Transition states in protein folding kinetics: Modeling -values of small -sheet proteins

¹ Max Planck Institute of Colloids and Interfaces

^* To whom correspondence should be addressed. E-mail: weikl{at}mpikg.mpg.de.

Submitted on March 30, 2007
Revised on June 5, 2007
Accepted on 19 September 2007

	Abstract

Small single-domain proteins often exhibit only a single free-energy barrier, or transition state, between the denatured and the native state. The folding kinetics of these proteins is usually explored via mutational analysis. A central question is which structural information on the transition state can be derived from the mutational data. In this article, we model and structurally interpret mutational -values for two small -sheet proteins, the PIN and the FBP WW domain. The native structure of these WW domains comprises two -hairpins that form a three-stranded -sheet. In our model, we assume that the transition state consists of two conformations in which either one of the hairpins is formed. Such a transition state has been recently observed in Molecular Dynamics folding-unfolding simulations of a small designed three-stranded -sheet protein. We obtain good agreement with the experimental data (i) by splitting up the mutation-induced free-energy changes into terms for the two hairpins and for the small hydrophobic core of the proteins, and (ii) by fitting a single parameter, the relative degree to which hairpin 1 and 2 are formed in the transition state. The model helps to understand how mutations affect the folding kinetics of WW domains, and captures also negative -values that have been difficult to interpret.

Key Words: WW domains, master equation, mutational analysis, protein folding, transition state, two-state proteins