Homodimeric complexes of the 90-231 human prion: a multilayered computational study based on FMO/GRID-DRY approach

The molecular interaction properties and aggregation capabilities disclosed by PrP-E200K, a pathogenic mutant of the human prion protein, were investigated in detail using multilayered computational approaches. In a previous work, we reported that the electrostatic complementarity between region1 (negative) and region3 (positive) has been assumed to lead to a head-to tail interaction between 120 and 231 PrP-E200K units and to initiation of the aggregation process. In this work, we extended the PrP-E200K structure by including the unstructured 90-120 segment which was found to assume different conformations. Plausible models of 90-231 PrP-E200K dimers were calculated and analyzed in depth to identify the nature of the involved protein-protein interactions. The unstructured 90-120 segment was found to extend the positively charged region3 involved in the association of PrP-E200K units which resulted to be driven by hydrophobic interactions. The combination of molecular dynamics, protein-protein docking, grid-based mapping, and fragment molecular orbital approaches allowed us to provide a plausible mechanism of the early state of 90-231 PrP-E200K aggregation, considered a preliminary step of amyloid conversion.