How Complex Is the Dynamics of Peptide Folding?

Classical molecular dynamics simulations of the folding of alanine peptides in aqueous solution are analyzed by constructing a deterministic model of the dynamics, using methods from nonlinear time series analysis. While the dimension of the free energy landscape increases with system size, a Lyapunov analysis shows that the effective dimension of the dynamic system is rather small and even decreases with chain length. The observed reduction of phase space is a nonlinear cooperative effect that is caused by intramolecular hydrogen bonds that stabilize the secondary structure of the peptides.