Structure of prion β-oligomers as determined by structural proteomics

Date

2017-09-07

Authors

Serpa, Jason John

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Abstract

The conversion of the native monomeric cellular prion protein (PrPC) into an aggregated pathological β-oligomeric (PrPβ) and an infectious form (PrPSc) is the central element in the development of prion diseases. The structure of the aggregates and the molecular mechanisms of the conformational change involved in this conversion are still unknown. My research hypothesis was that a specific structural rearrangement of normal PrPC monomers leads to the formation of new inter-subunit interaction interfaces in the prion aggregates, leading to aggregation. My approach was to use constraints obtained by structural proteomic methods to create a 3D model of urea-acid induced recombinant prion oligomers (PrPβ). My hypothesis was that this model would explain the mechanism of the conformational change involved in the conversion, the early formation of the β-structure nucleation site, and would describe the mode of assembly of the subunits within the oligomer. I applied a combination of limited proteolysis, surface modification, chemical crosslinking and hydrogen/deuterium exchange (HDX) with mass spectrometry for the differential characterization of the native and the urea-acid converted prion β-oligomer structures to get an insight into the mechanism of the conversion and aggregation. Using HDX, I detected a region of the protein in which backbone amides become more protected from exchange in PrPβ compared to PrPC. In order to obtain the inter-residue distance constraints to guide the assembly of the oligomer model, I then applied zero-length and short-range crosslinking to an equimolar mixture of 14N/15N-metabolically labeled β-oligomer thereby enabling the classification of the crosslinks as either intra-protein or inter-protein. Working with the Dokholyan group at the University of North Carolina at Chapel Hill, I was able to assemble a structure of the β-oligomer based on the combination of constraints obtained from all methods. By comparing the structures before and after the conversion, I was able to deduce the conformational change, that occurs during the conversion as the rearrangement and disassembly of the beta sheet 1– helix 1 – beta sheet 2 (β1-H1-β2) region from the helix 2 – helix 3 (H2-H3) core, forming new β-sheet nucleation site and resulting in the exposure of hydrophobic residues patches leading to formation of inter-protein contacts within aggregates.

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Keywords

β-oligomer, prion, PrP, HDX, hydrogen/deuterium exchange, crosslinking, mass spectrometry, limited proteolysis, surface modification, protein structure, proteomics, structural proteomics, prion structure, discrete molecular dynamics, CL-DMD, misfolding, aggregation

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