Structure of the Transition State for Folding of a Protein Derived from Experiment and Simulation

• Published in: Journal of molecular biology 1996-03, Vol.257 (2), p.430-440
• Main Authors: Daggett, Valerie, Li, Aijun, Itzhaki, Laura S., Otzen, Daniel E., Fersht, Alan R.
• Format: Article
• Language: English
• Subjects: alpha-helix; Amino Acid Sequence; beta-sheet; Chymotrypsin - antagonists & inhibitors; chymotrypsin inhibitors; Computer Simulation; folding nucleation; folding pathways; Hordeum - chemistry; Hordeum vulgare; Magnetic Resonance Spectroscopy; Models, Molecular; molecular conformation; molecular dynamics; Molecular Sequence Data; Peptides - chemistry; Plant Proteins; protein engineering; Protein Folding; Protein Structure, Secondary; simulation; structure; transition state structure
• ISSN: 0022-2836; 1089-8638
• DOI: 10.1006/jmbi.1996.0173

Independent experimental and theoretical studies of the unfolding of barley chymotrypsin inhibitor 2 (C/2) 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 Fvalues. The two are in good agreement overall (correlation coefficient=0.87), which suggests that the theoreticalmodels should provide a structural framework for interpretation of the Fvalues. 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 Fvalues 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 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 Fvalues 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.