ArticleProceedings of the National Academy of Sciences of the United States of America2012
Assembly of macromolecular complexes by satisfaction of spatial restraints from electron microscopy 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 26 papers.
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26 citing papers in PubMed.
- Accurate model and ensemble refinement using cryo-electron microscopy maps and Bayesian inference.PLoS computational biology · 2024Article
- SSEThread: Integrative threading of the DNA-PKcs sequence based on data from chemical cross-linking and hydrogen deuterium exchange.Progress in biophysics and molecular biology · 2019Article
- Archiving and disseminating integrative structure models.Journal of biomolecular NMR · 2019Article
- Single-Molecule 3D Images of "Hole-Hole" IgG1 Homodimers by Individual-Particle Electron Tomography.Scientific reports · 2019Article
- Review
- Computational modeling of RNA 3D structure based on experimental data.Bioscience reports · 2019Review
- A Hybrid Hamiltonian for the Accelerated Sampling along Experimental Restraints.International journal of molecular sciences · 2019Article
- Bayesian Weighing of Electron Cryo-Microscopy Data for Integrative Structural Modeling.Structure (London, England : 1993) · 2019Article
- The complex structure and function of Mediator.The Journal of biological chemistry · 2018Review
- The molecular architecture of the yeast spindle pole body core determined by Bayesian integrative modeling.Molecular biology of the cell · 2017Article
- Reconstruction of 3D structures of MET antibodies from electron microscopy 2D class averages.PloS one · 2017Article
- Metadynamic metainference: Enhanced sampling of the metainference ensemble using metadynamics.Scientific reports · 2016Article
- The molecular architecture of the Dam1 kinetochore complex is defined by cross-linking based structural modelling.Nature communications · 2015Article
- Dissecting Fission Yeast Shelterin Interactions via MICro-MS Links Disruption of Shelterin Bridge to Tumorigenesis.Cell reports · 2015Article
- Computational Refinement and Validation Protocol for Proteins with Large Variable Regions Applied to Model HIV Env Spike in CD4 and 17b Bound State.Structure (London, England : 1993) · 2015Article
- Determining protein complex structures based on a Bayesian model of in vivo Förster resonance energy transfer (FRET) data.Molecular & cellular proteomics : MCP · 2014Article
- Structural characterization by cross-linking reveals the detailed architecture of a coatomer-related heptameric module from the nuclear pore complex.Molecular & cellular proteomics : MCP · 2014Article
- Integrative structure-function mapping of the nucleoporin Nup133 suggests a conserved mechanism for membrane anchoring of the nuclear pore complex.Molecular & cellular proteomics : MCP · 2014Article
- Article
- Bayesian analysis of individual electron microscopy images: towards structures of dynamic and heterogeneous biomolecular assemblies.Journal of structural biology · 2013Article
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7 authors.
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Abstract
To obtain a structural model of a macromolecular assembly by single-particle EM, a large number of particle images need to be collected, aligned, clustered, averaged, and finally assembled via reconstruction into a 3D density map. This process is limited by the number and quality of the particle images, the accuracy of the initial model, and the compositional and conformational heterogeneity. Here, we describe a structure determination method that avoids the reconstruction procedure. The atomic structures of the individual complex components are assembled by optimizing a match against 2D EM class-average images, an excluded volume criterion, geometric complementarity, and optional restraints from proteomics and chemical cross-linking experiments. The optimization relies on a simulated annealing Monte Carlo search and a divide-and-conquer message-passing algorithm. Using simulated and experimentally determined EM class averages for 12 and 4 protein assemblies, respectively, we show that a few class averages can indeed result in accurate models for complexes of as many as five subunits. Thus, integrative structural biology can now benefit from the relative ease with which the EM class averages are determined.
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