Journal of Physical Chemistry B, Vol.106, No.34, 8796-8802, 2002
Two-dimensional correlation analysis of peptide unfolding: Molecular dynamics simulations of beta hairpins
We have studied the mechanism of formation of a 16-residue beta hairpin from the protein GB I using molecular dynamics simulations in an aqueous environment. Essential dynamics (ED) analysis was performed on the combined trajectories of two separate simulations at five different temperatures. Generalized 2D correlation analysis was performed using the displacements from the ED analysis as a dynamic spectrum. The results of the 2D correlation analysis illustrate the correlated structural changes as the temperature is increased. The asynchronous 2D correlation spectrum reveals the existence of sequential events in the unfolding of the peptide. The order of structural changes suggested by such an,analysis support the hydrophobic collapse mechanism of folding for the beta-hairpin fragment of protein GB1. The 2D correlation method combined with ED analysis can provide a useful scheme for studying the characteristics of dynamical structural changes which are important in understanding the function of protein and the mechanism of protein folding.