MDSPACE: Extracting Continuous Conformational Landscapes from Cryo-EM Single Particle Datasets Using 3D-to-2D Flexible Fitting based on Molecular Dynamics Simulation

Autor: Rémi Vuillemot, Alex Mirzaei, Mohamad Harastani, Ilyes Hamitouche, Léo Fréchin, Bruno P. Klaholz, Osamu Miyashita, Florence Tama, Isabelle Rouiller, Slavica Jonic
Přispěvatelé: Bioinformatique et BioPhysique [IMPMC] (IMPMC_BIBIP), Institut de minéralogie, de physique des matériaux et de cosmochimie (IMPMC), Muséum national d'Histoire naturelle (MNHN)-Institut de recherche pour le développement [IRD] : UR206-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN)-Institut de recherche pour le développement [IRD] : UR206-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), RIKEN Center for Computational Science [Kobe] (RIKEN CCS), RIKEN - Institute of Physical and Chemical Research [Japon] (RIKEN), Nagoya University Graduate School of Science, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Victoria, ANR-19-CE11-0008,EMBioMolMov,Décryptage des mouvements moléculaires continus des complexes biomacromoléculaires par de nouvelles méthodes d'analyse d'images de cryo-microscopie électronique(2019)
Rok vydání: 2023
Předmět:
continuous conformational variability
[SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry
Molecular Biology/Structural Biology [q-bio.BM]
principal component analysis
molecular dynamics simulation (MD simulation)
[SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry
Molecular Biology/Molecular biology
[INFO.INFO-SE]Computer Science [cs]/Software Engineering [cs.SE]
[INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation
[SDV.BBM.BP]Life Sciences [q-bio]/Biochemistry
Molecular Biology/Biophysics
3D-to-2D flexible fitting
[INFO.INFO-LG]Computer Science [cs]/Machine Learning [cs.LG]
Structural Biology
Cryo electron microscopy (cryo-EM)
[INFO.INFO-TI]Computer Science [cs]/Image Processing [eess.IV]
conformational landscapes
[INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM]
single particle analysis
Molecular Biology
Zdroj: Journal of Molecular Biology
Journal of Molecular Biology, 2023, pp.167951. ⟨10.1016/j.jmb.2023.167951⟩
ISSN: 0022-2836
1089-8638
Popis: International audience; 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.
Databáze: OpenAIRE
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