Fluorescence resonance energy transfer dynamics during protein folding: evidence of multistage folding kinetics

Fluorescence resonance energy transfer (FRET) during folding of a model protein, HP-36, is investigated by Brownian dynamics simulation. Computer simulations of this protein show that folding kinetics is non-exponential and multistage, after a fast initial hydrophobic collapse. This multistage dynamics can be captured in FRET with a suitably chosen donor- acceptor pair. In particular, we find that FRET can be sensitive to late stages of changes in the radius of gyration which is found to occur for this model protein. This late stage dynamics is driven by changes in the topological pair contact formation