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Adaptive sampling-based structural prediction reveals opening of a GABAA receptor through the αβ interface
KTH, School of Engineering Sciences (SCI), Applied Physics, Biophysics.ORCID iD: 0000-0003-3542-333X
KTH, School of Electrical Engineering and Computer Science (EECS), Computer Science, Computational Science and Technology (CST).
KTH, School of Engineering Sciences (SCI), Applied Physics, Biophysics. KTH, Centres, Science for Life Laboratory, SciLifeLab.ORCID iD: 0000-0003-2049-3378
KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences (SCI), Applied Physics, Biophysics. KTH Royal Inst Technol, Dept Appl Phys, SciLifeLab, Tomtebodavagen 23, S-17165 Stockholm, Sweden.;Stockholm Univ, Dept Biophys & Biochem, SciLifeLab, Tomtebodavagen 23, S-17165 Stockholm, Sweden..ORCID iD: 0000-0002-2734-2794
2025 (English)In: Science Advances, E-ISSN 2375-2548, Vol. 11, no 2, article id eadq3788Article in journal (Refereed) Published
Abstract [en]

gamma-Aminobutyric acid type A (GABAA) receptors are ligand-gated ion channels in the central nervous system with largely inhibitory function. Despite being a target for drugs including general anesthetics and benzodiazepines, experimental structures have yet to capture an open state of classical synaptic alpha 1 beta 2 gamma 2 GABAA receptors. Here, we use a goal-oriented adaptive sampling strategy in molecular dynamics simulations followed by Markov state modeling to capture an energetically stable putative open state of the receptor. The model conducts chloride ions with comparable conductance as in electrophysiology measurements. Relative to experimental structures, our open model is relatively expanded at both the cytoplasmic (-2 ') and central (9 ') gates, coordinated with distinctive rearrangements at the transmembrane alpha beta subunit interface. Consistent with previous experiments, targeted substitutions disrupting interactions at this interface slowed the open-to-desensitized transition rate. This work demonstrates the capacity of advanced simulation techniques to investigate a computationally and experimentally plausible functionally critical of a complex membrane protein yet to be resolved by experimental methods.

Place, publisher, year, edition, pages
American Association for the Advancement of Science (AAAS) , 2025. Vol. 11, no 2, article id eadq3788
National Category
Biophysics
Identifiers
URN: urn:nbn:se:kth:diva-359518DOI: 10.1126/sciadv.adq3788ISI: 001392723500018PubMedID: 39772677Scopus ID: 2-s2.0-85215122797OAI: oai:DiVA.org:kth-359518DiVA, id: diva2:1934900
Note

QC 20250205

Available from: 2025-02-05 Created: 2025-02-05 Last updated: 2025-02-05Bibliographically approved

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Haloi, NandanEriksson Lidbrink, SamuelHoward, Rebecca J.Lindahl, Erik

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Haloi, NandanEriksson Lidbrink, SamuelHoward, Rebecca J.Lindahl, Erik
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