Conformational Biases of α-Synuclein and Formation of Transient Knots

We study local conformational biases in the dynamics of alpha-synuclein by using all-atom simulations with explicit and implicit solvents. The biases are related to the frequency of the specific contact formation. In both approaches, the protein is intrinsically disordered, and its strongest bias is to make bend and turn local structures. The explicit-solvent conformations can be substantially more extended which allows for formation of transient trefoil knots, both deep and shallow, that may last for up to 5 mu s. The two-chain self-association events, both short- and long-lived, are dominated by formation of contacts in the central part of the sequence. This part tends to form helices when bound to a micelle.