BackgroundWe 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.ResultsWe 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.ConclusionsThis 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.
In a companion paper, we reported that pentapeptides from human poliovirus 1, Mahoney strain, occur repeatedly in human proteins for a total of more than 18,000 overlaps. In the present study, we describe the distribution of the polio pentapeptides throughout biochemical pathways and networks characterizing functions and tissues in the human host. The present study might be of help to better define the poliovirus-host relationships as well as for designing peptide modules with anti-polio activity.
In the present study, we analyze the peptide commonality between poliovirus polyprotein and the human proteins. We report on the following findings: (1) the extent of polio peptide overlap on the human proteome is high, and involves the entire viral polyprotein; (2) viral peptide matching affects human proteins linked to fundamental cellular functions. The data may help to further our understanding of the relationships between poliovirus and the human host.
In order to define poliovirus (PV) neurovirulence at the molecular level, we comparatively analyze the primary amino acid sequence of Mahoney, a neurovirulent PV strain, versus (i) Sabin, an attenuated PV strain, and (ii) IS1, a PV isolate obtained in temporal association to a paralysis event from a polio vaccinated subject. We identify and describe 12 pentapeptides that, originally present in the Mahoney sequence, are changed in the non-neurovirulent Sabin strain, and, successively, restored in IS1 strain.
Introduction 3. Extracting information from immunopeptidomes and related databanks using the low-similarity concept 4. Clostridium tetani toxin epitopes: a set of rare motifs 5. Anti-tetanus toxoid antibody CDR3 sequences: mirroring the epitopic peptide rarity 6. Bacillus anthracis toxin: epitopes and CDR3 sequences 7. Clostridium botulinum toxin: epitopes and CDR3 sequences 8. Perspectives 9. Contributions 10. References
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