Residue-Specific Description of Non-Native Transient Structures in the Ensemble ofAcid-Denatured Structures of the All-13 Protein c-src SH3t

摘要

Secondary chemical shift analysis has been used to characterize the unfolded state of acid-denatured c-src SH3. Even though native c-src SH3 adopts an all-fl fold, we found evidence of transienthelicity in regions corresponding to native loops. In particular, residues 40-46, connecting the n-src loop tothe third fi-strand, exhibited an apparent helicity of nearly 45%. Furthermore, the RT loop and the divergingturn appeared to adopt non-native-like helical conformations. Interestingly, none of the residues found intransient helical conformations exhibited significant 0-values [Riddle, D. S., et al. (1999) Nat. Struct. Biol. 6,1016-1024]. This indicated that the transient helicity has no influence or only a weak influence on the actualprotein folding reaction. The residual structural propensities were compared to those of other SH3 domains,revealing heterogeneity in the unfolded ensemble that clearly contrasts with the conserved character of thetopology of native state and transition state ensembles typical for SH3 domains.