ArticleProceedings of the National Academy of Sciences of the United States of America2005
Simulating movement of tRNA into the ribosome during decoding.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 135 papers.
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Who cites it
135 citing papers in PubMed, 282 citations in OpenAlex.
- Evolution of a core ribosomal innovation in octopus.Current biology : CB · 2026Article
- Evolution of a core ribosomal innovation in octopus.bioRxiv : the preprint server for biology · 2026Article
- An optimized contact map for GōMartini 3 enabling conformational changes in protein assemblies.Biophysical journal · 2026Article
- Human protein synthesis requires aminoacyl-tRNA pivoting during proofreading.Nature communications · 2025Article
- Supercomputing in the biological sciences: Toward Zettascale and Yottascale simulations.Current opinion in structural biology · 2024Review
- Loss of Conserved rRNA Modifications in the Peptidyl Transferase Center Leads to Diminished Protein Synthesis and Cell Growth in Budding Yeast.International journal of molecular sciences · 2024Article
- Tuning tRNAs for improved translation.Frontiers in genetics · 2024Review
- Endogenous trans-translation structure visualizes the decoding of the first tmRNA alanine codon.Frontiers in microbiology · 2024Article
- Geometric alignment of aminoacyl-tRNA relative to catalytic centers of the ribosome underpins accurate mRNA decoding.Nature communications · 2023Article
- Machines on Genes through the Computational Microscope.Journal of chemical theory and computation · 2023Review
- Computationally-guided design and selection of high performing ribosomal active site mutants.Nucleic acids research · 2022Article
- The Structural Dynamics of Translation.Annual review of biochemistry · 2022Review
- Getting to the bottom of lncRNA mechanism: structure-function relationships.Mammalian genome : official journal of the International Mammalian Genome Society · 2022Review
- Probing Interplays between Human XBP1u Translational Arrest Peptide and 80S Ribosome.Journal of chemical theory and computation · 2022Article
- Modeling the ribosome as a bipartite graph.PloS one · 2022Article
- The Peptidyl Transferase Center: a Window to the Past.Microbiology and molecular biology reviews : MMBR · 2021Article
- Article
- Elongation Factor Tu Switch I Element is a Gate for Aminoacyl-tRNA Selection.Journal of molecular biology · 2020Article
- Elongation factor-Tu can repetitively engage aminoacyl-tRNA within the ribosome during the proofreading stage of tRNA selection.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- tRNA Dissociation from EF-Tu after GTP Hydrolysis: Primary Steps and Antibiotic Inhibition.Biophysical journal · 2020Article
75 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Decoding is the key step during protein synthesis that enables information transfer from RNA to protein, a process critical for the survival of all organisms. We have used large-scale (2.64 x 10(6) atoms) all-atom simulations of the entire ribosome to understand a critical step of decoding. Although the decoding problem has been studied for more than four decades, the rate-limiting step of cognate tRNA selection has only recently been identified. This step, known as accommodation, involves the movement inside the ribosome of the aminoacyl-tRNA from the partially bound "A/T" state to the fully bound "A/A" state. Here, we show that a corridor of 20 universally conserved ribosomal RNA bases interacts with the tRNA during the accommodation movement. Surprisingly, the tRNA is impeded by the A-loop (23S helix 92), instead of enjoying a smooth transition to the A/A state. In particular, universally conserved 23S ribosomal RNA bases U2492, C2556, and C2573 act as a 3D gate, causing the acceptor stem to pause before allowing entrance into the peptidyl transferase center. Our simulations demonstrate that the flexibility of the acceptor stem of the tRNA, in addition to flexibility of the anticodon arm, is essential for tRNA selection. This study serves as a template for simulating conformational changes in large (>10(6) atoms) biological and artificial molecular machines.
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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.