How Cu(II) binding affects structure and dynamics of α-synuclein revealed by molecular dynamics simulations

We report accelerated molecular dynamics simulations of alpha-Synuclein and its complex with two Cu(II) ions bound to experimentally determined binding sites. Adding two Cu(II) ions, one bound to the N-terminal region and one to the C-terminus, decreases size and flexibility of the peptide while introducing significant new contacts within and between N-terminus and non-A beta component (NAC). Cu(II) ions also alter the pattern of secondary structure within the peptide, inducing more and longer-lasting elements of secondary structure such as beta-strands and hairpins. Free energy surfaces, obtained from reweighting the accelerated molecular dynamics boost po-tential, further demonstrate the restriction on size and flexibility that results from binding of copper ions.