Evolutionary Origin of a Secondary Structure: π-Helices as Cryptic but Widespread Insertional Variations of α-Helices That Enhance Protein Functionality

Formally annotated pi-helices are rare in protein structures but have been correlated with functional sites. Here, we analyze protein structures to show that pi-helices are the same as structures known as alpha-bulges, alpha-aneurisms, pi-bulges, and looping outs, and are evolutionarily derived by the insertion of a single residue into an alpha-helix. This newly discovered evolutionary origin explains both why pi-helices are cryptic, being rarely annotated despite occurring in 15% of known proteins, and why they tend to be associated with function. An analysis of pi-helices in the diverse ferritin-like superfamily illustrates their tendency to be conserved in protein families and identifies a putative pi-helix-containing primordial precursor, a missing link intermediary form of the ribonucleotide reductase family, vestigial pi-helices, and a novel function for pi-helices that we term a peristaltic-like shift. This new understanding of pi-helices paves the way for this generally overlooked motif to become a noteworthy feature that will aid in tracing the evolution of many protein families, guide investigations of protein and pi-helix functionality, and contribute additional tools to the protein engineering toolkit. (C) 2010 Elsevier Ltd. All rights reserved.