CryoEM reveals the stochastic nature of individual ATP binding events in a group II chaperonin

Yanyan Zhao, Michael F. Schmid, Judith Frydman and Wah Chiu ()
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Yanyan Zhao: Stanford University
Michael F. Schmid: SLAC National Accelerator Laboratory
Judith Frydman: Stanford University
Wah Chiu: Stanford University

Nature Communications, 2021, vol. 12, issue 1, 1-10

Abstract: Abstract Chaperonins are homo- or hetero-oligomeric complexes that use ATP binding and hydrolysis to facilitate protein folding. ATP hydrolysis exhibits both positive and negative cooperativity. The mechanism by which chaperonins coordinate ATP utilization in their multiple subunits remains unclear. Here we use cryoEM to study ATP binding in the homo-oligomeric archaeal chaperonin from Methanococcus maripaludis (MmCpn), consisting of two stacked rings composed of eight identical subunits each. Using a series of image classification steps, we obtained different structural snapshots of individual chaperonins undergoing the nucleotide binding process. We identified nucleotide-bound and free states of individual subunits in each chaperonin, allowing us to determine the ATP occupancy state of each MmCpn particle. We observe distinctive tertiary and quaternary structures reflecting variations in nucleotide occupancy and subunit conformations in each chaperonin complex. Detailed analysis of the nucleotide distribution in each MmCpn complex indicates that individual ATP binding events occur in a statistically random manner for MmCpn, both within and across the rings. Our findings illustrate the power of cryoEM to characterize a biochemical property of multi-subunit ligand binding cooperativity at the individual particle level.

Date: 2021
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DOI: 10.1038/s41467-021-25099-0

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