The dependence of the amino acid backbone conformation on the translated synonymous codon is not statistically significant.

Pablo Mier, Juan Cortés, Pau Bernadó, Javier González-Delgado, Pierre Neuvial

Journal: Proceedings of the National Academy of Sciences of the United States of America 2025;122(24):e2503264122

PMID: 40512784

Abstract

The correlation between synonymous codon usage and secondary structure in translated proteins has been widely demonstrated. This usage plays a capital role in tuning translational rates and protein folding kinetics, indirectly influencing multiple biological processes. A recent report [A. A. Rosenberg, A. Marx, A. M. Bronstein, , 2815 (2022).] suggests that the translated synonymous codon influences the [Formula: see text] dihedral angles within secondary structure elements. If true, this conclusion would have strong consequences in several scientific fields, including structural biology and protein design, where results would depend on DNA sequence rather than protein sequence. Here, we show that the original statistical methodology used in the referred study was formally incorrect. Furthermore, when using a correct approach, we demonstrate that the influence of the codon on the distribution of the dihedral angles is not statistically significant for any type of secondary structure.

Address: Université de Rennes, ENSAI, CNRS, CREST-UMR 9194, Rennes F-35000, France.; Andalusian Centre for Developmental Biology, Faculty of Experimental Sciences (Genetics Area), Universidad Pablo de Olavide, Seville 41013, Spain.; Centre de Biologie Structurale, Université de Montpellier, INSERM and CNRS, Montpellier F-34090, France.; Institut de Mathématiques de Toulouse, UMR5219, Université de Toulouse, CNRS, UPS, Toulouse Cedex 9 F-31062, France.; LAAS-CNRS, Université de Toulouse, CNRS, Toulouse F-31400, France.

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