CSAW: a dynamical model of protein folding

Kerson Huang

Published 2006-01-12Version 1

CSAW (conditioned self-avoiding walk) is a model of protein folding that combines SAW (self-avoiding walk) with Monte-Carlo. It simulates the Brownian motion of a chain molecule in the presence of interactions, both among chain residues, and with the environment. In a first model that includes the hydrophobic effect and hydrogen bonding, a chain of 30 residues folds into a native state with stable secondary and tertiary structures. The process starts with a rapid collapse into an intermediate "molten globule", which slowly decays into the native state afer a relatively long quiescent period. The behavior of the radius of gyration mimics experimental data.