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Identifying Conformational States of Macromolecules by Eigen-Analysis of Resampled Cryo-EM Images
- Source :
- Structure. 19(11):1582-1590
- Publication Year :
- 2011
- Publisher :
- Elsevier BV, 2011.
-
Abstract
- SummaryWe present the codimensional principal component analysis (PCA), a novel and straightforward method for resolving sample heterogeneity within a set of cryo-EM 2D projection images of macromolecular assemblies. The method employs PCA of resampled 3D structures computed using subsets of 2D data obtained with a novel hypergeometric sampling scheme. PCA provides us with a small subset of dominating “eigenvolumes” of the system, whose reprojections are compared with experimental projection data to yield their factorial coordinates constructed in a common framework of the 3D space of the macromolecule. Codimensional PCA is unique in the dramatic reduction of dimensionality of the problem, which facilitates rapid determination of both the plausible number of conformers in the sample and their 3D structures. We applied the codimensional PCA to a complex data set of Thermus thermophilus 70S ribosome, and we identified four major conformational states and visualized high mobility of the stalk base region.
- Subjects :
- Models, Molecular
Peptide Elongation Factor Tu
Biology
Article
Reduction (complexity)
Set (abstract data type)
03 medical and health sciences
Imaging, Three-Dimensional
Bacterial Proteins
RNA, Transfer
Structural Biology
Protein Interaction Domains and Motifs
Protein Structure, Quaternary
Projection (set theory)
Molecular Biology
030304 developmental biology
Complex data type
Analysis of Variance
Principal Component Analysis
0303 health sciences
Thermus thermophilus
Cryoelectron Microscopy
030302 biochemistry & molecular biology
Sample (graphics)
Hypergeometric distribution
Crystallography
Principal component analysis
Ribosome Subunits, Large
Biological system
Algorithms
Curse of dimensionality
Subjects
Details
- ISSN :
- 09692126
- Volume :
- 19
- Issue :
- 11
- Database :
- OpenAIRE
- Journal :
- Structure
- Accession number :
- edsair.doi.dedup.....2f4469e007f812c98864da4d873b2ba3
- Full Text :
- https://doi.org/10.1016/j.str.2011.10.003