ArticleNucleic acids research2010
Synonymous codon usage influences the local protein structure observed.
Article in Nucleic acids research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 71 papers, 1 of them a synthesis that pooled it.
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Who cites it
71 citing papers in PubMed, 1 synthesis or guideline pooled it, 174 citations in OpenAlex.
- Synonymous but Not Silent: The Codon Usage Code for Gene Expression and Protein Folding.Annual review of biochemistry · 2021Pooled it
- Codon Usage Pattern and its Influencing Factors for Mitochondrial CO Genes Among Different Subfamilies of Cerambycidae.Biochemical genetics · 2025Article
- NSUN2-tRNACellular & molecular biology letters · 2025Article
- The dependence of the amino acid backbone conformation on the translated synonymous codon is not statistically significant.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- The effectiveness of selection in a species affects the direction of amino acid frequency evolution.bioRxiv : the preprint server for biology · 2025Article
- AAV vector development, back to the future.Molecular therapy : the journal of the American Society of Gene Therapy · 2025Review
- DNA Sequence Changes Resulting from Codon Optimization Affect Gene Expression inJournal of fungi (Basel, Switzerland) · 2025Article
- Predicting gene sequences with AI to study codon usage patterns.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Are genomic language models all you need? Exploring genomic language models on protein downstream tasks.Bioinformatics (Oxford, England) · 2024Article
- Translation Rates and Protein Folding.Journal of molecular biology · 2024Review
- Re-examining Correlations Between Synonymous Codon Usage and Protein Bond Angles in Escherichia coli.Genome biology and evolution · 2024Article
- Specific codons control cellular resources and fitness.Science advances · 2024Article
- Machine Learning-Guided Protein Engineering.ACS catalysis · 2023Review
- Article
- Analysis of codon usage bias of WRKY transcription factors in Helianthus annuus.BMC genomic data · 2022Article
- Quantifying shifts in natural selection on codon usage between protein regions: a population genetics approach.BMC genomics · 2022Article
- Codon-specific Ramachandran plots show amino acid backbone conformation depends on identity of the translated codon.Nature communications · 2022Article
- Evolutionary dynamics of codon usages for peste des petits ruminants virus.Frontiers in veterinary science · 2022Article
- A synonymous mutation inMolecular therapy. Nucleic acids · 2021Article
- Identification of conserved slow codons that are important for protein expression and function.RNA biology · 2021Article
11 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Translation of mRNA into protein is a unidirectional information flow process. Analysing the input (mRNA) and output (protein) of translation, we find that local protein structure information is encoded in the mRNA nucleotide sequence. The Coding Sequence and Structure (CSandS) database developed in this work provides a detailed mapping between over 4000 solved protein structures and their mRNA. CSandS facilitates a comprehensive analysis of codon usage over many organisms. In assigning translation speed, we find that relative codon usage is less informative than tRNA concentration. For all speed measures, no evidence was found that domain boundaries are enriched with slow codons. In fact, genes seemingly avoid slow codons around structurally defined domain boundaries. Translation speed, however, does decrease at the transition into secondary structure. Codons are identified that have structural preferences significantly different from the amino acid they encode. However, each organism has its own set of 'significant codons'. Our results support the premise that codons encode more information than merely amino acids and give insight into the role of translation in protein folding.
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