ArticleRNA (New York, N.Y.)2011
Nucleotide modifications and tRNA anticodon-mRNA codon interactions on the ribosome.
Article in RNA (New York, N.Y.), 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed.
- Role of RNA modifications in blood development and regeneration.Experimental hematology · 2024Review
- tRNA epitranscriptome determines pathogenicity of the opportunistic pathogenProceedings of the National Academy of Sciences of the United States of America · 2024Article
- The Association Between Mitochondrial tRNAPharmacogenomics and personalized medicine · 2024Article
- Occurrence and stability of anion-π interactions between phosphate and nucleobases in functional RNA molecules.Nucleic acids research · 2022Article
- Selection of start codon during mRNA scanning in eukaryotic translation initiation.Communications biology · 2022Article
- Twice exploration of tRNA +1 frameshifting in an elongation cycle of protein synthesis.Nucleic acids research · 2021Article
- RNA modifications as a common denominator between tRNA and mRNA.Current genetics · 2021Review
- Ablation of Mto1 in zebrafish exhibited hypertrophic cardiomyopathy manifested by mitochondrion RNA maturation deficiency.Nucleic acids research · 2021Article
- Posttranscriptional modifications at the 37th position in the anticodon stem-loop of tRNA: structural insights from MD simulations.RNA (New York, N.Y.) · 2021Article
- A deafness-associated tRNA mutation caused pleiotropic effects on the m1G37 modification, processing, stability and aminoacylation of tRNAIle and mitochondrial translation.Nucleic acids research · 2021Article
- Arabidopsis TRM5 encodes a nuclear-localised bifunctional tRNA guanine and inosine-N1-methyltransferase that is important for growth.PloS one · 2019Article
- Deletion of Mtu1 (Trmu) in zebrafish revealed the essential role of tRNA modification in mitochondrial biogenesis and hearing function.Nucleic acids research · 2018Article
- RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.Chemical reviews · 2018Review
- A hypertension-associated mitochondrial DNA mutation introduces an mThe Journal of biological chemistry · 2018Article
- Occurrence and stability of lone pair-π stacking interactions between ribose and nucleobases in functional RNAs.Nucleic acids research · 2017Article
- A close-up view of codon selection in eukaryotic initiation.RNA biology · 2017Article
- The free energy of locking a ring: Changing a deoxyribonucleoside to a locked nucleic acid.Journal of computational chemistry · 2017Article
- Biochemical Evidence for a Nuclear Modifier Allele (A10S) in TRMU (Methylaminomethyl-2-thiouridylate-methyltransferase) Related to Mitochondrial tRNA Modification in the Phenotypic Manifestation of Deafness-associated 12S rRNA Mutation.The Journal of biological chemistry · 2017Article
- A deafness-associated tRNAAsp mutation alters the m1G37 modification, aminoacylation and stability of tRNAAsp and mitochondrial function.Nucleic acids research · 2016Article
- Structural effects of modified ribonucleotides and magnesium in transfer RNAs.Bioorganic & medicinal chemistry · 2016Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We have carried out molecular dynamics simulations of the tRNA anticodon and mRNA codon, inside the ribosome, to study the effect of the common tRNA modifications cmo(5)U34 and m(6)A37. In tRNA(Val), these modifications allow all four nucleotides to be successfully read at the wobble position in a codon. Previous data suggest that entropic effects are mainly responsible for the extended reading capabilities, but detailed mechanisms have remained unknown. We have performed a wide range of simulations to elucidate the details of these mechanisms at the atomic level and quantify their effects: extensive free energy perturbation coupled with umbrella sampling, entropy calculations of tRNA (free and bound to the ribosome), and thorough structural analysis of the ribosomal decoding center. No prestructuring effect on the tRNA anticodon stem-loop from the two modifications could be observed, but we identified two mechanisms that may contribute to the expanded decoding capability by the modifications: The further reach of the cmo(5)U34 allows an alternative outer conformation to be formed for the noncognate base pairs, and the modification results in increased contacts between tRNA, mRNA, and the ribosome.
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