA receptors (AMPARs). In this study, we present new structural data uncovering dynamic properties of the GluA2 and GluA3 AMPAR NTDs. GluA3 features a zipped-open dimer interface with unconstrained lower clamshell lobes, reminiscent of metabotropic GluRs (mGluRs). The resulting labile interface supports interprotomer rotations, which can be transmitted to downstream receptor segments. Normal mode analysis reveals two dominant mechanisms of AMPAR NTD motion: intraprotomer clamshell motions and interprotomer counter-rotations, as well as accessible interconversion between AMPAR and mGluR conformations. In addition, we detect electron density for a potential ligand in the GluA2 interlobe cleft, which may trigger lobe motions. Together, these data support a dynamic role for the AMPAR NTDs, which widens the allosteric landscape of the receptor and could provide a novel target for ligand development.

Global dynamics of GluA2 and GluA3 NTDs.
Global dynamics of GluA2 and GluA3 NTDs. (A) ANM predicts GluA2 and GluA3 NTDs to adopt classical clamshell motions. One of the dominant modes of motion predicted by ANM simulations for the GluA3 NTD monomer is a classical clamshell opening/closing with a large range of motion. The major deformation is an opening of the cleft (cleft opening angle shown as bars) along the ‘hinge’ axis; open (green) and closed (pink) states of GluA3 are shown. (B) Deformations within the dimer assembly are a bit different. The dominant mode is now an anti-correlated motion between the monomers along the axis denoted by the dashed red line, and manifests as a counter-rotation when viewed from the direction indicated by the black arrow. (C) Mobility profile of GluA2, GluA3 and GluK2 NTDs. Residue-specific fluctuations in mode 1 are shown for GluA2 (red), GluA3 (blue) and GluK2 (green; PDB 3H6G) NTDs. The correlation coefficients between the mobility distributions are as follows: 0.82 between GluA2 and GluA3, 0.86 between GluA2 and GluK2 and 0.94 between GluA3 and GluK2. Secondary structural segments that exhibit large fluctuations in the lower lobe (αF, αG and αI) are labelled. Upper and lower lobes are identified as brown and green bars below the x axis. (D) Dimer assemblies also show mobility. A GluA2 NTD dimer is shown with residues coloured by magnitude of the fluctuations from the first 10 modes of GNM, from least (blue) to most mobile (red). Note that the lower lobe is more mobile than the upper lobe, with the putative output region contacting the LBD exhibiting the most mobility