Kinetics of intramolecular contact formation in disordered peptides and unfolded proteins

The formation of intramolecular contacts between distant residues is, perhaps, the simplest among the elementary processes taking place during the folding of a protein. Quenching of the triplet state of tryptophan by close contact with cysteine after nanosecond laser excitation has been used to measure both equilibrium (reaction-limited) and dynamic (diffusion-limited) contact formation rates in model peptides and engineered proteins. The triplet quenching data and FRET end-to-end distances are analyzed by means of a chain model with realistic backbone conformations and simplified hard-sphere interaction between the residues. The effect of amino acid sequence on the chain swelling is discussed.