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Codon information value and codon transition-probability distributions in short-term evolution

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  • Jiménez-Montaño, M.A.
  • Coronel-Brizio, H.F.
  • Hernández-Montoya, A.R.
  • Ramos-Fernández, A.

Abstract

To understand the way the Genetic Code and the physical–chemical properties of coded amino acids affect accepted amino acid substitutions in short-term protein evolution, taking into account only overall amino acid conservation, we consider an underlying codon-level model. This model employs codon pair-substitution frequencies from an empirical matrix in the literature, modified for single-base mutations only. Ordering the degenerated codons according to their codon information value (Volkenstein, 1979), we found that three-fold and most of four-fold degenerated codons, which have low codon values, were best fitted to rank-frequency distributions with constant failure rate (exponentials). In contrast, almost all two-fold degenerated codons, which have high codon values, were best fitted to rank-frequency distributions with variable failure rate (inverse power-laws). Six-fold degenerated codons are considered to be doubly assigned. The exceptional behavior of some codons, including non-degenerate codons, is discussed.

Suggested Citation

  • Jiménez-Montaño, M.A. & Coronel-Brizio, H.F. & Hernández-Montoya, A.R. & Ramos-Fernández, A., 2016. "Codon information value and codon transition-probability distributions in short-term evolution," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 454(C), pages 117-128.
    • Handle: RePEc:eee:phsmap:v:454:y:2016:i:c:p:117-128
    DOI: 10.1016/j.physa.2016.02.043
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    References listed on IDEAS

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    1. Kim, J.K. & Yang, S.I. & Kwon, Y.H. & Lee, E.I., 2005. "Codon and amino-acid distribution in DNA," Chaos, Solitons & Fractals, Elsevier, vol. 23(5), pages 1795-1807.
    2. Anthony D. Keefe & Jack W. Szostak, 2001. "Functional proteins from a random-sequence library," Nature, Nature, vol. 410(6829), pages 715-718, April.
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