Molecular-level insights of early-stage prion protein aggregation on mica and gold surface determined by AFM imaging and molecular simulation

Direct observation of prion protein oligomer formation reveals an aggregation mechanism with multiple conformationally distinct species

“…PrP oligomerization has previously been followed either on a mica or gold surface. [54][55][56] However, it is unclear if the oligomers formed on a hydrophilic surface in these experiments eventually form brils or show similar structural characteristics to oligomers obtained in other studies. Furthermore, the use of truncated versions of PrP and the lack of co-factors may also contribute to increasing the chance of being trapped in local maxima.…”

Effect of the electrostatic surface potential on the oligomerization of full-length human recombinant prion protein at single-molecule level

“…16,50 The AFM images provide useful information not only for the single molecule ESP study but also for the thermodynamic and kinetic studies of the PrP aggregation process. 38,44…”

“…Moreover, in the acidic environment, the mica surface is negatively charged, so the positively charged surface of each oligomer will have stronger interactions with the substrate. 44 This interaction is another contribution to the specific patterns shown in AFM images. On the other hand, the hydrogen bonds depend on the AA residues on oligomer surfaces, and most of those residues were not be affected by the pH changes.…”

“…19,43 Therefore, it is feasible to explore the role of the ESP in the mechanism of full-length human recombinant prion protein (sequence: 23-231) oligomer aggregation via the AFM images of the PrP oligomers, which have their corresponding ESP distributions and may form specific patterns on different substrates, and under different pH conditions. 38,44 Here, the mica surface was used to mimic the hydrophilic surface of cell membrane. The PrP monomer (M) folding conformations at different pH values were predicted by molecular dynamics (MD); the structures of the dimer (D), and trimer (T) were obtained from molecular docking simulation using the M unit; 45 and the conformations of larger oligomers such as M-D and D-T were predicted with the help of high-resolution AFM images, by the same method used in previous publications.…”

“…The PrP monomer (M) folding conformations at different pH values were predicted by molecular dynamics (MD); the structures of the dimer (D), and trimer (T) were obtained from molecular docking simulation using the M unit; 45 and the conformations of larger oligomers such as M-D and D-T were predicted with the help of high-resolution AFM images, by the same method used in previous publications. 38,44 Based on these structures simulated by MD and docking, the ESP simulations were conducted, and the detailed aggregation mechanisms at single-molecule level have been established. 46 The combination of the surface morphology measurements and structural simulations successfully revealed the molecular basis of the ESP distributions involved in PrP oligomerization.…”