ArticleNucleic acids research2006
Molecular dynamics simulations of human tRNA Lys,3 UUU: the role of modified bases in mRNA recognition.
Article in Nucleic acids research, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed, 40 citations in OpenAlex.
- Thermophysical Properties of a tRNA Isodecoder.The journal of physical chemistry. B · 2026Article
- Structure-Based Simulations for Folding of a tRNA Isodecoder.Molecules (Basel, Switzerland) · 2026Article
- tRNA modifications in cancer: from molecular mechanisms to clinical translation.Biomarker research · 2026Review
- Accurately Modeling RNA Stem-Loops in an Implicit Solvent Environment.Journal of chemical information and modeling · 2024Article
- Adenine Methylation Enhances the Conformational Flexibility of an RNA Hairpin Tetraloop.The journal of physical chemistry. B · 2024Article
- Probing the structure of human tRNARSC advances · 2023Article
- Metabolic Analysis of Nucleosides/Bases in the Urine and Serum of Patients with Alcohol-Associated Liver Disease.Metabolites · 2022Article
- Review
- Posttranscriptional modifications at the 37th position in the anticodon stem-loop of tRNA: structural insights from MD simulations.RNA (New York, N.Y.) · 2021Article
- tRNA Biology in the Pathogenesis of Diabetes: Role of Genetic and Environmental Factors.International journal of molecular sciences · 2021Review
- Silencing of the tRNA Modification Enzyme Cdkal1 Effects Functional Insulin Synthesis in NIT-1 Cells: tRNAFrontiers in molecular biosciences · 2020Article
- Chemical and Conformational Diversity of Modified Nucleosides Affects tRNA Structure and Function.Biomolecules · 2017Review
- Structural effects of modified ribonucleotides and magnesium in transfer RNAs.Bioorganic & medicinal chemistry · 2016Article
- Additive CHARMM force field for naturally occurring modified ribonucleotides.Journal of computational chemistry · 2016Article
- From Prebiotics to Probiotics: The Evolution and Functions of tRNA Modifications.Life (Basel, Switzerland) · 2016Review
- Article
- Influence of Sequence and Covalent Modifications on Yeast tRNA Dynamics.Journal of chemical theory and computation · 2014Article
- Methylated nucleosides in tRNA and tRNA methyltransferases.Frontiers in genetics · 2014Review
- Human tRNA(Lys3)(UUU) is pre-structured by natural modifications for cognate and wobble codon binding through keto-enol tautomerism.Journal of molecular biology · 2012Article
- Identification of eukaryotic and prokaryotic methylthiotransferase for biosynthesis of 2-methylthio-N6-threonylcarbamoyladenosine in tRNA.The Journal of biological chemistry · 2010Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Accuracy in translation of the genetic code into proteins depends upon correct tRNA-mRNA recognition in the context of the ribosome. In human tRNA(Lys,3)UUU three modified bases are present in the anticodon stem-loop--2-methylthio-N6-threonylcarbamoyladenosine at position 37 (ms2t6A37), 5-methoxycarbonylmethyl-2-thiouridine at position 34 (mcm5s2U34) and pseudouridine (psi) at position 39--two of which, ms2t6A37 and mcm5s2U34, are required to achieve wild-type binding activity of wild-type human tRNA(Lys,3)UUU [C. Yarian, M. Marszalek, E. Sochacka, A. Malkiewicz, R. Guenther, A. Miskiewicz and P. F. Agris (2000) Biochemistry, 39, 13390-13395]. Molecular dynamics simulations of nine tRNA anticodon stem-loops with different combinations of nonstandard bases were performed. The wild-type simulation exhibited a canonical anticodon stair-stepped conformation. The ms2t6 modification at position 37 is required for maintenance of this structure and reduces solvent accessibility of U36. Ms2t6A37 generally hydrogen bonds across the loop and may prevent U36 from rotating into solution. A water molecule does coordinate to psi39 most of the simulation time but weakly, as most of the residence lifetimes are <40 ps.
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Registered trials
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