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The parallel beta-helix is a geometrically regular fold commonly found in the proteomes of bacteria, viruses, fungi, archaea, and 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 the end(s) by one or more secondary structures. Here, an in-depth classification of the diverse range of beta-helix cap structures reveals hidden commonalities in structural components and in interactions with the beta-helix core. Models of these commonalities, based on structural and sequence alignments, are developed as automated detectors for the different types of cap structures. Deletion of the detected C-terminal cap from the P.69T pertactin beta-helix resulted in pertactin aggregation and the formation of soluble oligomeric species, suggesting that beta-helix cap motifs can prevent specific, beta-sheet-mediated oligomeric interactions, similar to those observed in amyloid formation. The algorithm and analysis data can be found here. The README file is here. The pdb minus data used in testing is here.