Mechanisms of activation and desensitization of full-length glycine receptor in lipid nanodiscs

Abstract

Glycinergic synapses play a central role in motor control and pain processing in the central nervous system. Glycine receptors (GlyRs) are key players in mediating fast inhibitory neurotransmission at these synapses. While previous high-resolution structures have provided insights into the molecular architecture of GlyR, several mechanistic questions pertaining to channel function are still unanswered. Here, we present Cryo-EM structures of the full-length GlyR protein complex reconstituted into lipid nanodiscs that are captured in the unliganded (closed), glycine-bound (open and desensitized), and allosteric modulator-bound conformations. A comparison of these states reveals global conformational changes underlying GlyR channel gating and modulation. The functional state assignments were validated by molecular dynamics simulations, and the observed permeation events are in agreement with the anion selectivity and conductance of GlyR. These studies provide the structural basis for gating, ion selectivity, and single-channel conductance properties of GlyR in a lipid environment.

A critical residue in the α1M2–M3 linker regulating mammalian GABAA receptor pore gating by diazepam

“…Conversely, a more compact transmembrane domain may also enhance coupling with the BZD site (Kim et al, 2020). Valine and threonine residues in GlyR and AchR aligning with V279 ( Figure 1-figure supplement 1) adopt a similar conformation (Kumar et al, 2020;Nemecz et al, 2016;Du et al, 2015), suggesting that this residue has a conserved role in other pLGICs.…”

“…For example, a compression of the ends of the M2–M3 linker would cause the middle of the linker to be squeezed outward toward the neighboring γ 2 subunit, potentially enhancing intersubunit coupling. Comparison of GlyR structures in apo or antagonist-bound versus agonist-bound conformations indicates that intersubunit interactions between the M2–M3 linker in the vicinity of the valine aligning with V279 and the following serine, and the top of the M1 helix in the adjacent subunit are weakened during channel activation ( Du et al, 2015 ; Kumar et al, 2020 ). Thus, a stronger intersubunit coupling in this area could potentially both reduce unliganded opening and enhance coupling with rearrangements of the γ 2 subunit upon BZD binding.…”

Unmasking coupling between channel gating and ion permeation in the muscle nicotinic receptor

“…Structural and single channel functional studies on members of the muscle AChR have provided a picture of channel gating in which local agonist-induced structural changes propagate away from the binding site and produce motions in many parts of the protein ( Mukhtasimova et al, 2005 ; Mukhtasimova and Sine, 2007 ; Mukhtasimova et al, 2009 ; Mukhtasimova and Sine, 2018 ; Purohit and Auerbach, 2007a ; Purohit and Auerbach, 2007b ; Jha et al, 2007 ; Cadugan and Auerbach, 2010 ), ultimately resulting in dilation of the channel pore and permeation of hydrated ions. Recent cryo-electron microscopy studies have further clarified this picture by providing snapshots of the ‘closed’ and ‘open’ states of pLGICs, assigned based upon the size of the pore relative to the hydrated ions and molecular dynamics simulations of ion conduction ( Basak et al, 2018 ; Polovinkin et al, 2018 ; Kumar et al, 2020 ). Comparing the structures of these closed and open states, one sees that whereas the closed structures show narrow constrictions of the pore at the 9’ and −1’ positions, the open structures show expansion at these positions.…”

Molecular Simulations of Hydrophobic Gating of Pentameric Ligand Gated Ion Channels: Insights into Water and Ions

“…Here we will focus on the use of three different levels of computational study to explore the nature of the hydrophobic gate in these bilayer-embedded GlyR structures. 85 In particular, we will compare the closed (apo) state of the GlyR (PDB id 6UBS) with an open state of the channel (PDB id 6UD3) obtained by studying the GlyR in a complex with both the agonist (i.e., activator) glycine plus an open channel blocker, picrotoxin (PTX).…”

“… Application of three levels of simulation analysis to novel pLGIC channel structures. Figures modified with permission from ref ( 85 ). Copyright 2020 Nature Research.…”