Ruggedness in the folding landscape of protein L

Abstract

By exploring the folding pathways of the B1 domain of protein L with a series of equilibrium and rapid kinetic experiments, we have found its unfolded state to be more complex than suggested by two-state folding models. Using an ultrarapid mixer to initiate protein folding within approximately 2-4 microseconds, we observe folding kinetics by intrinsic tryptophan fluorescence and fluorescence resonance energy transfer. We detect at least two processes faster than 100 mus that would be hidden within the burst phase of a stopped-flow instrument measuring tryptophan fluorescence. Previously reported measurements of slow intramolecular diffusion are commensurate with the slower of the two observed fast phases. These results suggest that a multidimensional energy landscape is necessary to describe the folding of protein L, and that the dynamics of the unfolded state is dominated by multiple small energy barriers.