Structure-based prediction reveals capping motifs that inhibit β-helix aggregation

The parallel beta-helix is a geometrically regular fold commonly found in the proteomes of bacteria, viruses, fungi, archaea, and some vertebrates. beta-helix structure has been observed in monomeric units of some aggregated amyloid fibers. In contrast, soluble beta-helices, both right-and left-handed, are usually "capped" on each end by one or more secondary structures. Here, an in-depth classification of the diverse range of beta-helix cap structures reveals subtle commonalities in structural components and in interactions with the beta-helix core. Based on these uncovered commonalities, a toolkit of automated predictors was developed for the two distinct types of cap structures. In vitro deletion of the toolkit-predicted C-terminal cap from the pertactin beta-helix resulted in increased aggregation and the formation of soluble oligomeric species. These results suggest that beta-helix cap motifs can prevent specific, beta-sheet-mediated oligomeric interactions, similar to those observed in amyloid formation.