Nonequilibrium Dynamics of the Helix-Coil Transition in Polyalanine

TL;DR

This study uses molecular dynamics simulations to explore the nonequilibrium pathways and dynamics of the helix-coil transition in polyalanine, revealing the formation of short helices and the scaling of relaxation times.

Contribution

It provides detailed simulation-based insights into the nonequilibrium collapse process and the formation of different helical structures in polyalanine.

Findings

Short 3_10-helices form early in the transition.

The molecule becomes more aspherical during collapse.

Alpha-helix formation dominates in the final structure.

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 $3_{10}$-helices form, seemingly leading to the molecule becoming more aspherical midway through the collapse. After the completed collapse, the formation of $\alpha$-helices seems to become the prevalent ordering mechanism leading to helical bundles, a structure representative for the equilibrium behavior of longer chains. The dynamics of this transition is explored in terms of the power-law scaling of two associated relaxation times as a function of the chain length.