Structure of prion β‐oligomers as determined by short‐distance crosslinking constraint‐guided discrete molecular dynamics simulations

The conversion of the native monomeric cellular prion protein (PrP(C)) into an aggregated pathological β‐oligomeric form (PrP(β)) and an infectious form (PrP(Sc)) is the central element in the development of prion diseases. The structure of the aggregates and the molecular mechanisms of the conformational changes involved in the conversion are still unknown. We applied mass spectrometry combined with chemical crosslinking, hydrogen/deuterium exchange, limited proteolysis, and surface modification for the differential characterization of the native and the urea+acid‐converted prion β‐oligomer structures to obtain insights into the mechanisms of conversion and aggregation. For the determination of the structure of the monomer and the dimer unit of the β‐oligomer, we applied a recently‐developed approach for de novo protein structure determination which is based on the incorporation of zero‐length and short‐distance crosslinking data as intra‐ and inter‐protein constraints in discrete molecular dynamics simulations (CL‐DMD). Based on all of the structural‐proteomics experimental data and the computationally predicted structures of the monomer units, we propose the potential mode of assembly of the β‐oligomer. The proposed β‐oligomer assembly provides a clue on the β‐sheet nucleation site, and how template‐based conversion of the native prion molecule occurs, growth of the prion aggregates, and maturation into fibrils may occur.