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LipIDens : simulation assisted interpretation of lipid densities in cryo-EM structures of membrane proteins
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Ansell, T. Bertie, Song, Wanling, Coupland, Claire E., Carrique, Loïc, Corey, Robin A., Duncan, Anna L., Cassidy, C. Keith, Geurts, Maxwell M. G., Rasmussen, Tim, Ward, Andrew B., Siebold, Christian, Stansfeld, Phillip J. and Sansom, Mark S. P. (2023) LipIDens : simulation assisted interpretation of lipid densities in cryo-EM structures of membrane proteins. Nature Communications, 14 (1). 7774. doi:10.1038/s41467-023-43392-y ISSN 2041-1723.
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Official URL: https://doi.org/10.1038/s41467-023-43392-y
Abstract
Cryo-electron microscopy (cryo-EM) enables the determination of membrane protein structures in native-like environments. Characterising how membrane proteins interact with the surrounding membrane lipid environment is assisted by resolution of lipid-like densities visible in cryo-EM maps. Nevertheless, establishing the molecular identity of putative lipid and/or detergent densities remains challenging. Here we present LipIDens, a pipeline for molecular dynamics (MD) simulation-assisted interpretation of lipid and lipid-like densities in cryo-EM structures. The pipeline integrates the implementation and analysis of multi-scale MD simulations for identification, ranking and refinement of lipid binding poses which superpose onto cryo-EM map densities. Thus, LipIDens enables direct integration of experimental and computational structural approaches to facilitate the interpretation of lipid-like cryo-EM densities and to reveal the molecular identities of protein-lipid interactions within a bilayer environment. We demonstrate this by application of our open-source LipIDens code to ten diverse membrane protein structures which exhibit lipid-like densities.
Item Type: | Journal Article | |||||||||||||||||||||||||||||||||||||||||||||||||||
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Subjects: | Q Science > QP Physiology | |||||||||||||||||||||||||||||||||||||||||||||||||||
Divisions: | Faculty of Science, Engineering and Medicine > Science > Chemistry Faculty of Science, Engineering and Medicine > Science > Life Sciences (2010- ) |
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SWORD Depositor: | Library Publications Router | |||||||||||||||||||||||||||||||||||||||||||||||||||
Library of Congress Subject Headings (LCSH): | Lipids -- Simulation methods, Membrane proteins, Membrane lipids, Electron microscopy, Cryobiochemistry | |||||||||||||||||||||||||||||||||||||||||||||||||||
Journal or Publication Title: | Nature Communications | |||||||||||||||||||||||||||||||||||||||||||||||||||
Publisher: | Nature Publishing Group UK | |||||||||||||||||||||||||||||||||||||||||||||||||||
ISSN: | 2041-1723 | |||||||||||||||||||||||||||||||||||||||||||||||||||
Official Date: | 27 November 2023 | |||||||||||||||||||||||||||||||||||||||||||||||||||
Dates: |
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Volume: | 14 | |||||||||||||||||||||||||||||||||||||||||||||||||||
Number: | 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||
Article Number: | 7774 | |||||||||||||||||||||||||||||||||||||||||||||||||||
DOI: | 10.1038/s41467-023-43392-y | |||||||||||||||||||||||||||||||||||||||||||||||||||
Status: | Peer Reviewed | |||||||||||||||||||||||||||||||||||||||||||||||||||
Publication Status: | Published | |||||||||||||||||||||||||||||||||||||||||||||||||||
Access rights to Published version: | Open Access (Creative Commons) | |||||||||||||||||||||||||||||||||||||||||||||||||||
Date of first compliant deposit: | 6 December 2023 | |||||||||||||||||||||||||||||||||||||||||||||||||||
Date of first compliant Open Access: | 6 December 2023 | |||||||||||||||||||||||||||||||||||||||||||||||||||
RIOXX Funder/Project Grant: |
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