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-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.
Biocomputing Unit, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Campus de Cantoblanco, Madrid, Spain.
Carlos Oscar
CO
Sanchez Sorzano
Biocomputing Unit, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Campus de Cantoblanco, Madrid, Spain.
Ana Lucia
AL
Alvarez-Cabrera
Biocomputing Unit, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Campus de Cantoblanco, Madrid, Spain.
Mohsen
M
Kazemi
Biocomputing Unit, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Campus de Cantoblanco, Madrid, Spain.
Jose María
JM
Carazo
IMPMC, Sorbonne Universités, CNRS UMR 7590, Université Pierre et Marie Curie, Muséum National d'Histoire Naturelle, IRD UMR 206, Paris, France. Electronic address: slavica.jonic@impmc.upmc.fr.
Slavica
S
Jonić
D004548:Elasticity; D004926:Escherichia coli / Q000378:metabolism; D006801:Humans; D021621:Imaging, Three-Dimensional; D008854:Microscopy, Electron; D009690:Nucleic Acid Conformation; D011132:Polyribosomes / Q000737:chemistry / Q000378:metabolism; D011487:Protein Conformation; D012343:RNA, Transfer / Q000737:chemistry / Q000378:metabolism
D012343:RNA, Transfer