title: The oligodeoxynucleotide sequences corresponding to never-expressed peptide motifs are mainly located in the non-coding strand.
abstract: BACKGROUND
  We study the usage of specific peptide platforms in protein composition. Using the pentapeptide as a unit of length, we find that in the universal proteome many pentapeptides are heavily repeated (even thousands of times), whereas some are quite rare, and a small number do not appear at all. To understand the physico-chemical-biological basis underlying peptide usage at the proteomic level, in this study we analyse the energetic costs for the synthesis of rare and never-expressed versus frequent pentapeptides. In addition, we explore residue bulkiness, hydrophobicity, and codon number as factors able to modulate specific peptide frequencies. Then, the possible influence of amino acid composition is investigated in zero- and high-frequency pentapeptide sets by analysing the frequencies of the corresponding inverse-sequence pentapeptides. As a final step, we analyse the pentadecamer oligodeoxynucleotide sequences corresponding to the never-expressed pentapeptides.
  
  
  RESULTS
  We find that only DNA context-dependent constraints (such as oligodeoxynucleotide sequence location in the minus strand, introns, pseudogenes, frameshifts, etc.) provide a coherent mechanistic platform to explain the occurrence of never-expressed versus frequent pentapeptides in the protein world.
  
  
  CONCLUSIONS
  This study is of importance in cell biology. Indeed, the rarity (or lack of expression) of specific 5-mer peptide modules implies the rarity (or lack of expression) of the corresponding n-mer peptide sequences (with n < 5), so possibly modulating protein compositional trends. Moreover the data might further our understanding of the role exerted by rare pentapeptide modules as critical biological effectors in protein-protein interactions.
authors.affiliation: Department of Biochemistry and Molecular Biology Ernesto Quagliariello, University of Bari, Bari, Italy.
authors.forename: Giovanni
authors.initials: G
authors.lastname: Capone
authors.forename: Giuseppe
authors.initials: G
authors.lastname: Novello
authors.forename: Candida
authors.initials: C
authors.lastname: Fasano
authors.forename: Brett
authors.initials: B
authors.lastname: Trost
authors.forename: Mik
authors.initials: M
authors.lastname: Bickis
authors.forename: Anthony
authors.initials: A
authors.lastname: Kusalik
authors.forename: Darja
authors.initials: D
authors.lastname: Kanduc
mesh_terms: D020816:Amino Acid Motifs; D003062:Codon; D004247:DNA / Q000235:genetics*; D015870:Gene Expression; D009842:Oligopeptides / Q000737:chemistry* / Q000235:genetics*; D020543:Proteome / Q000032:analysis
chemical_list: D003062:Codon; D009842:Oligopeptides; D020543:Proteome; D004247:DNA