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bioRxiv · 10.1101/2021.01.04.425171

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

Rovsnik, U.·Zhuang, Y.·Forsberg, B. O.·Carroni, M.·Yvonnesdotter, L.·Howard, R. J.·Lindahl, E.
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Abstract

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 sidechain rearrangements at the subunit/domain interface, particularly involving functionally important residues in the {beta}1-{beta}2 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 support a dissection of protonation and activation steps in pH-stimulated conformational cycling in GLIC, including interfacial rearrangements largely conserved in the pentameric channel family.

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Rovsnik, U., Zhuang, Y., Forsberg, B. O., Carroni, M., Yvonnesdotter, L., Howard, R. J., Lindahl, E.. 2021-01-05. Dynamic closed states of a ligand-gated ion channel captured by cryo-EM and simulations. https://doi.org/10.1101/2021.01.04.425171

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