Details

Autor(en) / Beteiligte

• 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.

Titel

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

Ist Teil von

• Nature communications, 2023-11, Vol.14 (1), p.7774-7774, Article 7774

Ort / Verlag

London: Nature Publishing Group

Erscheinungsjahr

2023

Quelle

Alma/SFX Local Collection

Beschreibungen/Notizen

• 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.