Molecular dynamics simulation of the aggregation and folding mechanism of α-synuclein 47-56 in core peptide fragments induced by α-synuclein pentamer template.

The misfolding of intrinsically disordered α-synuclein protein, which can form β-sheet-rich fibrillar amyloid structures, is closely associated with Parkinson's disease (PD). The peptide α-synuclein 47-56 has been identified as the toxic core of α-synuclein and plays a pivotal role in the aggregation and misfolding processes of this protein. Investigating the template induction behavior of this peptide is crucial for elucidating the molecular mechanisms underlying α-synuclein misfolding and aggregation. To explore the molecular mechanism of the peptide α-synuclein 47-56, guided by the α-synuclein pentamer template, we conducted a 400 ns molecular dynamics simulation. In this simulation, the peptide α-synuclein 47-56 was positioned on both sides of the α-synuclein pentamers. Our results demonstrate distinct elongation characteristics of the peptide α-synuclein 47-56 on the two sides of the pentamer. The β-sheet structure readily formed on the left side of the α-synuclein pentamer, facilitating template induction. In contrast, the formation of β-sheet secondary structures was hindered on the right side of the α-synuclein pentamer. Furthermore, our analysis reveals that hydrogen bonding, electrostatic interactions, and van der Waals forces between the α-synuclein pentamer and monomer are crucial for β-sheet extension. Notably, we identified the α-synuclein 49-53 region as a key peptide segment in this process.