Activation of NMDA receptors and the mechanism of inhibition by ifenprodil

Abstract

SUMMARY The physiology of N-Methyl-D-aspartate (NMDA) receptors in mammals is fundamental to brain development and function. NMDA receptors are ionotropic glutamate receptors that function as heterotetramers composed mainly of GluN1 and GluN2 subunits. Activation of NMDA receptors requires binding of neurotransmitter agonists to a ligand-binding domain (LBD) and structural rearrangement of an amino terminal domain (ATD). Recent crystal structures of GluN1/GluN2B NMDA receptors in the presence of agonists and an allosteric inhibitor, ifenprodil, represent the allosterically inhibited state. However, how the ATD and LBD move to activate the NMDA receptor ion channel remains unclear. Here, we combine x-ray crystallography, single-particle electron cryomicroscopy, and electrophysiology to show that, in the absence of ifenprodil, the bi-lobed structure of GluN2 ATD adopts an open-conformation accompanied by rearrangement of the GluN1-GluN2 ATD heterodimeric interface, altering subunit orientation in the ATD and LBD and forming an active receptor conformation that gates the ion channel.

Structural modeling for the open state of an NMDA receptor

“…To help address how the ATD and LBD communicate with the TMD, we merged the refined open model with PDB entry 5FXG, which putatively represent the extracellular domains in the activated state (Tajima et al, 2016) (Fig. 6).…”

“…The template for the TMD was the chosen initial open model; the template for the ATD and LBD was PDB entry 5FXG, which is the structure for the extracellular domains of an activated GluN1/GluN2B receptor (Tajima et al, 2016). The targeted molecular dynamics simulation in vacuum was run using NAMD 2.11 (Phillips et al, 2005), for 1 ns with a time step of 1 fs at 310K.…”

Kinetic models for activation and modulation of NMDA receptor subtypes

“…A cryo-EM study of GluN1/GluN2B receptors revealed a diversity of structural configurations adopted by channels in the presence of agonist, which included for the first time a portion of active receptor [55 • ]. These groundbreaking reports permit for the first time the use of molecular modeling approaches to infer structures of the resting, and agonist-bound closed, open, and desensitized states.…”

Structure and symmetry inform gating principles of ionotropic glutamate receptors

“…Cryo-EM structures of NMDA receptors represent various conformations, including an agonist-bound inactive or perhaps desensitized-like state, an antagonist-bound inhibited state, an agonist/modulator bound state (Zhu et al, 2016) and an agonist-bound activated state (Tajima et al, 2016). Kainate GluK2 receptors were first captured in both the resting and the agonist-bound desensitized states by cryo-electron tomography at ~20 Å resolution (Schauder et al, 2013).…”