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Related Experiment Videos

Long-range order in the src SH3 folding transition state.

V P Grantcharova1, D S Riddle, D Baker

  • 1Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.

Proceedings of the National Academy of Sciences of the United States of America
|June 22, 2000
PubMed
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Protein folding pathways are investigated using the src SH3 domain. Results indicate a discrete order of structure assembly during folding, with the central beta-sheet forming early in the transition state ensemble.

Area of Science:

  • Protein folding dynamics
  • Biophysics
  • Structural biology

Background:

  • The src SH3 domain is a model system for studying protein folding.
  • Understanding the heterogeneity of folding transition states is crucial for protein folding research.
  • Previous studies utilized point mutagenesis to probe folding mechanisms.

Purpose of the Study:

  • To investigate the association of structural elements during protein folding.
  • To determine the degree of order in the folding transition state ensemble of the src SH3 domain.
  • To elucidate the role of specific structural elements and conformational entropy in protein folding.

Main Methods:

  • Double-mutant analysis of polar residues.
  • Introduction of glycine insertions in loops.

Related Experiment Videos

  • Disulfide crosslinking to stabilize or destabilize structural elements.
  • Kinetic analysis of folding and unfolding rates.

    • Main Results:

    • The hydrogen bond network between the distal beta-hairpin and diverging turn is formed in the folding transition state.
    • Modifications to the n-src loop and distal beta-hairpin affected folding rates but not unfolding rates, indicating pre-formed structure.
    • Crosslinking the RT loop or termini significantly slowed unfolding, suggesting their dissociation precedes the rate-limiting step.
    • The central three-stranded beta-sheet is formed in nearly all conformations of the folding transition state ensemble.

    Conclusions:

    • Protein folding of the src SH3 domain follows a discrete order of structure assembly.
    • The folding transition state ensemble is not highly heterogeneous; key structural elements are ordered early.
    • The central beta-sheet formation is a critical early event in the folding pathway.