PROTEIN-FOLDING FUNNELS - THE NATURE OF THE TRANSITION-STATE ENSEMBLE

Background: Energy landscape theory predicts that the folding funnel f or a small fast-folding alpha-helical protein will have a transition s tate half-way to the native state. Estimates of the position of the tr ansition state along an appropriate reaction coordinate can be obtaine d from linear free energy relationships observed for folding and unfol ding rate constants as a function of denaturant concentration. The exp erimental results of Huang and Gas for lambda repressor, Fersht and co llaborators for Cl2, and Gray and collaborators for cytochrome c indic ate a free energy barrier midway between the folded and unfolded regio ns. This barrier arises from an entropic bottleneck for the folding pr ocess. Results: In keeping with the experimental results, lattice simu lations based on the folding funnel description show that the transiti on state is not just a single conformation, but rather an ensemble of a relatively large number of configurations that can be described by s pecific values of one or a few order parameters (e.g. the fraction of native contacts). Analysis of this transition state or bottleneck regi on from our lattice simulations and from atomistic models for small oc -helical proteins by Boczko and Brooks indicates a broad distribution for native contact participation in the transition state ensemble cent ered around 50%. Importantly, however, the lattice-simulated transitio n state ensemble does include some particularly hot contacts, as seen in the experiments, which have been termed by others a folding nucleus . Conclusions: Linear free energy relations provide a crude spectrosco py of the transition state, allowing us to infer the values of a react ion coordinate based on the fraction of native contacts. This bottlene ck may be thought of as a collection of delocalized nuclei where diffe rent native contacts will have different degrees of participation. The agreement between the experimental results and the theoretical predic tions provides strong support for the landscape analysis. (C) Current Biology Ltd.