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Ansell, T. Bertie; Song, Wanling; Coupland, Claire E.; Carrique, Loic; Corey, Robin A.; Duncan, Anna L.; Cassidy, C. Keith; Geurts, Maxwell M. G.; Rasmussen, Tim; Ward, Andrew B.; Siebold, Christian; Stansfeld, Phillip J.; Sansom, Mark S. P.
Nature communications, 11/2023, Volume: 14, Issue: 1Journal Article
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.
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