Molecular dynamics study of the structural character of α-syn12 peptide bound to Synphilin-1 protein

Synphilin-1 is a novel α-synuclein interacting protein presenting in the Lewy bodies, the N-terminal 12 residues peptide of α-synuclein (α-syn12) can binding to the coiled-coil domain of Synphilin-1. However, the complex structure in water has not been determined by experimental methods, so that the possible structure of this complex and interaction sites have been studied by docking algorithms and molecular dynamics simulations (MD). We constructed the potential of mean force from the distributions of the backbone (ϕ, ψ) angles for the residues 2–11 of α-syn12 peptide and the free energy surface (FES) of the α-syn12 peptide based on two principle components (PC1 and PC2). The corresponding representative structure corresponds to the β hairpin structure with Turn9-6 and four hydrogen bonds (HB
4–11
, HB
6–9
, HB
9-6
and HB
11-4
). These results were consistent with conformation clusters.