Computational investigation of copper-mediated conformational changes in α-synuclein dimer

We report molecular dynamics simulation of dimers of alpha-synuclein, the peptide closely associated with onset of Parkinson's disease, both as metal-free dimer and with inter-chain bridging provided by Cu(ii) ions. Our investigation reveals that the presence of copper-induced inter-chain bridging not only stabilizes alpha-synuclein dimers, but also leads to enhanced beta-sheet formation at critical regions within the N-terminal and NAC regions of the protein. These contacts are larger and longer-lived in the presence of copper, and as a result each peptide chain is more extended and less flexible than in the metal-free dimer. The persistence of these inter-peptide contacts underscores their significance in stabilising the dimers, potentially influencing the aggregation pathway. Moreover, the increased flexibility in the two termini, as well as the absence of persistent contacts in the metal-free dimer, correlates with the presence of amorphous aggregates. This phenomenon is known to mitigate fibrillation, while their absence in the metal-bound dimer suggests an increased propensity to form fibrils in the presence of copper ions. MD simulations are used to examine the effect of bridging Cu(ii) ions on dimerization of alpha-synuclein.