STRUCTURE OF THE TRANSITION-STATE FOR FOLDING OF A PROTEIN-DERIVED FROM EXPERIMENT AND SIMULATION

Independent experimental and theoretical studies of the unfolding of b arley chymotrypsin inhibitor 2 (CI2) are compared in an attempt to der ive plausible three-dimensional structural models of the transition st ate. A very simple structure index is calculated along the sequence fo r the molecular dynamics-generated transition state models to facilita te comparison with the Phi(F) values. The two are in good agreement ov erall (correlation coefficient = 0.87), which suggests that the theore tical models should provide a structural framework for interpretation of the Phi(F) values. Both experiment and simulation indicate that the transition state is a distorted form of the native state in which the alpha-helix is weakened but partially intact and the beta-sheet is qu ite disrupted. As inferred from the Phi(F) values and observed directl y in the simulations, the unfolding of CI2 is cooperative and there is a ''folding core'' comprising a patch on the alpha-helix and a portio n of the beta-sheet, nucleated by interactions between Ala16, Ile49 an d other neighbouring residues. The protein becomes less structured rad iating away from this core. Overall the data indicate that CI2 folds b y a nucleation-collapse mechanism. In the absence of experimental info rmation, we have little confidence that the molecular dynamics simulat ions are correct, especially when only one or a few simulations are pe rformed. On the other hand, even though the experimentally derived Phi values may reflect the extent of overall structure formation, they do not provide an actual atomic-resolution three-dimensional structure o f the transition state. By combining the two approaches, however, we h ave a framework for interpreting Phi(F) values and can hopefully arriv e 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. (C) 1996 Academic Pr ess Limited