Stabilizing IκBα by “Consensus” Design

IκBα is the major regulator of transcription factor NF-κB function. The ankyrin repeat region of IκBα mediates specific interactions with NF-κB dimers, but ankyrin repeats 1, 5 and 6 display a highly dynamic character when not in complex with NF-κB. Using chemical denaturation, we show here that IκBα displays two folding transitions: a non-cooperative conversion under weak perturbation, and a major cooperative folding phase upon stronger insult. Taking advantage of a native Trp residue in ankyrin repeat (AR) 6 and engineered Trp residues in AR2, AR4 and AR5, we show that the cooperative transition involves AR2 and AR3, while the non-cooperative transition involves AR5 and AR6. The major structural transition can be affected by single amino acid substitutions converging to the “consensus” ankyrin repeat sequence, increasing the native state stability significantly. We further characterized the structural and dynamic properties of the native state ensemble of IκBα and the stabilized mutants by H/2H exchange mass spectrometry and NMR. The solution experiments were complemented with molecular dynamics simulations to elucidate the microscopic origins of the stabilizing effect of the consensus substitutions, which can be traced to the fast conformational dynamics of the folded ensemble.