title: "New view" of protein folding reconciled with the old through multiple unfolding simulations.
abstract: Twenty-four molecular dynamics trajectories of chymotrypsin inhibitor 2 provide a direct demonstration of the diversity of unfolding pathways. Comparison with experiments suggests that the transition state region for folding and unfolding occurs early with only 25 percent of the native contacts and that the root-mean-square deviations between contributing structures can be as large as 15 angstroms. Nevertheless, a statistically preferred unfolding pathway emerges from the simulations; disruption of tertiary interactions between the helix and a two-stranded portion of the beta sheet is the primary unfolding event. The results suggest a synthesis of the "new" and the classical view of protein folding with a preferred pathway on a funnel-like average energy surface.
authors.affiliation: Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.
authors.forename: T
authors.initials: T
authors.lastname: Lazaridis
authors.forename: M
authors.initials: M
authors.lastname: Karplus
mesh_terms: D003198:Computer Simulation; D008958:Models, Molecular; D010455:Peptides / Q000737:chemistry*; D010940:Plant Proteins; D011487:Protein Conformation; D011489:Protein Denaturation; D017510:Protein Folding; D017433:Protein Structure, Secondary; D013816:Thermodynamics
chemical_list: D010455:Peptides; D010940:Plant Proteins; C093336:chymotrypsin inhibitor 2