ArticleNature chemistry2023
Atomistic simulations of the Escherichia coli ribosome provide selection criteria for translationally active substrates.
Article in Nature chemistry, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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28 citing papers in PubMed.
- EF-P inhibits ribosomal α-hydroxy acid incorporation: strategic tRNA body selection for co-incorporating α-hydroxy acids and nonproteinogenic amino acids into depsipeptides.RNA (New York, N.Y.) · 2026Article
- 23S rRNA modifications stimulate catalytic activity and prevent the formation of alternative structures.Nucleic acids research · 2026Article
- Multiscale Modeling of the Bacterial Ribosome to Identify Potential Peptide Modulators and Their Allosteric Effects.Biochemistry · 2026Article
- A family of archaeal hibernation factors that bind in tandem and protect ribosomes in dormant cells.Nature communications · 2026Article
- Enhancing ribosomal translation of backbone-altering nonproteinogenic amino acids via YebC and YeeN.Nucleic acids research · 2026Article
- Ribosomal allostery as a potential regulator of bacterial dormancy.Nature communications · 2026Article
- Co-Translational Incorporation ofJournal of the American Chemical Society · 2026Article
- Co-Translational Incorporation of (Journal of the American Chemical Society · 2026Article
- Article
- Optimization of the genetic code expansion technology for intracellular labelling and single-molecule tracking of proteins in genomically re-codedRSC chemical biology · 2026Article
- A family of archaeal hibernation factors that bind in tandem and protect ribosomes in dormant cells.bioRxiv : the preprint server for biology · 2026Article
- Discovery of benzyl carbamate inhibitors of coronavirus MJournal of enzyme inhibition and medicinal chemistry · 2025Article
- Structural insights into context-specific inhibition of bacterial translation by macrolides.Nature communications · 2025Article
- Site-selective protein editing by backbone extension acyl rearrangements.Nature chemical biology · 2025Article
- Structure of an archaeal ribosome reveals a divergent active site and hibernation factor.Nature microbiology · 2025Article
- Mechanism of release factor-mediated peptidyl-tRNA hydrolysis on the ribosome.Science (New York, N.Y.) · 2025Article
- Direct and quantitative analysis of tRNA acylation using intact tRNA liquid chromatography-mass spectrometry.Nature protocols · 2025Review
- Monitoring monomer-specific acyl-tRNA levels in cells with PARTI.Nucleic acids research · 2025Article
- Principles of ion binding to RNA inferred from the analysis of a 1.55 Å resolution bacterial ribosome structure - Part I: Mg2.Nucleic acids research · 2025Article
- β-Amino Acids Reduce Ternary Complex Stability and Alter the Translation Elongation Mechanism.ACS central science · 2024Article
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7 authors.
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Abstract
As genetic code expansion advances beyond L-α-amino acids to backbone modifications and new polymerization chemistries, delineating what substrates the ribosome can accommodate remains a challenge. The Escherichia coli ribosome tolerates non-L-α-amino acids in vitro, but few structural insights that explain how are available, and the boundary conditions for efficient bond formation are so far unknown. Here we determine a high-resolution cryogenic electron microscopy structure of the E. coli ribosome containing α-amino acid monomers and use metadynamics simulations to define energy surface minima and understand incorporation efficiencies. Reactive monomers across diverse structural classes favour a conformational space where the aminoacyl-tRNA nucleophile is <4 Å from the peptidyl-tRNA carbonyl with a Bürgi-Dunitz angle of 76-115°. Monomers with free energy minima that fall outside this conformational space do not react efficiently. This insight should accelerate the in vivo and in vitro ribosomal synthesis of sequence-defined, non-peptide heterooligomers.
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