Folding landscapes of ankyrin repeat proteins: experiments meet theory

Abstract

Nearly 6% of eukaryotic protein sequences contain ankyrin repeat (AR) domains, which consist of several repeats and often function in binding. AR proteins show highly cooperative folding despite a lack of long-range contacts. Both theory and experiment converge to explain that formation of the interface between elements is more favorable than formation of any individual repeat unit. IkappaBalpha and Notch both undergo partial folding upon binding perhaps influencing the binding free energy. The simple architecture, combined with identification of consensus residues that are important for stability, has enabled systematic perturbation of the energy landscape by single point mutations that affect stability or by addition of consensus repeats. The folding energy landscapes appear highly plastic, with small perturbations re-routing folding pathways.

Figure 1

A) Structure of the Notch AR domain, 1OT8.pdb. A ribbon trace of the backbone is shown colored from red (AR1) to blue (AR7), the space-filling model is shown shaded. B) Contact map of the Notch AR domain colored according to A. C) Consensus sequences of stably folded ARs.

Figure 2

A) A schematic of the manner in which the free energy landscape of Notch was experimentally determined by obtaining an overall thermodynamic stability for each of the repeats in the domain. B) The free energy landscape of the Notch AR domain as experimentally determined.

Figure 3

Folding simulation of Notch using the Go-model energy function in which contacts are weighted according to the Miyzawa-Jernigan energies. The trajectory at an intermediate temperature is shown with snapshots of structures along the trajectory.