Nonequilibrium dynamics of the helix–coil transition in polyalanine

Abstract

In this work, the nonequilibrium pathways of the collapse of the helix-forming biopolymer polyalanine are investigated. To this end, the full time evolution of the helix–coil transition is simulated using molecular dynamics simulations. At the start of the transition, short 310-helices form, seemingly leading to the molecule becoming more aspherical midway through the collapse. After the completed collapse, the formation of α-helices becomes the prevalent ordering mechanism leading to helical bundles, a typical structural motif representative of the equilibrium behavior of longer chains. The dynamics of this transition is quantified in terms of the power-law scaling of two associated relaxation times as a function of chain length.