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TitleDiscovery of lipid binding sites in a ligand-gated ion channel by integrating simulations and cryo-EM.
Journal, issue, pagesElife, Vol. 12, Year 2024
Publish dateJan 30, 2024
AuthorsCathrine Bergh / Urška Rovšnik / Rebecca Howard / Erik Lindahl /
PubMed AbstractLigand-gated ion channels transduce electrochemical signals in neurons and other excitable cells. Aside from canonical ligands, phospholipids are thought to bind specifically to the transmembrane ...Ligand-gated ion channels transduce electrochemical signals in neurons and other excitable cells. Aside from canonical ligands, phospholipids are thought to bind specifically to the transmembrane domain of several ion channels. However, structural details of such lipid contacts remain elusive, partly due to limited resolution of these regions in experimental structures. Here, we discovered multiple lipid interactions in the channel GLIC by integrating cryo-electron microscopy and large-scale molecular simulations. We identified 25 bound lipids in the GLIC closed state, a conformation where none, to our knowledge, were previously known. Three lipids were associated with each subunit in the inner leaflet, including a buried interaction disrupted in mutant simulations. In the outer leaflet, two intrasubunit sites were evident in both closed and open states, while a putative intersubunit site was preferred in open-state simulations. This work offers molecular details of GLIC-lipid contacts particularly in the ill-characterized closed state, testable hypotheses for state-dependent binding, and a multidisciplinary strategy for modeling protein-lipid interactions.
External linksElife / PubMed:38289224 / PubMed Central
MethodsEM (single particle)
Resolution2.9 Å
Structure data

15649

8atg

EMDB-15649, PDB-8atg:
Pentameric ligand-gated ion channel GLIC with bound lipids
Method: EM (single particle) / Resolution: 2.9 Å

Chemicals

ChemComp-POV:
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / phospholipid*YM

Source
  • gloeobacter violaceus (bacteria)
KeywordsMEMBRANE PROTEIN / GLIC / ion channel / pentameric channel / proton-gated channel

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