Un-gating and allosteric modulation of a pentameric ligand-gated ion channel captured by molecular dynamics
Open accessAbstract
Pentameric ligand-gated ion channels (pLGICs) mediate intercellular communication at synapses through the opening of an ion pore in response to the binding of a neurotransmitter. Despite the increasing availability of high-resolution structures of pLGICs, a detailed understanding of the functional isomerization from closed to open (gating) and back is currently missing. Here, we provide the first atomistic description of the transition from open to closed (un-gating) in the glutamate-gated chloride channel (GluCl) from Caenorhabditis Elegans. Starting with the active-state structure solved in complex with the neurotransmitter L-glutamate and the positive allosteric modulator (PAM) ivermectin, we analyze the spontaneous relaxation of the channel upon removal of ivermectin by explicit solvent/membrane Molecular Dynamics (MD) simulations. The μs-long trajectories support the conclusion that ion-channel deactivation is mediated by two distinct quaternary transitions, i.e. a global receptor twisting followed by the radial expansion (or blooming) of the extracellular domain. At variance with previous models, we show that pore closing is exclusively regulated by the global twisting, which controls the position of the β1-β2 loop relative to the M2-M3 loop at the EC/TM domain interface. Additional simulations with L-glutamate restrained to the crystallographic binding mode and ivermectin removed indicate that the same twisting isomerization is regulated by agonist binding at the orthosteric site. These results provide a structural model for gating in pLGICs and suggest a plausible mechanism for the pharmacological action of PAMs in this neurotransmitter receptor family. The simulated un-gating converges to the X-ray structure of GluCl resting state both globally and locally, demonstrating the predictive character of state-of-art MD simulations.
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A more extended relaxation of GluCl in the absence of ivermectin captured the full closing motion consistent with the ligand-free GluCl X-ray structure.
“A more extended relaxation of the same channel in the absence of ivermectin captured the full closing motion that is consistent with the ligand-free GluCl X-ray structure (Martin et al., 2017).”
From Allostery in Its Many Disguises: From Theory to Applications (2019) · cites this paper as Martin et al., 2017
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- Authors
- Martin, N. E., Malik, S., Calimet, N., Changeux, J.-P., & Cecchini, M.
- Affiliations
- Centre National de la Recherche Scientifique (FR)
- Corresponding author
- Cecchini, Marco
- Venue
- PLoS Computational Biology
- Publisher
- Public Library of Science (PLoS)
- Published
- 2017-10-25
- Volume
- 13
- Issue
- 10
- Pages
- e1005784
- ISSN
- 1553-734X (ISSN-L)
- 1553-7358
- PMC
- PMC5673239
- OpenAlex
- W2765330520
- Cited by
- 38
- References
- 52
- Citations by year
- 2026: 1 · 2025: 2 · 2024: 1 · 2023: 5 · 2022: 2 · 2021: 6 · 2020: 2 · 2019: 9 · 2018: 9 · 2017: 1
- FWCI
- 2.35
- Type
- journal article
- Language
- en
- Update notices
- new_version (2017-11-06)
- Open access
- gold
- doi.org
- Licence
- Locations
- PLoS Computational Biology (publishedVersion, cc-by)
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- HAL (submittedVersion, other-oa)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- Figshare (submittedVersion, cc-by)
- Funders
- Agence Nationale de la Recherche (CSC-MCE-13)
- Horizon 2020 (HBP SGA1)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Nicotinic Acetylcholine Receptors Study
- Life Sciences › Neuroscience › Cellular and Molecular Neuroscience › Neuroscience and Neuropharmacology Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Receptor Mechanisms and Signaling
- Keywords
- pentameric ligand-gated ion channels, allosteric modulation, glutamate-gated chloride channels, ivermectin, positive allosteric modulators, channel deactivation, Caenorhabditis elegans, ion channel gating mechanism
- MeSH terms
- Allosteric Regulation, Allosteric Site, Binding Sites, Ivermectin, Ligands, Models, Chemical, Protein Binding, Protein Conformation, Ion Channel Gating, Chloride Channels, Neurotransmitter Agents, Glutamic Acid, Molecular Dynamics Simulation, Ligand-Gated Ion Channels
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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