Assembly of macromolecular complexes by satisfaction of spatial restraints from electron microscopy images

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 ima...

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Bibliographic Details
Published in:Proceedings of the National Academy of Sciences - PNAS 2012-11, Vol.109 (46), p.18821-18826
Main Authors: Velázquez-Muriel, Javier, Lasker, Keren, Russel, Daniel, Phillips, Jeremy, Webb, Benjamin M, Schneidman-Duhovny, Dina, Sali, Andrej
Format: Article
Language:English
Subjects:
Algorithms
Arithmetic mean
Atomic structure
Biological Sciences
crosslinking
Databases, Protein
Electron microscopy
Electrons
Fast Fourier transformations
Image reconstruction
Imaging, Three-Dimensional - methods
Microscopy, Electron - methods
Modeling
Molecules
Monte Carlo simulation
Multiprotein Complexes - chemistry
Multiprotein Complexes - ultrastructure
Pixels
Proteins
Proteomics
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Summary: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.
ISSN:0027-8424
1091-6490
DOI:10.1073/pnas.1216549109