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

[Display omitted] •MDSPACE extracts continuous conformational landscapes from single particle datasets.•It uses MD-simulation-based 3D-to-2D flexible fitting of an atomic structure to images.•It refines conformational landscapes using principal motion directions learned iteratively.•Its performance...

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Vydáno v:	Journal of molecular biology Ročník 435; číslo 9; s. 167951
Hlavní autoři:	Vuillemot, Rémi, Mirzaei, Alex, Harastani, Mohamad, Hamitouche, Ilyes, Fréchin, Léo, Klaholz, Bruno P., Miyashita, Osamu, Tama, Florence, Rouiller, Isabelle, Jonic, Slavica
Médium:	Journal Article
Jazyk:	angličtina
Vydáno:	Netherlands Elsevier Ltd 01.05.2023 Elsevier
Témata:	3D-to-2D flexible fitting Biochemistry, Molecular Biology Bioinformatics Biophysics Computer Science conformational landscapes continuous conformational variability cryo electron microscopy (cryo-EM) Cryoelectron Microscopy - methods Image Processing Life Sciences Machine Learning Modeling and Simulation Molecular biology Molecular Dynamics Simulation molecular dynamics simulation (MD simulation) Protein Conformation Single Molecule Imaging Software Engineering Structural Biology cryo electron microscopy (cryo-EM) 3D-to-2D flexible fitting molecular dynamics simulation (MD simulation) continuous conformational variability conformational landscapes Cryo electron microscopy (cryo-EM) single particle analysis principal component analysis
ISSN:	0022-2836, 1089-8638, 1089-8638
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Popis
Shrnutí:	[Display omitted] •MDSPACE extracts continuous conformational landscapes from single particle datasets.•It uses MD-simulation-based 3D-to-2D flexible fitting of an atomic structure to images.•It refines conformational landscapes using principal motion directions learned iteratively.•Its performance is shown with synthetic and experimental data. 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.
Bibliografie:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23
ISSN:	0022-2836 1089-8638 1089-8638
DOI:	10.1016/j.jmb.2023.167951