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Comparative Study
. 2012 Nov 7;20(11):1838-49.
doi: 10.1016/j.str.2012.08.012. Epub 2012 Sep 6.

Comparative dynamics of NMDA- and AMPA-glutamate receptor N-terminal domains

Anindita Dutta  1 , Indira H Shrivastava, Madhav Sukumaran, Ingo H Greger, Ivet Bahar
Affiliations
Comparative Study

Comparative dynamics of NMDA- and AMPA-glutamate receptor N-terminal domains

Anindita Dutta et al. Structure. .

Abstract

Ionotropic glutamate receptors (iGluRs) harbor two extracellular domains: the membrane-proximal ligand-binding domain (LBD) and the distal N-terminal domain (NTD). These are involved in signal sensing: the LBD binds L-glutamate, which activates the receptor channel. Ligand binding to the NTD modulates channel function in the NMDA receptor subfamily of iGluRs, which has not been observed for the AMPAR subfamily to date. Structural data suggest that AMPAR NTDs are packed into tight dimers and have lost their signaling potential. Here, we assess NTD dynamics from both subfamilies, using a variety of computational tools. We describe the conformational motions that underly NMDAR NTD allosteric signaling. Unexpectedly, AMPAR NTDs are capable of undergoing similar dynamics; although dimerization imposes restrictions, the two subfamilies sample similar, interconvertible conformational subspaces. Finally, we solve the crystal structure of AMPAR GluA4 NTD, and combined with molecular dynamics simulations, we characterize regions pivotal for an as-yet-unexplored dynamic spectrum of AMPAR NTDs.

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Figures

Figure 1
Figure 1
Structure of the GluA4 NTD Facilitates a Comparative Structural Analysis (A) Intact structure of GluA2 AMPAR (left) displaying the spatial arrangements of four subunits (two shown in gray and the others in blue and dark blue) that span the three domains (NTD, LBD, and TMD). The location of the NTD dimer resolved for GluA4 is enlarged. Subunits are symmetrically positioned, each consisting of an upper lobe (UL) and a lower lobe (LL); secondary structural features (helices αA, αB, αE, αF, αG, and αH and strands β1 and β2) are labeled. Interfacial interactions are highlighted. (B) UL dimerization interfaces of GluA1–A4 are largely conserved but LL packing shows heterogeneity. UL interfaces of GluA1–GluA2 (grays), GluA3 (green), and GluA4 (blue) have been artificially separated to show the structural conservation and orientations of key residues (shown in stick) making contacts across the interface. Two-fold axis of symmetry is shown as a dashed line. Superposition of LL shows distinct differences in interface packing that is most prominent in GluA3. (C) Intersubunit contacts at the UL and LL interfaces of GluA1–A4 NTDs. Atoms making interfacial contacts within 4.5Å are shown as spheres and colored from blue (one contact) to red (≥7 contacts). Calculated local contact density (LD) indices and empirically measured dimer dissociation constants (Kd) are also shown. The four NTDs are ranked by their homodimerization affinity. Note the LL interface is highly variable between AMPAR paralogs, whereas the UL interface is largely invariant. See also Figure S1 and Tables 1 and S1.
Figure 2
Figure 2
Global Dynamics of GluA4 Dimer in Comparison to other AMPAR NTDs Probed by ANM (A) Distribution of square displacements of residues in the most global (lowest frequency) mode intrinsically accessible to AMPAR NTD dimers (GluA1-AC, GluA1-BD [3SAJ], GluA2-AB [3HSY], GluA3-CD [3O21], and GluA4 [PDB ID code 4GPA]). The four subtypes show similar profile (see the high correlations listed in Table S2) but different size motions (see Table S3). (B) Shared mechanism of global motion: counterrotation of the two protomers (indicated by red arrows), depicted for GluA4 as a representative structure, from the front and side views. The diagram is color-coded from red (most mobile in mode 1) to blue (least mobile). The global mobility rank of the four AMPAR NTD dimers is GluA3-CD (0.110) > GluA1-BD (0.169) > GluA1-AC (0.184) ≈ GluA4-BA (0.187) > GluA2-AB (0.187). The numbers in parentheses indicate the global mode eigenvalues (see Experimental Procedures). See also Table S1.
Figure 3
Figure 3
Intrinsic Ability of NMDAR NTD to Undergo Cleft Motions (A) Deformation of NR2B subunit (PDB ID code 3JPW, pink) along ANM mode 2, leads to opening of the cleft (blue). (B) The time evolution of the cleft angle observed in the MD runs NMDA1 (pink, in presence of Zn2+) and NMDA2 (blue, in absence of Zn2+). The cartoon in the inset is the superposition of 50 ns snapshots from NMDA1 and NMDA2. It illustrates the opening of the cleft in the simulation performed without Zn2+ similar to the global reconfiguration predicted by the ANM for 3JPW in (A). The histograms in the inset are of the distribution of the angles sampled by NR2B in the two simulations: the average angle is 138° in NMDA1 and 121° in NMDA2. See also Table S4.
Figure 4
Figure 4
Comparing the Global Dynamics of NTD Protomers Resolved for AMPA and NMDA Receptors (A) Comparison of the mobility profiles as driven by the lowest frequency (most cooperative) mode of motion accessible to GluN2B (3JPW), GluN1 (3Q41-A), GluA2 (3HSY-B), and GluA3 (3O21-C) NTD monomers. The abscissa in (A) is labeled according to residues in GluA2. (B) Ribbon diagram of a representative AMPAR (GluA2) and an NMDAR (GluN2B) NTD monomer, colored by the mobility profile in mode 1. The arrows indicate the mechanism of motion (counterrotation of the two lobes). (C and D) Same as in (A) and (B), for ANM mode 2, a clamshell-like opening/closing of the two lobes. See also Tables S2 and S3.
Figure 5
Figure 5
Effect of Dimerization on the Intrinsic Dynamics of AMPAR and NMDAR NTD Monomers (A) Correlation between top 40 modes accessible to GluA2 protomer in isolation (3HSY-B; abscissa) and in the dimer (3HSY; ordinate). Darkest red and blue regions refer to strongest correlations (see the scale on the right). Clamshell motions (monomer mode 1) are maintained in the dimer but manifested by mode 2 (circled region). (B) Same as (A), for GluN2B (3QEL-D) monomer compared to GluN1/GluN2B heterodimer (3QEL). (C and D) Mobility profiles for GluA2 and GluN2B monomers in isolation and in the dimer, showing the suppression of mobilities (at the UL in particular) upon dimerization (see Figure S2 for GluA3 and GluN1). Insets show GluA2 and GluN2B monomers colored by their change in mobility upon dimerization, from most suppressed (red) to unaffected (blue).
Figure 6
Figure 6
Ease of Transition between Dimeric Conformers of NMDAR and AMPAR NTDs (A) Results are illustrated for the passage from GluN1 (NMDA) homodimeric conformer to GluA2 dimer conformer. The overlap (blue bars) represents the correlation cosine (see Experimental Procedures) for each of the top-ranking 80 ANM modes to the conformational change. The red curve represents the cumulative overlap, adding up the contribution of all modes starting from the low frequency end (mode 1). The dashed green curve displays the control, for random modes. The slowest mode predicted for GluN1 (PDB ID code 3Q41-AB) yields an overlap of ∼80%, indicating a strong predisposition of the GluN1 homodimer to assume the conformation of the GluA2 dimer. (B) Two transitional end points (orange, yellow) and an intermediate structure reached by moving exclusively along mode 1 (green). (C and D) Same as (A) and (B), for the change in the conformation of GluA3 homodimer (yellow) toward that of the heterodimer GluN1/GluN2B (PDB ID code 3QEL-CD, orange) along GluA3 ANM intermediate (green). See also Figure S3.
Figure 7
Figure 7
Lower Lobe Interface Instability of GluA3 Evidenced by Comparative Analysis of MD Simulations for GluA1–A4 (A) Distance between the mass centers of LLs, shown for GluA1–A4 NTDs as a function of simulation time. Results for the ULs are shown in the inset. Large fluctuations are observed in GluA3 LL-LL distance (blue trace). (B) Snapshots display GluA3 conformations at t = 0, 5.8, 15, and 60 ns (see colored circles in A). (C) Probe residues selected for monitoring the changes in interlobe cleft angle, shown for GluA3 NTD (3O21-CD). (D) Time evolution of interlobe angle for GluA3 protomers. Note the periodic opening/closing and the anticorrelation between the protomers. (E) These properties are contrasted to those observed for GluA2, where the angles exhibit minimal fluctuations. Histograms refer to interlobe angles for protomers A (dark blue) and B (cyan). See also Figures S4,S5 and,S7 and Table S4.
Figure 8
Figure 8
Critical Role of Interresidue Interactions at LL-LL Interface in Defining NTD Dimer Dynamics Results are presented for the mutants L144D (GluA2) and R163I (GluA3) to examine the significance of hydrophobic versus charged interactions in defining the distinctive dynamics of GluA3 and GluA2. (A) Time evolution of the closest interatomic distance between L144 residues on neighboring subunits for the wild-type (black) and between D144 pairs in the mutant (teal). Inset highlights the region of mutation. (B) Snapshots of wild-type GluA2 and L144D mutant at 100 ns, superimposed and viewed from bottom. (C and D) Same as (A) and (B) for GluA3 wild-type and mutant R163I. See also Figure S6 and Table S4.
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