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Large scale investigation of GPCR molecular dynamics data uncovers allosteric sites and lateral gateways
Univ Pompeu Fabra UPF, Dept Med & Life Sci, Barcelona, Spain.;Hosp del Mar Med Res Inst IMIM, Res Programme Biomed Informat GRIB, Barcelona, Spain..
Hosp del Mar Med Res Inst IMIM, Res Programme Biomed Informat GRIB, Barcelona, Spain.;InterAx Biotech AG, Villigen, Switzerland..
Univ Pompeu Fabra UPF, Dept Med & Life Sci, Barcelona, Spain.;Acellera Labs, Barcelona, Spain..
Hosp del Mar Med Res Inst IMIM, Res Programme Biomed Informat GRIB, Barcelona, Spain..
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2025 (English)In: Nature Communications, E-ISSN 2041-1723, Vol. 16, article id 2020Article in journal (Refereed) Published
Abstract [en]

G protein-coupled receptors (GPCRs) constitute a functionally diverse protein family and are targets for a broad spectrum of pharmaceuticals. Technological progress in X-ray crystallography and cryogenic electron microscopy has enabled extensive, high-resolution structural characterisation of GPCRs in different conformational states. However, as highly dynamic events underlie GPCR signalling, a complete understanding of GPCR functionality requires insights into their conformational dynamics. Here, we present a large dataset of molecular dynamics simulations covering 60% of currently available GPCR structures. Our analysis reveals extensive local "breathing" motions of the receptor on a nano- to microsecond timescale and provides access to numerous previously unexplored receptor conformational states. Furthermore, we reveal that receptor flexibility impacts the shape of allosteric drug binding sites, which frequently adopt partially or completely closed states in the absence of a molecular modulator. We demonstrate that exploring membrane lipid dynamics and their interaction with GPCRs is an efficient approach to expose such hidden allosteric sites and even lateral ligand entrance gateways. The obtained insights and generated dataset on conformations, allosteric sites and lateral entrance gates in GPCRs allows us to better understand the functionality of these receptors and opens new therapeutic avenues for drug-targeting strategies.

Place, publisher, year, edition, pages
Springer Nature, 2025. Vol. 16, article id 2020
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Molecular Biology Physical Chemistry
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URN: urn:nbn:se:uu:diva-552573DOI: 10.1038/s41467-025-57034-yISI: 001435269000011PubMedID: 40016203Scopus ID: 2-s2.0-85219637527OAI: oai:DiVA.org:uu-552573DiVA, id: diva2:1948237
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Novo Nordisk, NNF18OC0031226Available from: 2025-03-28 Created: 2025-03-28 Last updated: 2025-03-28Bibliographically approved

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