Document 
Eur. Phys. J. E 27, 197-204 (2008)
DOI: 10.1140/epje/i2007-10371-4
Dynamics of alpha helix formation in the CSAW model
J. Lei1 and K. Huang21 Zhou Pei-Yuan Center for Applied Mathematics, Tsinghua University, 100084, Beijing, China
2 Physics Department, Massachusetts Institute of Technology, 02139, Cambridge, MA, USA
jzlei@tsinghua.edu.cn
kerson@mit.edu
Received 10 October 2007 / Published online 30 September 2008
Abstract
We study the folding dynamics of polyalanine ( Ala20, 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 force 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, one near each end. The evolution of small- and large-scale structures involves different mechanisms. While the former can be described by rate equations that govern the growth of helical content, the latter is akin to the relaxation of an elastic solid.
Supplementary material in the form of a pdf file available from the journal web page at 10.1140/epje/i2007-10371-4 and are accessible for authorised users.
PACS87.14.E- - Proteins.
87.15.Cc - Folding: thermodynamics, statistical mechanics, models, and pathways.
87.15.A- - Theory, modeling, and computer simulation.
87.15.H- - Dynamics of biomolecules. Correspondence: jzlei@tsinghua.edu.cn
© EDP Sciences, Società Italiana di Fisica, Springer-Verlag 2008