ArticleJournal of molecular biology2008
Dynamics of Recognition between tRNA and elongation factor Tu.
Article in Journal of molecular biology, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
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Who cites it
44 citing papers in PubMed, 83 citations in OpenAlex.
- Transient ion-mediated interactions regulate subunit rotation in a eukaryotic ribosome.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Transient ion-mediated interactions regulate subunit rotation in a eukaryotic ribosome.bioRxiv : the preprint server for biology · 2025Article
- Direct RNA sequencing of the Escherichia coli epitranscriptome uncovers alterations under heat stress.Nucleic acids research · 2025Article
- Systematic analysis of the relationship between fold-dependent flexibility and artificial intelligence protein structure prediction.PloS one · 2024Article
- Tuning tRNAs for improved translation.Frontiers in genetics · 2024Review
- tRNA engineering strategies for genetic code expansion.Frontiers in genetics · 2024Review
- Customized synthesis of phosphoprotein bearing phosphoserine or its nonhydrolyzable analog.Synthetic and systems biotechnology · 2023Article
- Expansion of the genetic code through reassignment of redundant sense codons using fully modified tRNA.Nucleic acids research · 2022Article
- Early divergence of translation initiation and elongation factors.Protein science : a publication of the Protein Society · 2022Article
- Sulfur Availability Impacts Accumulation of the 2-Thiouridine tRNA Modification in Bacillus subtilis.Journal of bacteriology · 2022Article
- Review
- On the Track of the Missing tRNA Genes: A Source of Non-Canonical Functions?Frontiers in molecular biosciences · 2021Review
- Review
- Elongation Factor Tu Switch I Element is a Gate for Aminoacyl-tRNA Selection.Journal of molecular biology · 2020Article
- Strategies for in vitro engineering of the translation machinery.Nucleic acids research · 2020Review
- Role of Electrostatics in Protein-RNA Binding: The Global vs the Local Energy Landscape.The journal of physical chemistry. B · 2017Article
- Rationally evolving tRNAPyl for efficient incorporation of noncanonical amino acids.Nucleic acids research · 2015Article
- Efficient genetic encoding of phosphoserine and its nonhydrolyzable analog.Nature chemical biology · 2015Article
- Uncovering the thermodynamics of monomer binding for RNA replication.Journal of the American Chemical Society · 2015Article
- Structural Insights into tRNA Dynamics on the Ribosome.International journal of molecular sciences · 2015Review
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
Elongation factor Tu (EF-Tu) binds to all standard aminoacyl transfer RNAs (aa-tRNAs) and transports them to the ribosome while protecting the ester linkage between the tRNA and its cognate amino acid. We use molecular dynamics simulations to investigate the dynamics of the EF-Tu.guanosine 5'-triphosphate.aa-tRNA(Cys) complex and the roles played by Mg2+ ions and modified nucleosides on the free energy of protein.RNA binding. Individual modified nucleosides have pronounced effects on the structural dynamics of tRNA and the EF-Tu.Cys-tRNA(Cys) interface. Combined energetic and evolutionary analyses identify the coevolution of residues in EF-Tu and aa-tRNAs at the binding interface. Highly conserved EF-Tu residues are responsible for both attracting aa-tRNAs as well as providing nearby nonbonded repulsive energies that help fine-tune molecular attraction at the binding interface. In addition to the 3' CCA end, highly conserved tRNA nucleotides G1, G52, G53, and U54 contribute significantly to EF-Tu binding energies. Modification of U54 to thymine affects the structure of the tRNA common loop resulting in a change in binding interface contacts. In addition, other nucleotides, conserved within certain tRNA specificities, may be responsible for tuning aa-tRNA binding to EF-Tu. The trend in EF-Tu.Cys-tRNA(Cys) binding energies observed as the result of mutating the tRNA agrees with experimental observation. We also predict variations in binding free energies upon misacylation of tRNA(Cys) with d-cysteine or O-phosphoserine and upon changing the protonation state of l-cysteine. Principal components analysis in each case reveals changes in the communication network across the protein.tRNA interface and is the basis for the entropy calculations.
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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.