StructMap: Elastic Distance Analysis of Electron Microscopy Maps for Studying Conformational Changes

Single-particle electron microscopy (EM) has been shown to be very powerful for studying structures and associated conformational changes of macromolecular complexes. In the context of analyzing conformational changes of complexes, distinct EM density maps obtained by image analysis and three-dimens...

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Bibliographic Details
Published in:Biophysical journal 2016-04, Vol.110 (8), p.1753-1765
Main Authors: Sanchez Sorzano, Carlos Oscar, Alvarez-Cabrera, Ana Lucia, Kazemi, Mohsen, Carazo, Jose María, Jonić, Slavica
Format: Article
Language:English
Subjects:
Biological Physics
Biophysics
Density
Elasticity
Electron microscopes
Electrons
Escherichia coli - metabolism
Humans
Imaging, Three-Dimensional
Microscopy, Electron
Molecular physics
Nucleic Acid Conformation
Physics
Polyribosomes - chemistry
Polyribosomes - metabolism
Protein Conformation
Proteins
RNA, Transfer - chemistry
RNA, Transfer - metabolism
Three dimensional imaging
Visualization
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Summary:Single-particle electron microscopy (EM) has been shown to be very powerful for studying structures and associated conformational changes of macromolecular complexes. In the context of analyzing conformational changes of complexes, distinct EM density maps obtained by image analysis and three-dimensional (3D) reconstruction are usually analyzed in 3D for interpretation of structural differences. However, graphic visualization of these differences based on a quantitative analysis of elastic transformations (deformations) among density maps has not been done yet due to a lack of appropriate methods. Here, we present an approach that allows such visualization. This approach is based on statistical analysis of distances among elastically aligned pairs of EM maps (one map is deformed to fit the other map), and results in visualizing EM maps as points in a lower-dimensional distance space. The distances among points in the new space can be analyzed in terms of clusters or trajectories of points related to potential conformational changes. The results of the method are shown with synthetic and experimental EM maps at different resolutions.
ISSN:0006-3495
1542-0086
DOI:10.1016/j.bpj.2016.03.019