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Mechanical coupling maintains the fidelity of NMDA receptor–mediated currents

Nature Neuroscience volume 17, pages 914–922 (2014)Cite this article

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Abstract

The fidelity of integration of pre- and postsynaptic activity by NMDA receptors (NMDARs) requires a match between agonist binding and ion channel opening. To address how agonist binding is transduced into pore opening in NMDARs, we manipulated the coupling between the ligand-binding domain (LBD) and the ion channel by inserting residues in a linker between them. We found that a single residue insertion markedly attenuated the ability of NMDARs to convert a glutamate transient into a functional response. This was largely a result of a decreased likelihood of the channel opening and remaining open. Computational and thermodynamic analyses suggest that insertions prevent the agonist-bound LBD from effectively pulling on pore lining elements, thereby destabilizing pore opening. Furthermore, this pulling energy was more prominent in the GluN2 subunit. We conclude that an efficient NMDAR-mediated synaptic response relies on a mechanical coupling between the LBD and the ion channel.

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Figure 1: Single glycine insertions in either the GluN1 or GluN2A M3-S2 linker eliminates the fidelity of NMDAR-mediated currents.
Figure 2: Single glycine insertions in the M3-S2 linkers increase failure rate and latency to first opening and reduce channel open time.
Figure 3: M3-S2 insertions attenuate pore opening in all-atom MD simulations of modeled GluN1/GluN2A NMDARs.
Figure 4: Insertions at different points in the M3-S2 linker attenuate pore opening.
Figure 5: Additional insertions in the M3-S2 linkers further reduce pore opening.
Figure 6: Activation models for single glycine insertions in GluN1 or GluN2A.
Figure 7: The GluN2A subunit moves earlier and transduces more energy than the GluN1 subunit.

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Acknowledgements

We thank J. Howe, C. Grosman and Q. Gan for helpful discussions and/or comments on the manuscript, and J. Allopenna and M. Daniel for technical assistance. The authors thank XSEDE for providing computational resources through grant TG-MCB130127 on TACC Stampede. This work was supported by grants MH066892 (to L.P.W.) and GM088187 (to H.-X.Z.) and Predoctoral Fellowship NS077541 (to R.K.) from the US National Institutes of Health.

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Authors and Affiliations

  1. Graduate Program in Neuroscience, Stony Brook University, Stony Brook, New York, USA

    Rashek Kazi

  2. Medical Scientist Training Program, Stony Brook University, Stony Brook, New York, USA

    Rashek Kazi

  3. Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida, USA

    Jian Dai & Huan-Xiang Zhou

  4. Department of Neurobiology and Behavior, Stony Brook University, Stony Brook, New York, USA

    Cameron Sweeney & Lonnie P Wollmuth

  5. Center for Nervous System Disorders, Stony Brook University, Stony Brook, New York, USA

    Cameron Sweeney & Lonnie P Wollmuth

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Contributions

R.K., H.-X.Z. and L.P.W. designed the study. R.K. and C.S. carried out and analyzed the electrophysiology experiments. J.D. performed the computational studies, including modeling and molecular dynamic simulations. R.K. carried out secondary structure predictions. R.K., J.D., H.-X.Z. and L.P.W. wrote the paper.

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Correspondence to Lonnie P Wollmuth.

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Integrated supplementary information

Supplementary Figure 1 Manipulations in the M3-S2 linkers exert effects largely independent of LBD dynamics

(a–c) Single glycine insertions in GluN1 or GluN2A have no significant effect on deactivation rates, which for NMDARs are related to ligand unbinding and hence an index of LBD dynamics (Lester & Jahr, 1992, J. Neuroscience; Vance et al., 2011, Nat. Comm). (a) Representative macroscopic currents from outside-out patches in response to a 2 ms application of glutamate (1 mM). For GluN1/GluN2A(G645+1G), macroscopic currents with 2 ms applications could not be measured but could be using 10 ms applications (not shown). (b) Mean (± SEM, n ≥ 8) rates of deactivation for macroscopic (left) and summed currents of microscopic (1–2 channels, from Fig. 1) (right) patches for 2 ms applications. Rates were best fit using a biexponential function giving a fast (black) and slow (white) tau. (c) Mean (± SEM, n ≥ 4) rates of deactivation for outside-out patches/whole cell recordings following a 10 ms application of glutamate for GluN1/GluN2A or GluN1/GluN2A(G645+1G). Rates were best fit with a single exponential function. Deactivation rates in b & c were not significantly different. (d–g) Forcing the LBD into a closed clamshell configuration has no effect on open probability for M3-S2 insertion or deletion constructs, indicating that manipulations in the M3-S2 linkers do not affect LBD clamshell closure. (d & f) NMDAR LBDs were closed using two engineered cysteines (CC) across the cleft in either GluN1 (d) or GluN2A (f) (Blanke & VanDongen, 2008, J. Biol Chem; Kussius & Popescu, 2010, J. Neuroscience). Single-channel activity was recorded in the cell-attached configuration. For GluN1(CC)/GluN2A, the pipette solution contained glutamate (1 mM) with no added glycine. For GluN1/GluN2A(CC), the pipette solution contained glycine (0.1 mM) with no added glutamate. (e & g) Mean (± SEM, n ≥ 3) open probability for the control, +2G, and deletion constructs tested in the wild type LBD (black) or CC (grey) LBD background. Values for like manipulations in different backgrounds were not statistically different.

Supplementary Figure 2 Insertions ≤ 4 residues in the GluN1 M3-S2 primarily increase linker length (relates to Fig. 3).

To characterize the structural effects of insertions on secondary structure, we used homology modeling (PHYRE/SWISS-MODEL) (see Online Methods). (a–e) Homology models built using PHYRE/SWISS-MODEL modeling servers (a,c,e) or MODELLER (b,d) for GluN1(G6458+1G) (a & b), GluN1(G648+4G) (c & d), and GluN1(G648+6G) (e). +1G and +4G insertions predominantly increase the length of M3-S2 while the +6G insertion adds an additional local secondary structure (black arrow). The +4G model also shows a potential turn (grey arrow).

Supplementary Figure 3 Insertions in GluN2A M3-S2 increase linker length (relates to Fig. 3)

Same legend as Supplementary Fig. 3 except that modeling is for the GluN2A subunit. None of the insertions produced notable changes in secondary structures though +4G and +6G show a potential turn (grey arrows).

Supplementary Figure 4 M3-S2 insertions reduce the efficiency of pore widening (relates to Figs. 3 & 5)

(a–b) M3-S2 insertions reduce pore widening along the length of the pore. Left, Top-down view of the pore at the beginning (grey) and end (colored) of MD simulations for +1G or +4G insertions in GluN1 (a, blue) or GluN2A (b, pink). Right, Pore radius measurements for representative simulations along the z-axis at the beginning (black) and end (red) of the simulation. The arrow highlights the outermost ring formed by GluN1(V638) and GluN2A(I635) which was used for pore radius measurements in Figure 3c–e and Supplementary Figures 4c & 4d. (c) Additional insertions in the M3-S2 linker (+4G) further reduce pore widening compared to +1G insertions. Left, Overlaid structural snapshots of the ion channel pore (circle) for GluN1(G648+4G)/GluN2A and GluN1/GluN2A(G645+4G) at 0 ns (grey, faded) and after 65 ns of simulation (colored) with spheres highlighting α-carbons of the three gate-forming rings (Fig. 1e). Right, Change in pore radius from 0 ns to 65 ns. Shown are the filtered (solid line) and unfiltered (dots) traces for each construct. Pore radius was measured at the outermost ring. (d) Mean (± Standard Deviation) pore radius across the final 700 frames (35 ns) for GluN1/GluN2A (3.3 ± 0.4 Å), GluN1(G648+1G)/GluN2A (2.0 ± 0.4 Å), GluN1(G648+4G)/GluN2A (1.6 ± 0.6 Å), GluN1/GluN2A(G645+1G) (1.5 ± 0.3 Å), and GluN1/GluN2A(G645+4G) (1.1 ± 0.3 Å).

Supplementary Figure 5 Equilibrium open and closed time distributions for wild type and GluN1 insertion constructs (relates to Fig. 6)

Closed (left) and open (right) durations for GluN1/GluN2A (a) and GluN1(G648+nG)/GluN2A (b) where n = 1, 2, or 4. For all constructs, the closed-time distributions were best fit by five exponentials. Although there was considerable variation across patches in terms of the number of open state exponentials (2 to 4), we fitted all open state distributions with 2 exponentials to permit comparisons across different constructs. Insets, mean values (±SEM) for closed and open state durations (left, τ, ms) and occupancies (right, α, %).

Supplementary Figure 6 Equilibrium open and closed time distributions for wild type and GluN2A insertion manipulations (relates to Fig. 6)

Figure is same as Supplementary Fig. 6 but for insertions in the GluN2A subunit.

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Kazi, R., Dai, J., Sweeney, C. et al. Mechanical coupling maintains the fidelity of NMDA receptor–mediated currents. Nat Neurosci 17, 914–922 (2014). https://doi.org/10.1038/nn.3724

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