Transient helical structure during PI3K and Fyn SH3 domain folding

J Phys Chem B. 2013 May 2;117(17):4836-43. doi: 10.1021/jp400167s. Epub 2013 Apr 18.

Abstract

A growing list of proteins, including the β-sheet-rich SH3 domain, is known to transiently populate a compact α-helical intermediate before settling into the native structure. Examples have been discovered in cryogenic solvent as well as by pressure jumps. Earlier studies of λ repressor mutants showed that transient states with excess helix are robust in an all-α protein. Here we extend a previous study of src 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 β-sheet fold. We quantify helical structure by circular dichroism (CD), protein compactness by small-angle X-ray 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 α-rich transient misfolding could become a more subtle test for further force field improvements than observation of the native state alone.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Circular Dichroism
  • Guanidine / chemistry
  • Humans
  • Kinetics
  • Molecular Dynamics Simulation
  • Molecular Sequence Data
  • Phosphatidylinositol 3-Kinases / chemistry*
  • Phosphatidylinositol 3-Kinases / metabolism
  • Protein Refolding
  • Protein Structure, Secondary
  • Proto-Oncogene Proteins c-fyn / chemistry*
  • Proto-Oncogene Proteins c-fyn / metabolism
  • Scattering, Small Angle
  • Sequence Alignment
  • X-Ray Diffraction
  • src Homology Domains

Substances

  • Phosphatidylinositol 3-Kinases
  • FYN protein, human
  • Proto-Oncogene Proteins c-fyn
  • Guanidine