The statistical significance of selected sense-antisense peptide interactions

Christopher J.R. Illingworth, Sree V. Chintipalli, Stefano A. Serapian, Andrew D. Miller, Vaclav Veverka, Mark D. Carr, Christopher A. Reynolds

Research output: Contribution to journalArticlepeer-review

5 Citations (Scopus)


Sense and antisense peptides, encoded by sense and corresponding antisense DNA strands, are capable of specific interactions that could be a driving force to mediate protein-protein or protein-peptide binding associations. The complementary residue hypothesis suggests that these interactions are founded upon the sum of pairwise interactions between amino acids encoded by corresponding sense and antisense codons. Despite many successful experimental results obtained with the hypothesis, however, the physicochemical basis for these interactions is poorly understood. We examined the potential of the hypothesis for general identification of protein-protein interaction sites, and the possible role of the hypothesis in determining folding in a broad set of protein structures. In addition, we performed a structural study to investigate the binding of a complementary peptide to IL-1F2. Our results suggest that complementary residue pairs are no more frequent or conserved than average in protein-protein interfaces, and are statistically under-represented amongst contacting residue pairs in folded protein structures. Although our structural results matched experimental observations of binding between the peptide and IL-1F2, complementary residue interactions do not appear to be dominant in the bound structure. Overall, our data do not allow us to conclude that the complementary residue hypothesis accounts for specific sense-antisense peptide interactions.

Original languageEnglish
Pages (from-to)1440-1447
Number of pages8
JournalJournal of Computational Chemistry
Issue number16
Publication statusPublished - 4 Apr 2012
Externally publishedYes


  • Antisense peptides
  • Complementary residue pairs
  • Docking
  • Glide
  • IL-1F2
  • MI pairs
  • Molecular interactions
  • Protein peptide interaction
  • Protein-protein interactions
  • Sense peptides

ASJC Scopus subject areas

  • Chemistry(all)
  • Computational Mathematics


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