Time-resolved absorption and fluorescence spectroscopy are used to study the dynamics of protein structural changes subsequent to rapid mixing or excitation with short laser pulses. Kinetic models are used to fit and interpret the measured data. We have foccused on measuring the kinetics of loop formation for random peptides, and for both the cold shock protein from Thermotoga Maritima CspTm and the folding subdomain of villin. To measure loop formation, one position in the chain is labeled with tryptophan and another with cysteine or cystine. The trypophan, excited to its lowest triplet state by a 280-290 nm laser pulse, is efficiently quenched by the sulfur-containing residue upon loop formation. We had previously characterized this method for peptides having the sequence cys-(ala-gly-gln)j-trp, where the diffusion- and reaction-limited rates were obtained from measurements of the temperature- and viscosity-dependence of the quenching rates. The diffusion-limited rate is the rate of contact formation, while the reaction-limited rate provides information on the equilibrium end-to-end distribution. The turnover in the reaction-limited rate at short chain lengths was attributed to the stiffness of a chain having a persistence length of 0.65 nm. We have recently focused on using this technique to understand the dynamics of proteins and 'swollen' polypeptides. In 6 M guanidine hydrochloride (GdmCl), the peptides expand, the rates for slow down and the length-dependence of the reaction-limited rates increases for peptides longer than 10 amino acids as expected for chains 'swollen' by excluded volume. To further explore the effects of excluded volume we have carried out flourescence resonance energy transfer (FRET) experiments and added 'tails' at each end of an 11-residue peptide. The FRET results show that the average end-to-end distance of the 11-residue sequence dansyl-(ala-gly-gln)3-trp increases by about 15% in 6 M GdmCl. The rates for the peptides with tails are about a factor of 1.5 slower than that for the 11-mer. Simulations of wormlike chains that include excluded volume produce similar changes in the the end-to-end distances and the reaction-limited rates. We have used this technique to measure folding dynamics of the villin subdomain which has a tryptophan in position 23 and an N-terminal cysteine. The average rate for the unfolded chain is about 10 microseconds and increases with decreasing denaturant concentration, indicating a compaction of the unfolded protein as we had previously observed for the cold shock protein, CspTm. At intermediate denaturant concentrations the time course of the triplet decay consists of two relaxations, the rates and amplitudes of which reveal the fast kinetics for folding and unfolding of this protein. The folding rates obtained using a simple kinetic model are similar to those reported from laser induced temperature-jump experiments but differ significantly from those reported from dynamic NMR line shape analysis on a variant with methionine at the N-terminus, an issue that remains to be resolved. For the unfolded chain in 6 M GdmCl the quenching kinetics can be characterized by stretched-exponential decays, [exp(-kt)^B] with the exponent B ~ 0.8. The origin of this complexity is not yet clear, but it suggests that the unfolded protein must contain subpopulations with lifetimes comparable to the observed quenching rates (10 microseconds). When adjusted for segment length, the rate in the unfolded state is also slower than those observed for the (ala-gly-gln) peptides and for unfolded CspTm. The differences may result from the difference in the fraction of glycine residues.
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