Evolutionary origin of a secondary structure: π-helices as cryptic but widespread insertional variations of α-helices that enhance protein functionality

J Mol Biol. 2010 Nov 26;404(2):232-46. doi: 10.1016/j.jmb.2010.09.034. Epub 2010 Oct 1.


Formally annotated π-helices are rare in protein structures but have been correlated with functional sites. Here, we analyze protein structures to show that π-helices are the same as structures known as α-bulges, α-aneurisms, π-bulges, and looping outs, and are evolutionarily derived by the insertion of a single residue into an α-helix. This newly discovered evolutionary origin explains both why π-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 π-helices in the diverse ferritin-like superfamily illustrates their tendency to be conserved in protein families and identifies a putative π-helix-containing primordial precursor, a "missing link" intermediary form of the ribonucleotide reductase family, vestigial π-helices, and a novel function for π-helices that we term a "peristaltic-like shift." This new understanding of π-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 π-helix functionality, and contribute additional tools to the protein engineering toolkit.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Evolution, Molecular*
  • Ferritins / chemistry
  • Ferritins / genetics
  • Hydrogen Bonding
  • Models, Molecular
  • Molecular Sequence Data
  • Mutagenesis, Insertional
  • Phylogeny
  • Protein Structure, Secondary / genetics*
  • Proteins / chemistry*
  • Proteins / genetics*
  • Sequence Homology, Amino Acid
  • Thermodynamics


  • Proteins
  • Ferritins