Early stages of unwinding of zwitterionic α-helical homopolymeric peptides

Unwinding mechanisms of helices of the zwitterionic polyalanine, polyleucine, and polylysine were studied using classical molecular dynamics simulation at 300 K temperature. Interestingly the helices of polyalanine and polyleucine start to unwind from the terminals, which is further relayed to the middle of the chain with time. Polylysine helix also starts to unwind from the terminals of the α-helical chain but the unwinding is not relayed to the middle. The reason behind this observation is investigated whether the presence of –NH2 groups in the side chain of polylysine is influencing the unwinding. Two competitive mechanisms, fluctuation of the terminal residues and exchange of H-bonds between residues and water trigger the process of unwinding.