Journal Article

Dynamic closed states of a ligand-gated ion channel captured by cryo-EM and simulations

Forsberg, Björn O, Rovšnik, Urška, Yvonnesdotter, Linnea, Howard, Rebecca J, Zhuang, Yuxuan, Carroni, Marta, Lindahl, Erik

2021

Overview

Ligand-gated ion channels are critical mediators of electrochemical signal transduction across evolution. Biophysical and pharmacological characterization of these receptor proteins relies on high-quality structures in multiple, subtly distinct functional states. However, structural data in this family remain limited, particularly for resting and intermediate states on the activation pathway. Here, we report cryo-electron microscopy (cryo-EM) structures of the proton-activated Gloeobacter violaceus ligand-gated ion channel (GLIC) under three pH conditions. Decreased pH was associated with improved resolution and side chain rearrangements at the subunit/domain interface, particularly involving functionally important residues in the β1–β2 and M2–M3 loops. Molecular dynamics simulations substantiated flexibility in the closed-channel extracellular domains relative to the transmembrane ones and supported electrostatic remodeling around E35 and E243 in proton-induced gating. Exploration of secondary cryo-EM classes further indicated a low-pH population with an expanded pore. These results allow us to define distinct protonation and activation steps in pH-stimulated conformational cycling in GLIC, including interfacial rearrangements largely conserved in the pentameric channel family.

• Publisher: Life Science Alliance,Life Science Alliance LLC
• Subject: Bacterial Proteins - chemistry / Channel gating / Cryoelectron Microscopy / Crystallography / Cyanobacteria - chemistry / Cyanobacteria - metabolism / Datasets / Electron microscopy / Hydrogen bonds / Hydrogen-Ion Concentration / Interfaces / Ion channels / Ion channels (ligand-gated) / Ligand-Gated Ion Channels - chemistry / Ligands / Models, Molecular / Molecular Dynamics Simulation / Mutation / pH effects / Protein Conformation / Protein Domains / Protons / Signal transduction / Structure-function relationships