The GluN2B‐Glu413Gly NMDA receptor variant arising from a de novo GRIN2B mutation promotes ligand‐unbinding and domain opening

Abstract

N-methyl-D-aspartate (NMDA) receptors are transmembrane glutamate-binding ion channels that mediate neurotransmission in mammals. NMDA receptor subunits are tetrameric complexes of GluN1 and GluN2A-D subunits, encoded by the GRIN gene family. Of these subunits, GluN2B is suggested to be required for normal development of the central nervous system. A mutation identified in a patient with developmental delay, E413G, resides in the GluN2B ligand-binding domain and substantially reduces glutamate potency by an unknown mechanism. GluN2B Gly413, though near the agonist, is not in van der Waals contact with glutamate. Visual analysis of the GluN2B structure with the E413G mutation modeled suggests that replacement of Glu with Gly at this position increases solvent access to the ligand-binding domain. This was confirmed by molecular modeling, which showed that the ligand is more mobile in GluN2B-E413G than WT GluN2B. Evaluation of agonist occupancy using random accelerated molecular dynamics (RAMD) simulations predicts that the glutamate exits the binding-site more rapidly for GluN2B-E413G than WT receptors. This analysis was extended to other binding-site mutations, which produced qualitative agreement between experimentally determined EC values, deactivation time constants, and ligand motion within the binding-site. Furthermore, long sub-microsecond molecular dynamics simulations of the bi-lobed ligand-binding domain revealed that it adopted a cleft-open ligand-free state more often for GluN2B-E413G than wild-type GluN2B. This is consistent with the idea that L-glutamate binding is altered such that the ligand-binding domain occupies the open-cleft conformation associated with the closed channel.

The pathogenic S688Y mutation in the ligand-binding domain of the GluN1 subunit regulates the properties of NMDA receptors

“…Similarly, the NMDARs carrying several pathogenic mutations in the LBDs of GluN2A and GluN2B subunits exhibit clear correlation between the EC 50 for l -glutamate and surface expression 40 . For example, the pathogenic E413G mutation in GluN2B subunit profoundly reduced the surface delivery of NMDARs 40 , likely by promoting the unbinding of l -glutamate and opening of the LBD 67 . On the other hand, other pathogenic mutations within the LBDs of GluN2A and GluN2B subunits revealed no clear correlation between the receptor’s EC 50 for l -glutamate and surface expression, suggesting that additional mechanisms than the potency of l -glutamate regulate the surface delivery of the GluN1/GluN2 receptors 40 .…”

Distinct roles of GRIN2A and GRIN2B variants in neurological conditions

“…The E413G variant is in close proximity to the glutamate-binding site but is not in physical contact with the agonist glutamate. Modelling of the protein structure suggests that GluN2B-E413 can alter agonist dissociation by increasing the ability of water to compete with agonist binding, thereby accelerating glutamate unbinding and likely rendering the synaptic NMDAR response time course briefer than that for wild-type NMDARs 82, 95 .…”

A Mechanistic Model of NMDA and AMPA Receptor-Mediated Synaptic Transmission in Individual Hippocampal CA3-CA1 Synapses: A Computational Multiscale Approach

“…This kinetic feature, together with EC 50 values of the agonist, constitute a prominent quantitative feature used to perform functional analysis of ion channels [46]. Many published studies on rare NMDA receptor variants have tried to assess the severity of a certain mutation, considering its impact on both glutamate potency and deactivation time constant [25,[47][48][49].…”

“…We used our model to predict the glutamate affinity (K d ) and the weighted deactivation time constant (τ w ) in NMDA receptor variants, based on the EC 50 values that have been reported in different experimental and computational studies [25,47,48,50]. In particular, we focused on two rare variants: Glu413Gly and Cys461Phe that fall inside the GluN2B binding pocket (Figure 9).…”

“…In particular, we focused on two rare variants: Glu413Gly and Cys461Phe that fall inside the GluN2B binding pocket (Figure 9). These variants have been shown to decrease the glutamate potency, which may result from a decrease in the glutamate affinity [47,48,50,51]. Figure 9.…”