PerspectiveImmunology

Rewilding immunology

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Science  03 Jul 2020:
Vol. 369, Issue 6499, pp. 37-38
DOI: 10.1126/science.abb8664

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  • Forbidden Order in coding sequences of viruses
    • Pratibha ., Associate Professor, INDIAN INSTITUTE OF TECHNOLOGY ROORKEE INDIA
    • Other Contributors:
      • Cyril Shaju, PhD Student, Dept of Earth Sciences, Indian Institute of Technology Roorkee, India
      • Kamal ., Professor, Dept of Earth Sciences, Indian Institute of Technology Roorkee, India

    In his perspective, “Rewilding immunology” (3 July 2020, DOI: 10.1126/science.abb8664), Flies et al. emphasize shifting the focus of immunological research to new models and interdisciplinary studies.
    We recently have looked at the amino acid sequences from a different angle.
    Based on the chemical properties of the side chain of an amino acid in a coding sequence of a species, we generated a sequence of N (non-polar), P (polar), A (acidic), and B (basic) like NBNNPAAABBNPNNNPABBABABAA…………… where each letter represents amino acid with one of the chemical properties listed above. Theoretically, all combinations of N,B, A, and P are possible in this sequence, what we found that in this sequence of thousands of letters, some particular order is prohibited by nature. So we looked at the other side of the coin.
    We generate chaos game representation plots for the species and look for the forbidden combinations. Here we look at the sub-sequences of a particular length (order) of N, B, A and P, which are prohibited by the species. For example, the Human Adeno Virus, we get a quadruplet BABA that is not permitted. It means that a basic side chain (B) followed by an acidic one (A) followed by a basic (B) one CANNOT be followed by an acidic (A) side chain in the protein sequence. The fourth member has to be one of the nonpolar (N), polar (P), or basic (B).
    We also analyzed SARS-CoV-2 and 20 other viruses. Although five such quadruplets are forbidden in C...

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    Competing Interests: None declared.

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