Dynamics of Alpha-Helix Formation in the CSAW Model

TL;DR

This study investigates the folding dynamics of a polyalanine peptide using the CSAW model, revealing the sequence of structural formation, nucleation points, and distinct mechanisms for small and large scale structure evolution.

Contribution

It introduces the application of the CSAW model to analyze alpha-helix formation, highlighting the sequence of structure development and nucleation points.

Findings

Large structures form before small structures.

Helix nucleation occurs at two separate points.

Different mechanisms govern small and large scale structure evolution.

Abstract

We study the folding dynamics of polyalanine (Ala$_{20}$), a protein fragment with 20 residues whose native state is a single alpha helix. We use the CSAW model (conditioned self-avoiding walk), which treats the protein molecule as a chain in Brownian motion, with interactions that include hydrophobic forces and internal hydrogen bonding. We find that large scale structures form before small scale structures, and obtain the relevant relaxation times. We find that helix nucleation occurs at two separate points on the protein chain. The evolution of small and large scale structures involve different mechanisms. While the former can be describe by rate equations governing the growth of helical content, the latter is akin to the relaxation of an elastic solid.