Forbidden penta-peptides

There are 3,200,000 amino acid sequences of length 5 (penta-peptides). Statistically, we expect to see a distribution of penta-peptides that is determined by the frequency of the participating amino acids. We show, however, that not only are there thousands of such penta-peptides that are absent from all known proteomes, but many of them are coded for multiple times in the non-coding genomic regions. This suggests a strong selection process that prevents these peptides from being expressed. We also show that the characteristics of these forbidden penta-peptides vary among different phylogenetic groups (e.g., eukaryotes, prokaryotes, and archaea). Our analysis provides the first steps toward understanding the "grammar" of the forbidden penta-peptides. Published by Cold Spring Harbor Laboratory Press.