Yanyan Zhao

All Publications

• Cost-benefit analysis of cryogenic electron tomography subtomogram averaging of chaperonin MmCpn at near atomic resolution. Structure (London, England : 1993) Zhao, Y., Schmid, M. F., Chiu, W. 2024

  Abstract

  Cryogenic electron microscopy single particle analysis (cryoEM-SPA) has evolved into a routine approach for determining macromolecule structures to near-atomic resolution. Cryogenic electron tomography subtomogram averaging (cryoET-STA) toward a similar resolution, in contrast, is still under active development. Here, we use the archeal chaperonin MmCpn as a model macromolecule to quantitatively investigate the resolution limiting factors of cryoET-STA in terms of cumulative electron dose, ice thickness, subtomogram numbers, and tilt angle ranges. By delineating the feasibility and experimental factors of attaining near atomic resolution structure with cryoET-STA, especially the effect of electron damage through the tilt series and inelastic scattering at various ice thickness, we encourage a customized tilt series collection strategy for efficient throughput. This study provides a biophysical basis for the application of cryoET-STA (for highly symmetric molecules like MmCpn) toward high resolution and the rationales in using cryoET-STA to achieve an efficient outcome at the desired resolution.

  View details for DOI 10.1016/j.str.2024.11.008

  View details for PubMedID 39644888

• Visualizing nucleation, condensation and propagation of β-tubulin folding in chaperonin TRiC. bioRxiv : the preprint server for biology Zhao, Y., Schmid, M. F., Chiu, W. 2024

  Abstract

  The folding nucleus (FN) initiates protein folding and enables an efficient folding pathway. Here we directly visualize the tubulin FN consisting of a nonnative, partially assembled Rossmann fold, in the closed chamber of human chaperonin TRiC. Chaperonin TRiC interacts with non-natively folded secondary structural elements, stabilizing the nucleus for transition into its first native domain. Through progressive folding, the unfolded sequence goes through drastic spatial arrangement in the TRiC chamber to sample the conformational space, mediated by the highly dynamic CCT tails. The observed presence of individual nonnative secondary structures first in the nonnative FN and then around the incrementally folded native domains supports the hypothesis that tubulin folding in TRiC is a hierarchical process of nucleation, condensation and propagation in cooperation with TRiC subunits.

  View details for DOI 10.1101/2024.10.13.618036

  View details for PubMedID 39464091

  View details for PubMedCentralID PMC11507676

• Structural visualization of the tubulin folding pathway directed by human chaperonin TRiC/CCT. Cell Gestaut, D., Zhao, Y., Park, J., Ma, B., Leitner, A., Collier, M., Pintilie, G., Roh, S. H., Chiu, W., Frydman, J. 2022; 185 (25): 4770-4787.e20

  Abstract

  The ATP-dependent ring-shaped chaperonin TRiC/CCT is essential for cellular proteostasis. To uncover why some eukaryotic proteins can only fold with TRiC assistance, we reconstituted the folding of β-tubulin using human prefoldin and TRiC. We find unstructured β-tubulin is delivered by prefoldin to the open TRiC chamber followed by ATP-dependent chamber closure. Cryo-EM resolves four near-atomic-resolution structures containing progressively folded β-tubulin intermediates within the closed TRiC chamber, culminating in native tubulin. This substrate folding pathway appears closely guided by site-specific interactions with conserved regions in the TRiC chamber. Initial electrostatic interactions between the TRiC interior wall and both the folded tubulin N domain and its C-terminal E-hook tail establish the native substrate topology, thus enabling C-domain folding. Intrinsically disordered CCT C termini within the chamber promote subsequent folding of tubulin's core and middle domains and GTP-binding. Thus, TRiC's chamber provides chemical and topological directives that shape the folding landscape of its obligate substrates.

  View details for DOI 10.1016/j.cell.2022.11.014

  View details for PubMedID 36493755

  View details for PubMedCentralID PMC9735246

• A very special chaperonin: How does TRiC/CCT achieve tubulin folding? Gestaut, D., Zhao, Y., Park, J., Ma, B., Leitner, A., Collier, M., Aebersold, R., Roh, S., Chiu, W., Frydman, J. WILEY. 2021: 149

  View details for Web of Science ID 000711562500319

• CryoEM reveals the stochastic nature of individual ATP binding events in a group II chaperonin. Nature communications Zhao, Y., Schmid, M. F., Frydman, J., Chiu, W. 2021; 12 (1): 4754

  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.

  View details for DOI 10.1038/s41467-021-25099-0

  View details for PubMedID 34362932