Folding dynamics of proteins from denatured to native state: principal component analysis

Abstract

Several trajectories starting from random configurations and ending in the native state for chymotrypsin inhibitor 2, CI2, are generated using a Go-type model where the backbone torsional angles execute random jumps on which a drift towards their native values is superposed. Bond lengths and bond angles are kept fixed, and the size of the backbone atoms and side groups are recognized. The large datasets obtained are analyzed using a particular type of principal component analysis known as Karhunen - Loeve expansion (KLE). Trajectories are decomposed separately into modes in residue space and time space. General features of different folding trajectories are compared in the modal space and relationships between the structure of CI2 and its folding dynamics are obtained. Dynamic scaling and order reduction of the folding trajectories are discussed. A continuous wavelet transform is used to decompose the nonstationary folding trajectories into windows exhibiting different features of folding dynamics. Analysis of correlations confirms the known two-state nature of folding of CI2. All of the conserved residues of the protein are shown to be stationary in the small modes of the residue space. The sequential nature of folding is shown by examining the slow modes of the trajectories. The present model of protein folding dynamics is compared with the simple Rouse model of polymer dynamics. Principal component analysis is shown to be a very effective tool for the characterization of the general folding features of proteins.