MDSPACE: Extracting continuous conformational landscapes from cryo-EM single particle datasets using 3D-to-2D flexible fitting based on Molecular Dynamics simulation.

Date publication

janvier 2023

Journal

Journal of molecular biology

Auteurs

Membres identifiés du Cancéropôle Est :
Dr KLAHOLZ Bruno

Tous les auteurs :
Vuillemot R, Mirzaei A, Harastani M, Hamitouche I, Fréchin L, Klaholz BP, Miyashita O, Tama F, Rouiller I, Jonic S

Lien Pubmed

https://www.ncbi.nlm.nih.gov/pubmed/36638910

Résumé

This article presents an original approach for extracting atomic-resolution landscapes of continuous conformational variability of biomolecular complexes from cryo electron microscopy (cryo-EM) single particle images. This approach is based on a new 3D-to-2D flexible fitting method, which uses molecular dynamics (MD) simulation and is embedded in an iterative conformational-landscape refinement scheme. This new approach is referred to as MDSPACE, which stands for Molecular Dynamics simulation for Single Particle Analysis of Continuous Conformational hEterogeneity. The article describes the MDSPACE approach and shows its performance using synthetic and experimental datasets. Running title: MDSPACE.

Mots clés

3D-to-2D flexible fitting, Cryo electron microscopy (cryo-EM), conformational landscapes, continuous conformational variability, molecular dynamics simulation (MD simulation), principal component analysis, single particle analysis

Référence

J Mol Biol. 2023 01 10;:167951