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We began analyzing https://www.nature.com/articles/nsmb.2466, but it redirected us to https://www.nature.com/articles/nsmb.2466. The analysis below is for the second page.

Title[redir]:
Evolutionary conservation of codon optimality reveals hidden signatures of cotranslational folding | Nature Structural & Molecular Biology
Description:
Rare or nonoptimal codons that cause ribosomes to pause have been suggested to be important determinants of cotranslational folding. A revised translational efficiency scale, which considers tRNA abundance as well as codon usage and codon-tRNA interaction, now suggests a correlation between optimal or nonoptimal codon usage and secondary structure of the nascent polypeptide. The choice of codons can influence local translation kinetics during protein synthesis. Whether codon preference is linked to cotranslational regulation of polypeptide folding remains unclear. Here, we derive a revised translational efficiency scale that incorporates the competition between tRNA supply and demand. Applying this scale to ten closely related yeast species, we uncover the evolutionary conservation of codon optimality in eukaryotes. This analysis reveals universal patterns of conserved optimal and nonoptimal codons, often in clusters, which associate with the secondary structure of the translated polypeptides independent of the levels of expression. Our analysis suggests an evolved function for codon optimality in regulating the rhythm of elongation to facilitate cotranslational polypeptide folding, beyond its previously proposed role of adapting to the cost of expression. These findings establish how mRNA sequences are generally under selection to optimize the cotranslational folding of corresponding polypeptides.

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article, google, scholar, cas, nature, protein, codon, folding, biol, access, mol, cotranslational, translation, ribosome, cell, translational, struct, content, usage, sci, nat, res, usa, cookies, data, frydman, efficiency, structure, gene, nucleic, acids, privacy, analysis, molecular, biology, evolutionary, optimality, open, synonymous, proteins, tunnel, proc, natl, acad, information, structural, pechmann, judith, codons, local,

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nature portfolio permissions reprints designed research privacy policy advertising nature 475 nature 449 nature social media author information authors position-specific gap penalties position-specific scoring matrices pathogenic exon-skipping variants coding sequence–dependent degradation author correspondence mistranslation-induced protein misfolding springerlink instant access ribosome-mediated translational pause personal data permissions protein domain organization data protection article pechmann judith frydman gratefully acknowledge support translational protein folding privacy european economic area genome-wide analysis synonymous codon usage pdb related databases data competing financial interests codon usage preferences nascent polypeptide folding unwind messenger rna coding-sequence evolution translational folding intermediates translational folding pathway explore content subscription content molecular bases ribosome exit port ribosomal exit tunnel transfer rna genes ribosome exit tunnel issue learn institutional subscriptions read β-sheet signals structurally sensitive sites

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