Lateral fenestrations in the extracellular domain of the glycine receptor contribute to the main chloride permeation pathway

Abstract

Glycine receptors (GlyRs) are ligand-gated ion channels mediating signal transduction at chemical synapses. Since the early patch-clamp electrophysiology studies, the details of the ion permeation mechanism have remained elusive. Here, we combine molecular dynamics simulations of a zebrafish GlyR-α1 model devoid of the intracellular domain with mutagenesis and single-channel electrophysiology of the full-length human GlyR-α1. We show that lateral fenestrations between subunits in the extracellular domain provide the main translocation pathway for chloride ions to enter/exit a central water-filled vestibule at the entrance of the transmembrane channel. In addition, we provide evidence that these fenestrations are at the origin of current rectification in known anomalous mutants and design de novo two inward-rectifying channels by introducing mutations within them. These results demonstrate the central role of lateral fenestrations on synaptic neurotransmission.

Wordom update 2: A user-friendly program for the analysis of molecular structures and conformational ensembles

“…Recently, using an original combination of in-silico electrophysiology and polyatomic anion permeation simulations, we have provided evidence that none of the early cryo-EM structures of the glycine receptor is physiologically relevant and identified an alternative open-channel state by MD simulations, which was ion-conductive and anion-selective in semi-quantitative agreement with experiments [40] . Analysis tools to display the morphology of the ion pore and quantify both ion and water fluxes through it are critically important for a structure-to-function annotation as well as the exploration of the ion-permeation mechanism(s) [116] .…”