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© Structural Dynamics Of Macromolecules
The structure of a bacterial analog of the nicotinic receptor (one color per subunit) inserted into the cell membrane (grey and orange). A representation of the volume accessible to ions is shown in yellow.
Publication : Proceedings of the National Academy of Sciences of the United States of America

String method solution of the gating pathways for a pentameric ligand-gated ion channel

Scientific Fields
Diseases
Organisms
Applications
Technique

Published in Proceedings of the National Academy of Sciences of the United States of America - 09 May 2017

Lev B, Murail S, Poitevin F, Cromer BA, Baaden M, Delarue M, Allen TW

Link to Pubmed [PMID] – 28487483

Proc. Natl. Acad. Sci. U.S.A. 2017 05;114(21):E4158-E4167

Pentameric ligand-gated ion channels control synaptic neurotransmission by converting chemical signals into electrical signals. Agonist binding leads to rapid signal transduction via an allosteric mechanism, where global protein conformational changes open a pore across the nerve cell membrane. We use all-atom molecular dynamics with a swarm-based string method to solve for the minimum free-energy gating pathways of the proton-activated bacterial GLIC channel. We describe stable wetted/open and dewetted/closed states, and uncover conformational changes in the agonist-binding extracellular domain, ion-conducting transmembrane domain, and gating interface that control communication between these domains. Transition analysis is used to compute free-energy surfaces that suggest allosteric pathways; stabilization with pH; and intermediates, including states that facilitate channel closing in the presence of an agonist. We describe a switching mechanism that senses proton binding by marked reorganization of subunit interface, altering the packing of β-sheets to induce changes that lead to asynchronous pore-lining M2 helix movements. These results provide molecular details of GLIC gating and insight into the allosteric mechanisms for the superfamily of pentameric ligand-gated channels.

https://www.ncbi.nlm.nih.gov/pubmed/28487483