Transient Helical Structure during PI3K and Fyn SH3 Domain Folding

Abstract

A growing list of proteins, including the beta-sheet-rich SH3 domain, is known to transiently populate a compact alpha-helical intermediate before settling into the native structure. Examples have been discovered in cryogenic solvent as well as by pressure jumps. Earlier studies of lambda repressor mutants showed that transient states with excess helix are robust in an all-alpha protein. Here we extend a,previous study of STC SH3 domain to two new SH3 sequences, phosphatidylinositol 3-kinase (PI3K) and a Fyn mutant, to see how robust such helix rich transients are to sequence variations in this beta-sheet fold. We quantify helical structure by circular dichroism (CD), protein compactness by small angle Xray scattering (SAXS), and transient helical populations by cryo-stopped-flow CD. Our results show that transient compact helix rich intermediates are easily accessible on the folding landscape of different SH3 domains. In molecular dynamics simulations, force field errors are often blamed for transient non-native structure. We suggest that experimental examples of very fast alpha-rich, transient misfolding could become a more subtle test for further force field improvements than observation of the native state alone.