Identification of Minimally Interacting Modules in an Intrinsically Disordered Protein

The conformational characterization of intrinsically disordered proteins (IDPs) is complicated by their conformational heterogeneity and flexibility. If an IDP could somehow be divided into smaller fragments and reconstructed later, theoretical and spectroscopic studies could probe its conformational variability in detail. Here, we used replica molecular-dynamics simulations and network theory to explore whether such a divide-and-conquer strategy is feasible for alpha-synuclein, a prototypical IDP. We characterized the conformationar variability of alpha-synuclein by conducting >100 unbiased all-atom molecular-dynamics simulations, for a total of >10 mu s of trajectories. In these simulations, alpha-synuclein formed a heterogeneous ensemble of collapsed coil states in an aqueous environment. These states were stabilized by heterogeneous contacts between sequentially distant regions. We find that alpha-synuclein contains residual secondary structures in the collapsed states, and the heterogeneity in the collapsed state makes it feasible to split alpha-synuclein into sequentially contiguous minimally interacting fragments. This study reveals previously unknown characteristics of alpha-synuclein and provides a new (to our knowledge) approach for studying other IDPs.