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Parallel folding pathways in the SH3 domain protein.

A R Lam1, J M Borreguero, F Ding

  • 1Center for Polymer Studies, Department of Physics, Boston University, Boston, MA 02215, USA. arlam@buphy.bu.edu

Journal of Molecular Biology
|September 29, 2007
PubMed
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Researchers characterized the protein transition-state ensemble (TSE) using simulations. They discovered multiple folding pathways, suggesting TSEs in related proteins might reveal alternative folding routes.

Area of Science:

  • Computational biophysics
  • Protein folding dynamics
  • Molecular modeling

Background:

  • Understanding protein folding is essential for molecular biology.
  • The transition-state ensemble (TSE) represents a critical, yet challenging, intermediate state in protein folding.
  • Characterizing the TSE is key to deciphering the mechanisms of protein folding.

Purpose of the Study:

  • To determine the transition-state ensemble (TSE) of the src-SH3 domain protein.
  • To investigate the structural properties and folding pathways within the TSE.
  • To explore the potential for designing novel folding pathways.

Main Methods:

  • Extensive molecular dynamics simulations using the Go model.
  • Calculation of folding probabilities for candidate TSE conformations.

Related Experiment Videos

  • Analysis of structural ensembles and identification of folding pathways.

    • Main Results:

    • The TSE of src-SH3 features a stable hydrophobic core with dynamic surrounding structures.
    • Three distinct, parallel folding pathways were identified within the TSE.
    • One pathway aligns with experimental data, while two others represent less preferred routes.

    Conclusions:

    • The study reveals the structural heterogeneity and multi-pathway nature of the protein TSE.
    • Designing specific amino acid interactions can steer protein folding through alternative pathways.
    • Experimentally observed TSEs in homologous proteins and circular permutants may reflect inherent alternative folding pathways.