β-Bulge triggers route-switching on the functional landscape of interleukin-1β

Proteins fold into three-dimensional structures in a funneled energy landscape. This landscape is also used for functional activity. Frustration in this landscape can arise from the competing evolutionary pressures of biological function and reliable folding. Thus, the ensemble of partially folded states can populate multiple routes on this journey to the native state. Although protein folding kinetics experiments have shown the presence of such routes for several proteins, there has been sparse information about the structural diversity of these routes. In addition, why a given protein populates a particular route more often than another protein of similar structure and sequence is not clear. Whereas multiple routes are observed in theoretical studies on the folding of interleukin-1 beta (IL-1 beta), experimental results indicate one dominant route where the central portion of the protein folds first, and is then followed by closure of the barrel in this beta-trefoil fold. Here we show, using a combination of computation and experiment, that the presence of functionally important regions like the beta-bulge in the signaling protein IL-1 beta strongly influences the choice of folding routes. By deleting the beta-bulge, we directly observe the presence of route-switching. This route-switching provides a direct link between route selection and the folding and functional landscapes of a protein.