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Protein Science (2007), 16:2251-2259. Published by Cold Spring Harbor Laboratory Press. Copyright © 2007 The Protein Society
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Forbidden penta-peptides

Tamir Tuller1, Benny Chor1, and Nathan Nelson2

1 School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel
2 The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel

(RECEIVED June 12, 2007; FINAL REVISION July 9, 2007; ACCEPTED July 9, 2007)

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.

Keywords: short peptides; proteomes; evolutionary selection; protein grammar; phylogenetic groups


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