Identification of a pre-active conformation of a pentameric channel receptor
- Institut Pasteur, France
- Weill Cornell Medicine, United States
- Université Paris-Sud, France
- Inserm U1024, CNRS 8197, Institute of Biology, Ecole Normale Supérieure, France
Abstract
Pentameric ligand-gated ion channels (pLGICs) mediate fast chemical signalling through global allosteric transitions. Despite the existence of several high-resolution structures of pLGICs, their dynamical properties remain elusive. Using the proton-gated channel GLIC, we engineered multiple fluorescent reporters, each incorporating a bimane and a tryptophan/tyrosine, whose close distance causes fluorescence quenching. We show that proton application causes a global compaction of the extracellular subunit interface, coupled to an outward motion of the M2-M3 loop near the channel gate. These movements are highly similar in lipid vesicles and detergent micelles. These reorganizations are essentially completed within 2 ms and occur without channel opening at low proton concentration, indicating that they report a pre-active intermediate state in the transition pathway towards activation. This provides a template to investigate the gating of eukaryotic neurotransmitter receptors, for which intermediate states also participate in activation.
Article and author information
Author details
Pierre-Jean Corringer
Funding
Agence Nationale de la Recherche (Pentagate)
- Anaïs Menny
- Solène N Lefebvre
- Emmanuelle Drège
- Zaineb Fourati
- Marc Delarue
- Delphine Joseph
- Pierre-Jean Corringer
Centre National de la Recherche Scientifique (UMR 3571)
- Anaïs Menny
- Solène N Lefebvre
- Delphine Joseph
Institut Pasteur
- Anaïs Menny
- Solène N Lefebvre
- Zaineb Fourati
- Marc Delarue
- Pierre-Jean Corringer
Université Pierre et Marie Curie (PhD student fellowship)
- Anaïs Menny
- Solène N Lefebvre
Fondation pour la Recherche Médicale (DEQ20140329497)
- Anaïs Menny
- Pierre-Jean Corringer
National Institutes of Health (R01 GM088352)
- Crina M Nimigean
Centre National de la Recherche Scientifique (UMR 8076)
- Emmanuelle Drège
- Delphine Joseph
Centre National de la Recherche Scientifique (UMR 3528)
- Zaineb Fourati
- Marc Delarue
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Copyright
© 2017, Menny et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
Metrics
-
- 2,056
- views
-
- 528
- downloads
-
- 43
- citations
Views, downloads and citations are aggregated across all versions of this paper published by eLife.
Download links
A two-part list of links to download the article, or parts of the article, in various formats.
Downloads (link to download the article as PDF)
Open citations (links to open the citations from this article in various online reference manager services)
Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)
Identification of a pre-active conformation of a pentameric channel receptor
eLife 6:e23955.
https://doi.org/10.7554/eLife.23955
Further reading
-
- Biochemistry and Chemical Biology
- Structural Biology and Molecular Biophysics
African trypanosomes are the causative agents of neglected tropical diseases affecting both humans and livestock. Disease control is highly challenging due to an increasing number of drug treatment failures. African trypanosomes are extracellular, blood-borne parasites that mainly rely on glycolysis for their energy metabolism within the mammalian host. Trypanosomal glycolytic enzymes are therefore of interest for the development of trypanocidal drugs. Here, we report the serendipitous discovery of a camelid single-domain antibody (sdAb aka Nanobody) that selectively inhibits the enzymatic activity of trypanosomatid (but not host) pyruvate kinases through an allosteric mechanism. By combining enzyme kinetics, biophysics, structural biology, and transgenic parasite survival assays, we provide a proof-of-principle that the sdAb-mediated enzyme inhibition negatively impacts parasite fitness and growth.
-
- Structural Biology and Molecular Biophysics
The relationship between protein dynamics and function is essential for understanding biological processes and developing effective therapeutics. Functional sites within proteins are critical for activities such as substrate binding, catalysis, and structural changes. Existing computational methods for the predictions of functional residues are trained on sequence, structural, and experimental data, but they do not explicitly model the influence of evolution on protein dynamics. This overlooked contribution is essential as it is known that evolution can fine-tune protein dynamics through compensatory mutations either to improve the proteins’ performance or diversify its function while maintaining the same structural scaffold. To model this critical contribution, we introduce DyNoPy, a computational method that combines residue coevolution analysis with molecular dynamics simulations, revealing hidden correlations between functional sites. DyNoPy constructs a graph model of residue–residue interactions, identifies communities of key residue groups, and annotates critical sites based on their roles. By leveraging the concept of coevolved dynamical couplings—residue pairs with critical dynamical interactions that have been preserved during evolution—DyNoPy offers a powerful method for predicting and analysing protein evolution and dynamics. We demonstrate the effectiveness of DyNoPy on SHV-1 and PDC-3, chromosomally encoded β-lactamases linked to antibiotic resistance, highlighting its potential to inform drug design and address pressing healthcare challenges.
