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

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

Physica A: Statistical Mechanics and its Applications, 2016, vol. 454, issue C, 117-128

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.

Keywords: Codon; Value of information; Fitting; Power law; Exponential; Reduced empirical matrix (search for similar items in EconPapers)
Date: 2016
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Persistent link: https://EconPapers.repec.org/RePEc:eee:phsmap:v:454:y:2016:i:c:p:117-128

DOI: 10.1016/j.physa.2016.02.043

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