Dynamics of Alpha-Helix Formation in the CSAW Model

Details Dynamics of Alpha-Helix Formation in the CSAW Model Dynamics of Alpha-Helix Formation in the CSAW Model

2007-06-22

arxiv.org/abs/0706.3256v3

The European physical Journal E, 2008, vol. 27(2), pp. 197-204

Physics

Condensed Matter

Soft Condensed Matter

18 pages, 10 figures

Scientific paper

10.1140/epje/i2007-10371-4

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.

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