ArticleBiophysical journal2005
Comparison of tRNA motions in the free and ribosomal bound structures.
Article in Biophysical journal, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed, 46 citations in OpenAlex.
- Modeling conformational transitions in DNA, RNA, and protein-nucleic acid complexes.Nucleic acids research · 2026Article
- Comparative Analysis of Structural and Dynamical Features of Ribosome Upon Association With mRNA Reveals Potential Role of Ribosomal Proteins.Frontiers in molecular biosciences · 2021Article
- RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.Chemical reviews · 2018Review
- Directional Force Originating from ATP Hydrolysis Drives the GroEL Conformational Change.Biophysical journal · 2017Article
- Protocols for Molecular Dynamics Simulations of RNA Nanostructures.Methods in molecular biology (Clifton, N.J.) · 2017Article
- Cellular Delivery of RNA Nanoparticles.ACS combinatorial science · 2016Review
- Ribosome Mechanics Informs about Mechanism.Journal of molecular biology · 2016Review
- Elastic network models for RNA: a comparative assessment with molecular dynamics and SHAPE experiments.Nucleic acids research · 2015Article
- Exploring the balance between folding and functional dynamics in proteins and RNA.International journal of molecular sciences · 2015Article
- Functional Importance of Mobile Ribosomal Proteins.BioMed research international · 2015Review
- Influence of Sequence and Covalent Modifications on Yeast tRNA Dynamics.Journal of chemical theory and computation · 2014Article
- Elastic network models capture the motions apparent within ensembles of RNA structures.RNA (New York, N.Y.) · 2014Article
- Computational and experimental characterization of RNA cubic nanoscaffolds.Methods (San Diego, Calif.) · 2014Article
- Fast fitting to low resolution density maps: elucidating large-scale motions of the ribosome.Nucleic acids research · 2014Article
- Simulating movement of tRNA through the ribosome during hybrid-state formation.The Journal of chemical physics · 2013Article
- Connecting the kinetics and energy landscape of tRNA translocation on the ribosome.PLoS computational biology · 2013Article
- A computational investigation on the connection between dynamics properties of ribosomal proteins and ribosome assembly.PLoS computational biology · 2012Article
- A-site residues move independently from P-site residues in all-atom molecular dynamics simulations of the 70S bacterial ribosome.PloS one · 2012Article
- Key intermolecular interactions in the E. coli 70S ribosome revealed by coarse-grained analysis.Journal of the American Chemical Society · 2011Article
- Changes in dynamics upon oligomerization regulate substrate binding and allostery in amino acid kinase family members.PLoS computational biology · 2011Article
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Authors and funding
2 authors at 2 institutions in 1 country.
Funding
Abstract
A general method is presented that allows the separation of the rigid body motions from the nonrigid body motions of structural subunits when bound in a complex. The application presented considers the motions of the tRNAs: free, bound to the ribosome and to a synthase. We observe that both the rigid body and nonrigid body motions of the structural subunits are highly controlled by the large ribosomal assembly and are important for the functional motions of the assembly. For the intact ribosome, its major parts, the 30S and the 50S subunits, are found to have counterrotational motions in the first few slowest modes, which are consistent with the experimentally observed ratchet motion. The tRNAs are found to have on average approximately 72-75% rigid body motions and principally translational motions within the first 100 slow modes of the complex. Although the three tRNAs exhibit different apparent total motions, after the rigid body motions are removed, the remaining internal motions of all three tRNAs are essentially the same. The direction of the translational motions of the tRNAs are in the same direction as the requisite translocation step, especially in the first slowest mode. Surprisingly the small intrinsically flexible mRNA has all of its internal motions completely inhibited and shows mainly a rigid-body translation in the slow modes of the ribosome complex. On the other hand, the required nonrigid body motions of the tRNA during translocation reveal that the anticodon-stem-loop, as well as the acceptor arm, of the tRNA enjoy a large mobility but act as rigid structural units. In summary, the ribosome exerts its control by enforcing rigidity in the functional parts of the tRNAs as well as in the mRNA.
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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.