Perturbations in inter-domain associations may trigger the onset of pathogenic transformations in PrP^C: insights from atomistic simulations

Abstract

Conversion of the predominantly α-helical cellular prion protein (PrP(C)) to the misfolded β-sheet enriched Scrapie form (PrP(Sc)) is a critical event in prion pathogenesis. However, the conformational triggers that lead to the isoform conversion (PrP(C) to PrP(Sc)) remain obscure, and conjectures about the role of unusually hydrophilic, short helix H1 of the C-terminal globular domain in the transition are varied. Helix H1 is anchored to helix H3 via a few stabilizing polar interactions. We have employed fully atomistic molecular dynamics simulations to study the effects triggered by a minor perturbation in the network of these non-bonded interactions in PrP(C). The elimination of just one of the key H1-H3 hydrogen bonds led to a cascade of conformational changes that are consistent with those observed in partially unfolded intermediates of PrP(C), with pathogenic mutations and in low pH environments. Our analyses reveal that the perturbation results in the enhanced conformational flexibility of the protein. The resultant enhancement in the dynamics leads to overall increased solvent exposure of the hydrophobic core residues and concomitant disruption of the H1-H3 inter-domain salt bridge network. This study lends credence to the hypothesis that perturbing the cooperativity of the stabilizing interactions in the PrP(C) globular domain can critically affect its dynamics and may lead to structural transitions of pathological relevance.

Structural insight into the antiprion compound inhibition mechanism of native prion folding over misfolding

“…As expected, the benchmark simulation of the inactive compound BMD01 displayed a similar helical loss compared to free PrP C and the active compound GN8 retained the helical content (Figure S2D). As in earlier simulation studies, the end of the α1 region, which consists of residues 154–156, formed continued 3 10 ‐helix in antiprion compound‐stabilized PrP C , while in the absence of an antiprion compound, these residues mostly adopted a helical conformation …”

“…However, these regions are unstable in PrP C and experience large conformational changes in the absence of antiprion compounds, as demonstrated in a previous study . Although it is well established that hydrophobic core interactions in PrP C are the driving force in prion folding, we observed that these interactions are conserved in the presence of antiprion compounds. Therefore, we performed a simulation of PrP C with the well‐determined antiprion compound, GN8, to evaluate the accuracy of our procedure; the results were similar to those obtained using our discovered antiprion compounds.…”

“…The NMR structure of the prion (1AG2), previously used to identify two active compounds, and the NMR‐determined GN8 compound were used to perform explicit‐solvent atomic MD simulations at acidic pH (Figure ) . It should be noted that because the ligand‐binding regions are located in the C‐terminal of PrP C , we omitted the unstructured N‐terminal to reduce the simulation time, as simulations using the C‐terminal alone were successfully performed in previous studies . Because an acidic pH misfolding mechanism has been widely studied for PrP C using MD simulations, we were interested in determining how antiprion compounds promote native PrP C folding over misfolding.…”

“…Misfolding events of PrP C to PrP Sc have been achieved via acidic pH, high temperature, or point mutations using biophysical and theoretical methods . Previous simulation studies have elucidated the structural details of misfolding and the conformational transition of secondary structural elements using the aforementioned techniques . In addition to point mutations and high temperature, acidic pH simulations have often been used as a key factor for inducing the misfolding of prions.…”

Interdomain salt‐bridges in the Ebola virus protein VP40 and their role in domain association and plasma membrane localization

“…Salt‐bridge ionic interactions are important for protein stability, conformational specificity, and for positioning key residues that are essential for protein folding and function . Salt‐bridge interactions can provide the structural specificity required for proper folding of individual domains as well as guiding domain–domain association.…”