Helix-coil kinetics: Folding time scales for helical peptides from a sequential kinetic model

In this paper we describe the development of a simple model for peptide helix folding kinetics. This model is based upon a master equation treatment of the evolution of kinetic states describing the number of alpha-helical hydrogen bonds present in the folding polypeptide versus time. The equilibrium aspects of the model are assumed to obey the Zimm-Bragg model for helix to coil transitions. Barrier heights for individual hydrogen bond formation events are taken from recent calculations on the thermodynamic barrier associated with helix propagation. The resulting kinetic treatment suggests that the coil to helix folding transition should occur on a time scale of 20-70 ns under refolding conditions, depending on the peptide length and the specific values of the Zimm-Bragg constants sigma and s used to represent the equilibrium aspects of folding. Helix unfolding is seen to occur on a somewhat shorter time scale for these peptides. The overall picture suggests that helix-coil dynamics are faster than the microsecond time scales suggested by earlier experiments and that they may be probed by fast T-jump experiments on a nanosecond time scale.