A structurally derived model of subunit‐dependent NMDA receptor function

Alasdair J Gibb,Pieter Burger,Dennis C Liotta,Steven A Kell,Chris Butch,Katie M Vance,Stephen F Traynelis,Miranda J Mcdaniel,Kevin K Ogden

doi:10.1113/jp276093

Alasdair J Gibb, Pieter Burger + Show 7 more

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https://doi.org/10.1113/jp276093

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Abstract

Key points The kinetics of NMDA receptor (NMDAR) signalling are a critical aspect of the physiology of excitatory synaptic transmission in the brain.Here we develop a mechanistic description of NMDAR function based on the receptor tetrameric structure and the principle that each agonist‐bound subunit must undergo some rate‐limiting conformational change after agonist binding, prior to channel opening.By fitting this mechanism to single channel data using a new MATLAB‐based software implementation of maximum likelihood fitting with correction for limited time resolution, rate constants were derived for this mechanism that reflect distinct structural changes and predict the properties of macroscopic and synaptic NMDAR currents.The principles applied here to develop a mechanistic description of the heterotetrameric NMDAR, and the software used in this analysis, can be equally applied to other heterotetrameric glutamate receptors, providing a unifying mechanistic framework to understanding the physiology of glutamate receptor signalling in the brain. NMDA receptors (NMDARs) are tetrameric complexes comprising two glycine‐binding GluN1 and two glutamate‐binding GluN2 subunits. Four GluN2 subunits encoded by different genes can produce up to 10 different di‐ and triheteromeric receptors. In addition, some neurological patients contain a de novo mutation or inherited rare variant in only one subunit. There is currently no mechanistic framework to describe tetrameric receptor function that can be extended to receptors with two different GluN1 or GluN2 subunits. Here we use the structural features of glutamate receptors to develop a mechanism describing both single channel and macroscopic NMDAR currents. We propose that each agonist‐bound subunit undergoes some rate‐limiting conformational change after agonist binding, prior to channel opening. We hypothesize that this conformational change occurs within a triad of interactions between a short helix preceding the M1 transmembrane helix, the highly conserved M3 motif encoded by the residues SYTANLAAF, and the linker preceding the M4 transmembrane helix of the adjacent subunit. Molecular dynamics simulations suggest that pre‐M1 helix motion is uncorrelated between subunits, which we interpret to suggest independent subunit‐specific conformational changes may influence these pre‐gating steps. According to this interpretation, these conformational changes are the main determinants of the key kinetic properties of NMDA receptor activation following agonist binding, and so these steps sculpt their physiological role. We show that this structurally derived tetrameric model describes both single channel and macroscopic data, giving a new approach to interpreting functional properties of synaptic NMDARs that provides a logical framework to understanding receptors with non‐identical subunits.

Highlights

N-Methyl-D-aspartate (NMDA) receptors are a subtype of ionotropic glutamate receptor with important roles in excitatory synaptic transmission, synaptic plasticity, learning and memory (Bliss & Collingridge, 1993; Cull-Candy & Leszkiewicz, 2004; Traynelis et al 2010; Paoletti et al 2013)
We evaluated the properties of unitary currents in outside-out patch clamp recordings of single rat GluN1/GluN2A receptors expressed in HEK cells
We idealized these recordings at a resolution of 50 μs for open and closed times to obtain a sequence of 121,125 lifetimes as the receptor alternates between open and closed conformations of the pore (Fig. 1A)

Summary

Introduction

N-Methyl-D-aspartate (NMDA) receptors are a subtype of ionotropic glutamate receptor with important roles in excitatory synaptic transmission, synaptic plasticity, learning and memory (Bliss & Collingridge, 1993; Cull-Candy & Leszkiewicz, 2004; Traynelis et al 2010; Paoletti et al 2013). The receptor complex undergoes a transition to fourfold symmetry approaching the ion channel pore, where linker regions connect the ligand binding domains to the highly conserved transmembrane domains (Karakas & Furukawa, 2014; Lee et al 2014). This region includes the signature M3 gating motif (SYTANLAAF) as well as a critically positioned two-turn cuff helix that lies parallel to the plasma membrane and is in van der Waals contact with the M3 transmembrane helix that occludes the pore in the closed state (Sobolevsky et al 2009; Karakas et al 2015; Tajima et al 2016). Receptors composed of two identical GluN1 and two identical GluN2 subunits likely show equivalence in the rates of conformational change within subunit dimer pairs, while receptors with non-identical GluN1 or GluN2 subunits (often referred to as triheteromeric receptors) will lack this symmetry (Luet al. 2017)

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