Spin Label Scanning Reveals Likely Locations of β-Strands in the Amyloid Fibrils of the Ure2 Prion Domain.

Jingzhou Wang,Matthew Nguyen,Tiffany San Fung,Tiffany Yuwen Lin,Frederick Hsu,Yoon Kyung Lee,Zhefeng Guo,Giovanna Park

doi:10.1021/acsomega.9b04358

Jingzhou Wang, Matthew Nguyen + Show 6 more

Open Access

https://doi.org/10.1021/acsomega.9b04358

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Journal: ACS omega	Publication Date: Mar 11, 2020
Citations: 10	License type: cc-by

Affiliation: University of California, Los Angeles

Abstract

In yeast, the formation of Ure2 fibrils underlies the prion state [URE3], in which the yeast loses the ability to distinguish good nitrogen sources from bad ones. The Ure2 prion domain is both necessary and sufficient for the formation of amyloid fibrils. Understanding the structure of Ure2 fibrils is important for understanding the propagation not only of the [URE3] prion but also of other yeast prions whose prion domains share similar features, such as the enrichment of asparagine and glutamine residues. Here, we report a structural study of the amyloid fibrils formed by the Ure2 prion domain using site-directed spin labeling and electron paramagnetic resonance (EPR) spectroscopy. We completed a spin label scanning of all the residue positions between 2 and 80 of the Ure2 prion domain. The EPR data show that the Ure2 fibril core consists of residues 8–68 and adopts a parallel in-register β-sheet structure. Most of the residues show strong spin–exchange interactions, suggesting that there are only short turns and no long loops in the fibril core. Based on the strength of spin–exchange interactions, we determined the likely locations of the β-strands. EPR data also show that the C-terminal region of the Ure2 prion domain is more disordered than the N-terminal region. The roles of hydrophobic and charged residues are analyzed. Overall, the structure of Ure2 fibrils appears to involve a balance of stabilizing interactions, such as asparagine ladders, and destabilizing interactions, such as stacking of charged residues.

Highlights

Prions are infectious proteins that propagate the prion state by converting the prion protein from a non-prion conformation to a prion conformation.[1,2] In mammals, prions are the basis of transmissible encephalopathies, including the Creutzfeldt− Jakob disease in humans,[3] bovine spongiform encephalopathies in cattle,[4] and chronic wasting disease in deer and elk.[5]
To study the structure of amyloid fibrils formed by the yeast prion protein Ure[2], we prepared spin-labeled Ure[2] fibrils in a phosphate-buffered saline (PBS) buffer at 37 °C without agitation
The electron paramagnetic resonance (EPR) spectra at labeling sites 2−15 were taken from the study of Ngo et al.,[26] but all other samples were prepared in this study

Summary

Introduction

Prions are infectious proteins that propagate the prion state by converting the prion protein from a non-prion conformation to a prion conformation.[1,2] In mammals, prions are the basis of transmissible encephalopathies, including the Creutzfeldt− Jakob disease in humans,[3] bovine spongiform encephalopathies in cattle,[4] and chronic wasting disease in deer and elk.[5]. The EPR data show that the Ure[2] fibril core consists of residues 8−68 and adopts a parallel in-register β-sheet structure. Article paramagnetic resonance (EPR)[25,26] shows that the amyloid fibrils of Ure[2] prion domain adopt a parallel in-register β-sheet structure, but the detailed locations of β-strands and turns are still lacking.

Results

Conclusion