Comparative all-atomic study of unfolding pathways for proteins chymotrypsin inhibitor 2 and barnase

The features of transition states and intermediates are important in the study on protein folding. However, transition states and intermediates could not be obviously identified from trajectories obtained by dynamic simulations. In this work, a different method to identify and characterize the transition states and intermediates by combining the root mean square deviation of C(alpha) atoms and the similarity factor Q to the native state is proposed. The unfolding processes based on all-atomic simulations for proteins chymotrypsin inhibitor 2 and barnase are studied, and the related transition states and intermediates are identified by observing an unfolding factor U = 1-F. Comparisons between the conformational cluster analysis and experimental results are also made. The various analyses on the unfolding behaviors indicate that our method can well define the transition states and intermediates, and the factor U (or F) can be used as a reaction coordinate of the folding and unfolding process. It is also found that three-state folding proteins might experience more complicated pathways and have more rugged energy landscapes than two-state folding proteins.