title: Transient helical structure during PI3K and Fyn SH3 domain folding.
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.
authors.affiliation: Department of Physics, Kansai Medical University, 2-5-1 Shinmachi, Hirakata, 573-1010, Japan.
authors.forename: Yoshitaka
authors.initials: Y
authors.lastname: Matsumura
authors.forename: Masaji
authors.initials: M
authors.lastname: Shinjo
authors.forename: Seung Joong
authors.initials: SJ
authors.lastname: Kim
authors.forename: Nobuyuki
authors.initials: N
authors.lastname: Okishio
authors.forename: Martin
authors.initials: M
authors.lastname: Gruebele
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Kihara
mesh_terms: D000595:Amino Acid Sequence; D002942:Circular Dichroism; D019791:Guanidine / Q000737:chemistry; D006801:Humans; D007700:Kinetics; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D019869:Phosphatidylinositol 3-Kinases / Q000737:chemistry* / Q000378:metabolism; D058849:Protein Refolding; D017433:Protein Structure, Secondary; D051076:Proto-Oncogene Proteins c-fyn / Q000737:chemistry* / Q000378:metabolism; D053838:Scattering, Small Angle; D016415:Sequence Alignment; D014961:X-Ray Diffraction; D018909:src Homology Domains
chemical_list: D019869:Phosphatidylinositol 3-Kinases; C494957:FYN protein, human; D051076:Proto-Oncogene Proteins c-fyn; D019791:Guanidine
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