LipIDens: simulation assisted interpretation of lipid densities in cryo-EM structures of membrane proteins.
Nat Commun
; 14(1): 7774, 2023 Nov 27.
Article
em En
| MEDLINE
| ID: mdl-38012131
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.
Texto completo:
1
Base de dados:
MEDLINE
Assunto principal:
Simulação de Dinâmica Molecular
/
Proteínas de Membrana
Idioma:
En
Ano de publicação:
2023
Tipo de documento:
Article
País de afiliação:
Reino Unido