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Structure of the transition state for folding of a protein derived from experiment and simulation

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  • Valerie Daggett, University of Washington
  • ,
  • Aijun Li, University of Washington
  • ,
  • Laura S. Itzhaki, University of Cambridge
  • ,
  • Daniel E. Otzen
  • Alan R. Fersht, University of Cambridge

Independent experimental and theoretical studies of the unfolding of barley chymotrypsin inhibitor 2 (CI2) are compared in an attempt to derive plausible three-dimensional structural models of the transition state. A very simple structure index is calculated along the sequence for the molecular dynamics-generated transition state models to facilitate comparison with the Φ(F) values. The two are in good agreement overall (correlation coefficient = 0.87), which suggests that the theoretical models should provide a structural framework for interpretation of the Φ(F) values. Both experiment and simulation indicate that the transition state is a distorted form of the native state in which the α-helix is weakened but partially intact and the β-sheet is quite disrupted. As inferred from the (I)F values and observed directly in the simulations, the unfolding of CI2 is cooperative and there is a 'folding core' comprising a patch on the α-helix and a portion of the β-sheet, nucleated by interactions between Ala16, Ile49 and other neighbouring residues. The protein becomes less structured radiating away from this core. Overall the data indicate that CI2 folds by a nucleation-collapse mechanism. In the absence of experimental information, we have little confidence that the molecular dynamics simulations are correct, especially when only one or a few simulations are performed. On the other hand, even though the experimentally derived Φ values may reflect the extent of overall structure formation, they do not provide an actual atomic-resolution three-dimensional structure of the transition state. By combining the two approaches, however, we have a framework for interpreting Φ(F) values and can hopefully arrive at a more trustworthy model of the transition state. The process is in some ways similar to the combination of molecular dynamics and NMR data to solve the tertiary structure of proteins.

Original languageEnglish
JournalJournal of Molecular Biology
Pages (from-to)430-440
Number of pages11
Publication statusPublished - 29 Mar 1996

    Research areas

  • Folding nucleation, Folding pathways, Molecular dynamics, Protein engineering, Transition state structure

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