Piecing Together the History of Protein Folds From a Fragmented Evolutionary Record

Protein folds are structural units defined by the number, type, arrangement, and orientation of their core secondary structural elements. The universe of protein folds is highly interconnected. Local sequence similarities, referred to as sequence motifs, link structurally distinct folds. Sequence and structure motifs reveal deep evolutionary relationships that can help us understand the evolutionary mechanisms shaping protein structures over time. This work analyses structural divergence in folds that contain the β-hammerhead motif. Sequence and structure-based analyses reveal deep evolutionary relationships between 3-fold superfamilies: Beta Barrel (CATH superfamily 2.40.50.100); Distorted Sandwich (CATH superfamily 2.70.70.100); and Alpha-Beta Complex (CATH superfamily 3.90.1170.30). The patterns of fold divergence and motif degeneration are discussed in the context of fold evolution.