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 tryptophan at one end of a flexible peptide and cysteine at the other, the triplet decay rate is identical to the rate of quenching by cysteine. We show that this rate is also close to the diffusion-limited rate of contact formation. The length dependence of this end-to-end contact rate was studied in a series of Cys-(Ala-Gly-Gln)(k)-Trp peptides, with k varying from 1 to 6. The rate decreases from ∼1/(40 ns) for k = 1 to ∼1/(140 ns) for k = 6, approaching the length dependence expected for a random coil (n(−3/2)) for the longest peptides.