Classification of images of biomolecular assemblies: a study of ribosomes and ribosomal subunits of Escherichia coli

Abstract

K E Y WORDS. Correspondence analysis, hierarchical ascendant classification, image analysis, electron microscopy. SUMMARY Images of macromolecules obtained in the electron microscope are subjected to correspondence analysis. The structure inherent in the data in the resulting low-dimensional factor space is characterized by a mixed classification method which combines the dynamic clouds clustering technique with hierarchical ascendant classification (HAC). For our data, the rejection of marginal clusters obtained by dynamic clouds clustering appears as a crucial prerequisite for a stable performance of HAC.The method is applied to two sets of 204 and 177 images that show the 70s ribosome of Escherichia coli, in the range of overlap views as defined by A. Verschoor and co-workers, and to two sets of 480 and 496 images of the 50s subunit of E . coli depleted of L7/L12 proteins in the well-defined crown view. Reproducible classes are obtained, which are characterized by images reconstituted from factorial coordinates. These classes appear to be related to different orientations on the specimen grid (in the case of the 70s particle) and to different conformational states (50s subunit).

Proteomics and electron microscopic characterization of the unusual mitochondrial ribosome-related 45S complex in Leishmania tarentolae

“…From a total of 128 micrographs, the110 best ones were scanned on a Zeiss flatbed scanner, with a step size of 14 μm, corresponding to 2.76 Å on the object scale. From the originally windowed 24,826 images from the scanned micrographs, 12,678 images were manually selected and subjected to reference-free alignment and two-dimensional correspondence analysis [28] using SPIDER [29].…”

Aminosulfonate Modulated pH-induced Conformational Changes in Connexin26 Hemichannels

“…Correlation-averaged unit cells were 6-fold symmetrized. To assess the standard deviation k,l , individual unit cells were extracted according to the coordinates of their correlation peaks and were aligned angularly as well as translationally before single particle averaging (31). The S.D.…”

Isolation and Structural Characterization of Trimeric Cyanobacterial Photosystem I Complex with the Help of Recombinant Antibody Fragments

“…Intermediate references were constructed from the sums of the best particles as estimated from their correlation with the reference. In the next step, over 60% of the aligned particles were submitted to multivariate statistical analysis and automatic classification (Frank et al, 1987;van Heel, 1984). The six largest classes were then averaged individually and used as references for further refinement.…”

“…Topview particles were selected from electron micrographs of isolated trimeric PSI complexes (control, absence of the Fv fragment) and of the PSIEv complexes for image processing. After a first cycle of angular and translational alignments, multivariate statistical analysis and classification of the projections were performed according to the method of van Heel (1984) and Frank et al (1987). Averages from the six largest classes were used as reference for a subsequent alignment procedure (Figs 7 and 8).…”