LipIDens: simulation assisted interpretation of lipid densities in cryo-EM structures of membrane proteins

T. Bertie Ansell, Wanling Song, Claire E. Coupland, Loic Carrique, Robin A. Corey, Anna L. Duncan, C. Keith Cassidy, Maxwell M. G. Geurts, Tim Rasmussen, Andrew B. Ward, Christian Siebold, Phillip J. Stansfeld and Mark S. P. Sansom ()
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T. Bertie Ansell: University of Oxford
Wanling Song: University of Oxford
Claire E. Coupland: University of Oxford
Loic Carrique: University of Oxford
Robin A. Corey: University of Oxford
Anna L. Duncan: University of Oxford
C. Keith Cassidy: University of Oxford
Maxwell M. G. Geurts: University of Oxford
Tim Rasmussen: Universität Würzburg, Haus D15
Andrew B. Ward: The Scripps Research Institute
Christian Siebold: University of Oxford
Phillip J. Stansfeld: University of Warwick
Mark S. P. Sansom: University of Oxford

Nature Communications, 2023, vol. 14, issue 1, 1-14

Abstract: 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.

Date: 2023
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DOI: 10.1038/s41467-023-43392-y

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