A Combined Solid‐State NMR and MD Characterization of the Stability and Dynamics of the HET‐s(218‐289) Prion in its Amyloid Conformation

Dynamic and rigid: The prion HET‐s(218–289) consists, in its amyloid form as shown here, of highly ordered and rigid parts and a very dynamic loop, which could be of great importance for fibril formation. Indeed, MD simulations explain the experimental NMR results and describe the dynamics of the salt‐bridge network that stabilizes the amyloid fibril, a feature not easily accessible by experiment. magnified image The three‐dimensional structure of amyloid fibrils of the prion‐forming part of the HET‐s protein [HET‐s(218–289)], as determined by solid‐state NMR, contains rigid and remarkably well‐ordered parts, as witnessed by the narrow solid‐state NMR line widths for this system. On the other hand, high‐resolution magic‐angle‐spinning (HRMAS) NMR results have shown that HET‐s(218–289) amyloid fibrils contain highly flexible parts as well. Here, we further explore this unexpected behaviour using solid‐state NMR and molecular dynamics (MD). The NMR data provide new information on order and dynamics in the rigid and flexible parts of HET‐s(218–289), respectively. The MD study addresses whether or not small multimers, in an amyloid conformation, are stable on the 10 ns timescale of the MD run and provides insight into the dynamic parameters on the nanosecond timescale. The atom‐positional, root‐mean‐squared fluctuations (RMSFs) and order parameters S2 obtained are in agreement with the NMR data. A flexible loop and the N terminus exhibit dynamics on the ps–ns timescale, whereas the hydrophobic core of HET‐s(218–289) is rigid. The high degree of order in the core region of HET‐s(218–289) amyloids, as observed in the MD simulations, is in agreement with the narrow, solid‐state, NMR lines. Finally, we employed MD to predict the behaviour of the salt‐bridge network in HET‐s(218–289), which cannot be obtained easily by experiment. Simulations at different temperatures indicated that the network is highly dynamic and that it contributes to the thermostability of the HET‐s(218–289) amyloids.