title: Folding Kinetics and Unfolded State Dynamics of the GB1 Hairpin from Molecular Simulation.
abstract: The C-terminal β-hairpin of protein G is a 16-residue peptide that folds in a two-state fashion akin to many larger proteins. However, with an experimental folding time of ∼6 μs, it remains a challenging system for all-atom, explicitly solvated, molecular dynamics simulations. Here, we use a large simulation data set (0.7 ms total) of the hairpin at 300 and 350 K to interpret its folding via a master equation approach. We find a separation of over an order of magnitude between the longest and second longest relaxation times, with the slowest relaxation corresponding to folding. However, in spite of this apparent two-state dynamics, the folding rate determined based on a first-passage time analysis depends on the initial conditions chosen, with a nonexponential distribution of first passage times being obtained in some cases. Using the master equation model, we are now able to account quantitatively for the observed distribution of first passage times. The deviation from the expected exponential distribution for a two-state system arises from slow dynamics in the unfolded state, associated with formation and melting of helical structures. Our results help to reconcile recent findings of slow dynamics in unfolded proteins with observed two-state folding kinetics. At the same time, they indicate that care is required in estimating folding kinetics from many short folding simulations. Last, we are able to use the master equation model to obtain details of the folding mechanism and folding transition state, which appear consistent with the "zipper" mechanism inferred from the experiment.
authors.affiliation: Cambridge University, Department of Chemistry, Lensfield Road Cambridge CB2 1EW, United Kingdom.
authors.forename: David
authors.initials: D
authors.lastname: De Sancho
authors.affiliation: Department of Chemical Engineering, 111 Research Drive, Iacocca Hall, Bethlehem, Pennsylvania 18015, United States.
authors.forename: Jeetain
authors.initials: J
authors.lastname: Mittal
authors.affiliation: Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States.
authors.forename: Robert B
authors.initials: RB
authors.lastname: Best