Determination of the Near-Atomic Structure of Non-Purified Oligomeric E. coli Proteins

Abstract

The roughly purified extract of E. coli proteins has been studied by cryoelectron microscopy, the class-sums containing 2D projections of two proteins (β-galactosidase and 2-oxoglutarate dehydrogenase complex catalytic domain (ODC-CD)), identified in an extract by tandem mass spectrometry, have been distinguished. The structures of these proteins have been solved at near-atomic resolution. De novo simulation of the ODC-CD structure yielded an atomic model that revealed differences in the positions of some amino acid residues of the active center, in comparison with the known crystal structures.

Preparation and characterization of inactivated tick-borne encephalitis virus samples for single-particle imaging at the European XFEL

“…High concentration and homogeneity are necessary for cryo-EM, cryo-TM and SPI experiments at XFELs. Advanced computational classification approaches have been developed for cryo-EM data analysis, allowing samples to be successfully 'purified' in silico (Lyumkis, 2019) or even the structure of one protein in a mixture with another to be solved (Pichkur et al, 2021). In SPI experiments, sample-sized impurities may produce parasitic scattering and decrease the hit rate.…”

Preparation and Characterization of Inactivated Tick-Borne Encephalitis Virus Samples for Single Particle Imaging at European XFEL

“…High concentration and homogeneity is necessary both for cryo-EM single particle analysis and SPI experiment at XFELs. Advanced computational classification approaches are developed for the cryo-EM data analysis, allowing to successfully “purify” sample in silico (Lyumkis, 2019) or even solve the structure of one protein from the mixture with another one (Pichkur et al ., 2021). In SPI experiments, sample-sized impurities may produce parasitic scattering and along with aggregates may reduce target concentration in the sample considerably.…”