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.
Hegger
Rainer
R
Institute of Physical and Theoretical Chemistry, J.W. Goethe University, Max-von-Laue-Strasse 7, 60438 Frankfurt, Germany. hegger@theochem.uni-frankfurt.de
Altis
Alexandros
A
Nguyen
Phuong H
PH
Stock
Gerhard
G
D003198:Computer Simulation; D008956:Models, Chemical; D008958:Models, Molecular; D017711:Nonlinear Dynamics; D010455:Peptides / Q000737:chemistry*; D017510:Protein Folding
D010455:Peptides; C019529:polyalanine