Flexibly varying folding mechanism of a nearly symmetrical protein: B domain of protein A

The folding pathway of the B domain of protein A is the pathway most intensively studied by computer simulations. Recent systematic measurement of (D values by Sato et al. [Sato, S., Religa, T. L., Daggett, V., & Fersht, A. R. (2004) Proc. Natl Acad. Sci. USA 101, 6952-6956], however, has shown that none of the published computational predictions is consistent with the detailed features of the experimentally observed folding mechanism. In this article we use a statistical mechanical model of folding to show that sensitive dependence of multiple transition state ensembles on temperature and the denaturant concentration is the key to resolving the inconsistency among simulations and the experiment. Such sensitivity in multiple transition state ensembles is a natural consequence of symmetry-breaking in a nearly symmetrical protein.