The alpha-helix folds on the millisecond time scale

It has long been believed that nucleation of the alpha-helix is a very fast reaction, occurring in around 10(-7) s. We show here that helix nucleation, in fact, takes place on the millisecond time scale. The rate of alpha-helix nucleation in two polyalanine-based peptides and in lysine and glutamic acid homopolymers was measured directly by stopped-flow deep UV CD with synchrotron radiation as the light source. Synchrotron radiation CD gives far superior signal to noise than a conventional instrument. The 16-aa AK peptide folds with first-order kinetics and a rate constant of 15 s-1 at 0 degrees C. The rate-determining step is presumably the initiation of a new helix, which occurs at least 10(5) times slower than expected. Helix folding occurs in at least two steps on the millisecond time scale for the longer peptides, with a transient overshoot of helix content significantly greater than at equilibrium, similar to that seen in the folding of several proteins. We suggest that the overshoot is caused by the formation of a single long helix followed by its breakage into the two or more helices present at equilibrium.