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Probing a moving target with a plastic unfolding intermediate of an ankyrin-repeat protein

Repeat proteins are composed of tandem arrays of 30- to 40-residue structural motifs and are characterized by short-range interactions between residues close in sequence. Here we have investigated the equilibrium unfolding of D34, a 426-residue fragment of ankyrinR that comprises 12 ankyrin repeats. We show that D34 unfolds via an intermediate in which the C-terminal half of the protein is structured and the N-terminal half is unstructured. Surprisingly, however, we find that we change the unfolding process when we attempt to probe it. Single-site, moderately destabilizing mutations at the C terminus result in different intermediates dominating. The closer to the C terminus the mutation, the fewer repeats are structured in the intermediate; thus, structure in the intermediate frays from the site of the mutation. This behavior contrasts with the robust unfolding of globular proteins in which mutations can destabilize an intermediate but do not cause a different intermediate to be populated. We suggest that, for large repeat arrays, the energy landscape is very rough, with many different low-energy species containing varying numbers of folded modules so the species that dominates can be altered easily by single, conservative mutations. The multiplicity of partly folded states populated in the equilibrium unfolding of D34 is also mirrored by the kinetic folding mechanism of ankyrin-repeat proteins in which we have observed that parallel pathways are accessible from different initiation sites in the structure.