Alpha secondary structures generate weak but recurrent periodicity in proteins.

Weak but recurrent periodic patterns characterize numerous actual proteins: the rate at which similarity occurs between residues i and i + 4 or i + 7 or i + 11 is very often slightly higher than predicted by chance. That result could indicate that numerous actual proteins derive from ancestral clearcut periodic sequences. Nevertheless, it is shown that this recurrent periodic pattern occurs much more significantly when analyses are restricted to the alpha-helical portions of proteins while it never occurs when beta-stranded subsequences are taken into account. This preferential location of periodicity inside protein subregions corresponding to alpha helices suggests that the recurrent pattern of weak periodicity could result from an ubiquitous physical property of alpha helices. The regular alternation of hydrophobicity, which is most often displayed by alpha helices, could then be the origin of weak periodicity.