ArticleProceedings of the National Academy of Sciences of the United States of America2012
Multiscale natural moves refine macromolecules using single-particle electron microscopy projection images.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Hierarchical natural move Monte Carlo refines flexible RNA structures into cryo-EM densities.RNA (New York, N.Y.) · 2020Article
- HLA-DM Stabilizes the Empty MHCII Binding Groove: A Model Using Customized Natural Move Monte Carlo.Journal of chemical information and modeling · 2019Article
- Structural insights into species-specific features of the ribosome from the human pathogen Mycobacterium tuberculosis.Nucleic acids research · 2017Article
- Reconstruction of 3D structures of MET antibodies from electron microscopy 2D class averages.PloS one · 2017Article
- Massively parallel unsupervised single-particle cryo-EM data clustering via statistical manifold learning.PloS one · 2017Article
- Modeling Functional Motions of Biological Systems by Customized Natural Moves.Biophysical journal · 2016Article
- Exploring peptide/MHC detachment processes using hierarchical natural move Monte Carlo.Bioinformatics (Oxford, England) · 2016Article
- Single-Particle Refinement and Variability Analysis in EMAN2.1.Methods in enzymology · 2016Review
- Structure of Ribosomal Silencing Factor Bound to Mycobacterium tuberculosis Ribosome.Structure (London, England : 1993) · 2015Article
- Bayesian analysis of individual electron microscopy images: towards structures of dynamic and heterogeneous biomolecular assemblies.Journal of structural biology · 2013Article
- Computational methods for constructing protein structure models from 3D electron microscopy maps.Journal of structural biology · 2013Article
- Conformational States of macromolecular assemblies explored by integrative structure calculation.Structure (London, England : 1993) · 2013Article
- Assembly of macromolecular complexes by satisfaction of spatial restraints from electron microscopy images.Proceedings of the National Academy of Sciences of the United States of America · 2012Article
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3 authors.
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Abstract
The method presented here refines molecular conformations directly against projections of single particles measured by electron microscopy. By optimizing the orientation of the projection at the same time as the conformation, the method is well-suited to two-dimensional class averages from cryoelectron microscopy. Such direct use of two-dimensional images circumvents the need for a three-dimensional density map, which may be difficult to reconstruct from projections due to structural heterogeneity or preferred orientations of the sample on the grid. Our refinement protocol exploits Natural Move Monte Carlo to model a macromolecule as a small number of segments connected by flexible loops, on multiple scales. After tests on artificial data from lysozyme, we applied the method to the Methonococcus maripaludis chaperonin. We successfully refined its conformation from a closed-state initial model to an open-state final model using just one class-averaged projection. We also used Natural Moves to iteratively refine against heterogeneous projection images of Methonococcus maripaludis chaperonin in a mix of open and closed states. Our results suggest a general method for electron microscopy refinement specially suited to macromolecules with significant conformational flexibility. The algorithm is available in the program Methodologies for Optimization and Sampling In Computational Studies.
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