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Forbidden penta-peptides.

Tamir Tuller1, Benny Chor, Nathan Nelson

  • 1School of Computer Science, Tel Aviv University, Tel Aviv, Israel. tamirtul@post.tau.ac.il

Protein Science : a Publication of the Protein Society
|September 26, 2007
PubMed
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Thousands of penta-peptides are absent from proteomes, suggesting selection against their expression. These "forbidden" penta-peptides show varying characteristics across different life forms, hinting at a genomic grammar.

Area of Science:

  • Genomics
  • Proteomics
  • Bioinformatics

Background:

  • The theoretical number of possible penta-peptides (amino acid sequences of length 5) is 3,200,000.
  • The distribution of penta-peptides in proteomes is expected to correlate with amino acid frequencies.

Purpose of the Study:

  • To investigate the presence and distribution of penta-peptides across known proteomes.
  • To identify penta-peptides that are unexpectedly absent from all proteomes.
  • To explore the genomic coding and phylogenetic characteristics of these absent penta-peptides.

Main Methods:

  • Statistical analysis of amino acid sequences.
  • Comparative genomics across eukaryotic, prokaryotic, and archaeal proteomes.
  • Identification of penta-peptides absent from known proteomes.

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Main Results:

  • Thousands of possible penta-peptides are absent from all known proteomes.
  • Many of these absent penta-peptides are encoded multiple times in non-coding genomic regions.
  • The characteristics of these "forbidden" penta-peptides differ significantly among major phylogenetic groups.

Conclusions:

  • A strong selection process appears to prevent the expression of specific penta-peptides.
  • The observed patterns suggest an underlying "grammar" governing penta-peptide occurrence and avoidance.
  • Further research into this forbidden penta-peptide grammar could reveal fundamental biological principles.