ArticleBiophysical journal2005
Hinge-like motions in RNA kink-turns: the role of the second a-minor motif and nominally unpaired bases.
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 41 papers.
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Who cites it
41 citing papers in PubMed, 95 citations in OpenAlex.
- The Kink-Turn 7 Motif: An Additional Test for RNA Force Field Performance.Journal of chemical theory and computation · 2025Article
- Effects of Molecular Crowding on the Structure, Folding, Stability, and Catalysis of RNA.Sub-cellular biochemistry · 2025Review
- Dynamics and Function of sRNA/mRNAs Under the Scrutiny of Computational Simulation Methods.Methods in molecular biology (Clifton, N.J.) · 2024Article
- RNA kink-turns are highly anisotropic with respect to lateral displacement of the flanking stems.Biophysical journal · 2022Article
- Simulation Study of the Plasticity of k-Turn Motif in Different Environments.Biophysical journal · 2020Article
- RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.Chemical reviews · 2018Review
- The RNA 3D Motif Atlas: Computational methods for extraction, organization and evaluation of RNA motifs.Methods (San Diego, Calif.) · 2016Review
- Major centers of motion in the large ribosomal RNAs.Nucleic acids research · 2015Article
- New molecular engineering approaches for crystallographic studies of large RNAs.Current opinion in structural biology · 2014Review
- Candidate RNA structures for domain 3 of the foot-and-mouth-disease virus internal ribosome entry site.Nucleic acids research · 2013Article
- Structure and mechanical properties of the ribosomal L1 stalk three-way junction.Nucleic acids research · 2012Article
- Molecular dynamics simulations of G-DNA and perspectives on the simulation of nucleic acid structures.Methods (San Diego, Calif.) · 2012Review
- Molecular Mechanics Investigation of an Adenine-Adenine Non-Canonical Pair Conformational Change.Journal of chemical theory and computation · 2011Article
- Spatial code recognition in neuronal RNA targeting: role of RNA-hnRNP A2 interactions.The Journal of cell biology · 2011Article
- Interactions of cations with RNA loop-loop complexes.Biophysical journal · 2011Article
- Quantum chemical studies of nucleic acids: can we construct a bridge to the RNA structural biology and bioinformatics communities?The journal of physical chemistry. B · 2010Article
- Structure of the K-turn U4 RNA: a combined NMR and SANS study.Nucleic acids research · 2010Article
- Molecular dynamics simulations suggest that RNA three-way junctions can act as flexible RNA structural elements in the ribosome.Nucleic acids research · 2010Article
- A structural database for k-turn motifs in RNA.RNA (New York, N.Y.) · 2010Article
- Protonation states of the key active site residues and structural dynamics of the glmS riboswitch as revealed by molecular dynamics.The journal of physical chemistry. B · 2010Article
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Authors and funding
4 authors at 3 institutions in 2 countries.
Funding
Abstract
Kink-turn (K-turn) motifs are asymmetric internal loops found at conserved positions in diverse RNAs, with sharp bends in phosphodiester backbones producing V-shaped structures. Explicit-solvent molecular dynamics simulations were carried out for three K-turns from 23S rRNA, i.e., Kt-38 located at the base of the A-site finger, Kt-42 located at the base of the L7/L12 stalk, and Kt-58 located in domain III, and for the K-turn of human U4 snRNA. The simulations reveal hinge-like K-turn motions on the nanosecond timescale. The first conserved A-minor interaction between the K-turn stems is entirely stable in all simulations. The angle between the helical arms of Kt-38 and Kt-42 is regulated by local variations of the second A-minor (type I) interaction between the stems. Its variability ranges from closed geometries to open ones stabilized by insertion of long-residency waters between adenine and cytosine. The simulated A-minor geometries fully agree with x-ray data. Kt-58 and Kt-U4 exhibit similar elbow-like motions caused by conformational change of the adenosine from the nominally unpaired region. Despite the observed substantial dynamics of K-turns, key tertiary interactions are stable and no sign of unfolding is seen. We suggest that some K-turns are flexible elements mediating large-scale ribosomal motions during the protein synthesis cycle.
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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.