Measuring the rate of intramolecular contact formation in polypeptides

Formation of a specific contact between two residues of a polypeptide chain is an important elementary process in protein folding. Here we describe a method for studying contact formation between tryptophan and cysteine based on measurements of the lifetime of the tryptophan triplet state. With tryp tophan at one end of a flexible peptide and cysteine at the other, the trip let decay rate is identical to the rate of quenching by cysteine. We show t hat this rate is also close to the diffusion-limited rate of contact format ion. The length dependence of this end-to-end contact rate was studied in a series of Cys-(Ala-Gly-Gln)(kappa)-Trp peptides, with k varying from 1 to 6. The rate decreases from similar to 1/(40 ns) for k = 1 to similar to 1/( 140 ns) for k = 6. approaching the length dependence expected for a random coil (n(-3/2)) for the longest peptides.