Proceedings of the National Academy of Sciences · 2017 · 106 citations · 37 references
Protein AssemblyBiomolecular Structure PredictionMolecular BiologyConformation ClassProtein FoldingSingle Particle BiophysicsProtein X-ray CrystallographyMulti-protein AssemblyBiophysicsBiochemistryIdentical SubunitsMacromolecular MachineConformational StudyProtein ModelingCrystallographyStructural BiologyNatural SciencesMolecular BiophysicsMedicineAdjacent SubunitsIndividual Groel Oligomers
Cryo‑EM is an emerging tool for resolving structures of conformationally heterogeneous particles, but each structure is derived from an average of many particles presumed to have identical conformations. We performed a 3.5‑Å cryo‑EM reconstruction with imposed D7 symmetry and mapped each subunit conformation class to its location within each GroEL oligomer. Focused classification of the 14 subunits in each oligomer revealed three dominant classes of subunit conformations, each resembling a distinct GroEL crystal structure, with differences arising from apical domain orientations; the spatial distributions varied among oligomers, most containing 10–12 subunits of the three classes, and adjacent subunits were more likely to share the same class, demonstrating cryo‑EM’s utility for revealing structure dynamics within a single protein oligomer.
Single-particle electron cryo-microscopy (cryo-EM) is an emerging tool for resolving structures of conformationally heterogeneous particles; however, each structure is derived from an average of many particles with presumed identical conformations. We used a 3.5-Å cryo-EM reconstruction with imposed D7 symmetry to further analyze structural heterogeneity among chemically identical subunits in each GroEL oligomer. Focused classification of the 14 subunits in each oligomer revealed three dominant classes of subunit conformations. Each class resembled a distinct GroEL crystal structure in the Protein Data Bank. The conformational differences stem from the orientations of the apical domain. We mapped each conformation class to its subunit locations within each GroEL oligomer in our dataset. The spatial distributions of each conformation class differed among oligomers, and most oligomers contained 10-12 subunits of the three dominant conformation classes. Adjacent subunits were found to more likely assume the same conformation class, suggesting correlation among subunits in the oligomer. This study demonstrates the utility of cryo-EM in revealing structure dynamics within a single protein oligomer.
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