Extracting function from a β-trefoil folding motif

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Abstract
Despite having remarkably similar three-dimensional structures and stabilities, IL-1β promotes signaling, whereas IL-1Ra inhibits it. Their energy landscapes are similar and have coevolved to facilitate competitive binding to the IL-1 receptor. Nevertheless, we find that IL-1Ra folds faster than IL-1β. A structural alignment of the proteins shows differences mainly in two loops, a β-bulge of IL-1β and a loop in IL-1Ra that interacts with residue K145 and connects β-strands 11 and 12. Bioassays indicate that inserting the β-bulge from IL-1β confers partial signaling capability onto a K145D mutant of IL-1Ra. Based on the alignment, mutational assays and our computational folding results, we hypothesize that functional regions are not central to the β-trefoil motif and cause slow folding. The IL-1β β-bulge facilitates activity and replacing it by the IL-1Ra β-turn results in a hybrid protein that folds faster than IL-1β. Inserting the β11–β12 connecting-loop, which aids inhibition, into either IL-1β or the hybrid protein slows folding. Thus, regions that aid function (either through activity or inhibition) can be inferred from folding traps via structural differences. Mapping functional properties onto the numerous folds determined in structural genomics efforts is an area of intense interest. Our studies provide a systematic approach to mapping the functional genomics of a fold family.

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