The oligodeoxynucleotide sequences corresponding to never-expressed peptide motifs are mainly located in the non-coding strand.

BMC Bioinformatics
Giovanni CaponeDarja Kanduc

Abstract

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. 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 pentape...Continue Reading

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Citations

May 19, 2012·Immunopharmacology and Immunotoxicology·Guglielmo Lucchese
Sep 11, 2012·Journal of Basic Microbiology·Giovanni CaponeDarja Kanduc
Nov 16, 2014·Bioinformatics·Baris E SuzekUNKNOWN UniProt Consortium
May 26, 2018·Current Drug Discovery Technologies·Darja Kanduc
Apr 6, 2011·The Protein Journal·Yongchao DouJun Wang
Oct 13, 2018·Scientific Reports·Jarosław PoznańskiMarcin Grynberg
Apr 8, 2021·Expert Review of Proteomics·Darja Kanduc
Jul 30, 2020·Pathobiology : Journal of Immunopathology, Molecular and Cellular Biology·Darja Kanduc

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Software Mentioned

blastn
Perfect Peptide Match
BLAST
Spartan
Sequence Manipulation Suite Reverse Translate
ProtScale

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