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

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, <i>Nat. Commun.</i> <b>13</b>, 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.

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Publication Details

Journal
Proceedings of the National Academy of Sciences
Published
2025-06-13
DOI
https://doi.org/10.1073/pnas.2503264122
Primary Topic
RNA and protein synthesis mechanisms
Type
article
Field-Weighted Citation Impact
0.00

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article

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

Pau Bernadó, Javier González-Delgado, Pierre Neuvial, Juan Cortés et al.
Proceedings of the National Academy of Sciences
RNA and protein synthesis mechanisms
article

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

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

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, <i>Nat. Commun.</i> <b>13</b>, 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.

Proceedings of the National Academy of SciencesVol. 122(24)
Centre National de la Recherche Scientifique (FR), Inserm (FR), Université Fédérale de Toulouse Midi-Pyrénées (FR), Université de Montpellier (FR), École Nationale de la Statistique et de l'Analyse de l'Information (FR), Centre for Research in Engineering Surface Technology (IE), Centro Andaluz de Biología del Desarrollo (ES), Centre de Recherche en Économie et Statistique (FR), Université de Rennes (FR), Institut de Mathématiques de Toulouse (FR), Universidad Pablo de Olavide (ES)
Agence Nationale de la Recherche
Openalex Percentile: Top 88%
RNA and protein synthesis mechanisms
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