ArticleProceedings of the National Academy of Sciences of the United States of America2009
Dynamical networks in tRNA:protein complexes.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 381 papers, 1 of them a synthesis that pooled it.
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Who cites it
381 citing papers in PubMed, 1 synthesis or guideline pooled it, 822 citations in OpenAlex.
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- Network analysis of correlated conformational dynamics across the evolution of influenza A virus NS1.bioRxiv : the preprint server for biology · 2026Article
- Time-Dependent Voronoi Analysis of Amino Acid Side-Chain Packing in Simulations.Journal of computational chemistry · 2026Article
- Deciphering the allosteric landscape of 5-HTPharmacological reports : PR · 2026Article
- A dynamically frustrated allosteric checkpoint consistent with conformational proofreading in CRISPR-Cas9.Nucleic acids research · 2026Article
- Integrating NMR and contact-response analysis reveals the allosteric network driving domain closure in Enzyme I.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Effects of a cancer-associated mutation and multiple serine phosphorylation on poly(ADP-ribose) polymerase 2.Biophysical journal · 2026Article
- Residue Interaction Network Reveals Allosteric Pathways Linking Orthosteric and Intracellular Sites in Class A GPCRs.Journal of chemical information and modeling · 2026Article
- Article
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- A pore-facing glycan constrains GABACommunications biology · 2026Article
- Directional information flow as a tool for analyzing protein allostery.bioRxiv : the preprint server for biology · 2026Article
- Molecular mechanisms of native ligand selectivity in catecholamine G protein-coupled receptors.Nature communications · 2026Article
- Mapping Allosteric Communication in the Nucleosome with Conditional Activity.Journal of chemical information and modeling · 2026Article
- Mechanism of Hsp70 activation: How J-domain proteins push for ATP hydrolysis.PLoS computational biology · 2026Article
- Coupling high-throughput protease enzymology with viral replication reveals biochemical constraints of viral fitness.bioRxiv : the preprint server for biology · 2026Article
- Framework for Quantifying the Efficiency of Competing Signal Transmission Modes in Proteins.Journal of the American Chemical Society · 2026Article
- The Allosteric Regulation of the DNA-Binding Domain of p53 by the Intrinsically Disordered C-Terminal Domain.Pharmaceuticals (Basel, Switzerland) · 2026Article
- Allosteric Activation through Coordinated Energy Landscape Reweighting and Information Flow.Computational and structural biotechnology journal · 2026Article
321 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Community network analysis derived from molecular dynamics simulations is used to identify and compare the signaling pathways in a bacterial glutamyl-tRNA synthetase (GluRS):tRNA(Glu) and an archaeal leucyl-tRNA synthetase (LeuRS):tRNA(Leu) complex. Although the 2 class I synthetases have remarkably different interactions with their cognate tRNAs, the allosteric networks for charging tRNA with the correct amino acid display considerable similarities. A dynamic contact map defines the edges connecting nodes (amino acids and nucleotides) in the physical network whose overall topology is presented as a network of communities, local substructures that are highly intraconnected, but loosely interconnected. Whereas nodes within a single community can communicate through many alternate pathways, the communication between monomers in different communities has to take place through a smaller number of critical edges or interactions. Consistent with this analysis, there are a large number of suboptimal paths that can be used for communication between the identity elements on the tRNAs and the catalytic site in the aaRS:tRNA complexes. Residues and nucleotides in the majority of pathways for intercommunity signal transmission are evolutionarily conserved and are predicted to be important for allosteric signaling. The same monomers are also found in a majority of the suboptimal paths. Modifying these residues or nucleotides has a large effect on the communication pathways in the protein:RNA complex consistent with kinetic data.
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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.