ArticleNature communications2022
Codon-specific Ramachandran plots show amino acid backbone conformation depends on identity of the translated codon.
Article in Nature communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
18 citing papers in PubMed, 45 citations in OpenAlex.
- Synonymous Gene Recoding Affects the Accuracy of Protein Quantification Measurements.The AAPS journal · 2026Article
- Synonymous mutations in essential genes infrequently produce fitness effects in human cell lines.Nucleic acids research · 2026Article
- mRNA Cancer Vaccines: From Pandemic Paradigm to Personalized Oncology Therapeutics.Cancer innovation · 2025Review
- Detecting Interspecific Positive Selection Using Convolutional Neural Networks.Molecular biology and evolution · 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
- Identification of clade-defining single nucleotide polymorphisms for improved rabies virus surveillance.New microbes and new infections · 2024Article
- A dataset of alternately located segments in protein crystal structures.Scientific data · 2024Article
- Translation Rates and Protein Folding.Journal of molecular biology · 2024Review
- Variability in SOD1-associated amyotrophic lateral sclerosis: geographic patterns, clinical heterogeneity, molecular alterations, and therapeutic implications.Translational neurodegeneration · 2024Review
- Re-examining Correlations Between Synonymous Codon Usage and Protein Bond Angles in Escherichia coli.Genome biology and evolution · 2024Article
- Mechanisms and pathology of protein misfolding and aggregation.Nature reviews. Molecular cell biology · 2023Review
- Machine Learning-Guided Protein Engineering.ACS catalysis · 2023Review
- An amino-domino model described by a cross-peptide-bond Ramachandran plot defines amino acid pairs as local structural units.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Machine learning classifiers predict key genomic and evolutionary traits across the kingdoms of life.Scientific reports · 2023Article
- Clinical and Therapeutic Evaluation of the Ten Most PrevalentBiomedicines · 2023Article
- Augmenting tomato functional genomics with a genome-wide induced genetic variation resource.Frontiers in plant science · 2023Article
- Local Backbone Geometry Plays a Critical Role in Determining Conformational Preferences of Amino Acid Residues in Proteins.Biomolecules · 2022Article
- Non-Equilibrium Protein Folding and Activation by ATP-Driven Chaperones.Biomolecules · 2022Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Synonymous codons translate into chemically identical amino acids. Once considered inconsequential to the formation of the protein product, there is evidence to suggest that codon usage affects co-translational protein folding and the final structure of the expressed protein. Here we develop a method for computing and comparing codon-specific Ramachandran plots and demonstrate that the backbone dihedral angle distributions of some synonymous codons are distinguishable with statistical significance for some secondary structures. This shows that there exists a dependence between codon identity and backbone torsion of the translated amino acid. Although these findings cannot pinpoint the causal direction of this dependence, we discuss the vast biological implications should coding be shown to directly shape protein conformation and demonstrate the usefulness of this method as a tool for probing associations between codon usage and protein structure. Finally, we urge for the inclusion of exact genetic information into structural databases.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.