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Transient non-native burial of a Trp residue occurs initially during the unfolding of a SH3 domain.

The detection and characterization of non-native interactions in a partially unfolded form of any protein are important not only with regard to how they might facilitate folding but also in the context of their possible role in driving the protein toward amyloid fibril formation. The SH3 domain of PI3 kinase is known to unfold via an early, partially unfolded intermediate. In this study, the kinetics of unfolding of this protein in guanidine hydrochloride was studied by monitoring the fluorescence of its sole tryptophan residue, W53. W53 is fully solvent-exposed in both the native and unfolded states, as indicated by a similar wavelength (356-357 nm) of maximal fluorescence emission, and a similar quantum yield of fluorescence. W53 becomes partially buried in the unfolding intermediate, as seen in the 6-7 nm blue shift in its wavelength of maximal fluorescence emission in the intermediate, and in the transient initial increase in the quantum yield of its fluorescence during unfolding. It appears that W53 is engaged in non-native interactions in the unfolding intermediate. It is also shown that the transition from the native state to the unfolding intermediate occurs as a gradual and not an all-or-none transition.