The Glycine-Rich Region as a Flexible Molecular Glue Promoting hPrP_106–145 Aggregation into β-Sheet Structures

The abnormal aggregation of human prion protein (hPrP) into cross-β fibrillar amyloid deposits is associated with prion diseases such as Creutzfeldt-Jakob disease and fatal familial insomnia. However, the molecular mechanisms underlying the early stages of prion aggregation remain poorly understood. In this study, we employed multiple long-time scale atomistic discrete molecular dynamics (DMD) simulations to investigate the conformational dynamics of hPrP_106-145, a critical fragment with intrinsic aggregation propensity and key involvement in infectivity. Our results revealed that the hPrP_106-145 monomer primarily adopted a helical conformation in the alanine-rich region (residues 109-118), while the remaining sequence was largely unstructured, exhibiting dynamic β-sheet formation around residues ¹²⁰AVV¹²², ¹²⁸YVL¹³⁰, and ¹³⁸IIH¹⁴⁰. Upon dimerization, β-sheet formation was significantly enhanced, particularly around ¹³⁸IIH¹⁴⁰, which displayed the highest β-sheet propensity and interpeptide contact frequency, underscoring its pivotal role in aggregate stabilization. The glycine-rich region (residues 119-131) was found to facilitate aggregation by conferring structural flexibility due to glycine's minimal steric hindrance. This flexibility allowed hydrophobic and aromatic residues to collapse dynamically, forming transient intra- and interpeptide β-sheets. These interactions acted as a molecular glue, promoting aggregation while maintaining structural adaptability. Although β-sheet formation lowered potential energy, excessive β-sheet content resulted in significant entropic loss, highlighting a trade-off between stability and conformational entropy. Overall, this study provides molecular insights into the early nucleation events of hPrP_106-145 aggregation, emphasizing the critical role of glycine-mediated flexibility. Our findings deepen the understanding of prion misfolding and offer a computational framework for exploring glycine-rich peptide phase separation in amyloid-related disorders.