ArticleBiophysical journal2004
Long-residency hydration, cation binding, and dynamics of loop E/helix IV rRNA-L25 protein complex.
Article in Biophysical journal, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Deciphering hydration patterns across RNA conformations: Insights into water-mediated RNA recognition.Current research in structural biology · 2026Article
- Delta SARS-CoV-2 s2m Structure, Dynamics, and Entropy: Consequences of the G15U Mutation.ACS physical chemistry Au · 2023Article
- Structural, Dynamical, and Entropic Differences between SARS-CoV and SARS-CoV-2 s2m Elements Using Molecular Dynamics Simulations.ACS physical chemistry Au · 2023Article
- Role of salt-bridging interactions in recognition of viral RNA by arginine-rich peptides.Biophysical journal · 2021Article
- RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.Chemical reviews · 2018Review
- Structural study of the Fox-1 RRM protein hydration reveals a role for key water molecules in RRM-RNA recognition.Nucleic acids research · 2017Article
- The RNA 3D Motif Atlas: Computational methods for extraction, organization and evaluation of RNA motifs.Methods (San Diego, Calif.) · 2016Review
- Higher order structural effects stabilizing the reverse Watson-Crick Guanine-Cytosine base pair in functional RNAs.Nucleic acids research · 2014Article
- Article
- Dynamics of the base of ribosomal A-site finger revealed by molecular dynamics simulations and Cryo-EM.Nucleic acids research · 2010Article
- Molecular dynamics simulations of nucleic acid-protein complexes.Current opinion in structural biology · 2008Review
- The conformational landscape of the ribosomal protein S15 and its influence on the protein interaction with 16S RNA.Biophysical journal · 2007Article
- Review
- Elastic properties of ribosomal RNA building blocks: molecular dynamics of the GTPase-associated center rRNA.Nucleic acids research · 2007Article
- Trapped water molecules are essential to structural dynamics and function of a ribozyme.Proceedings of the National Academy of Sciences of the United States of America · 2006Article
- Cations and hydration in catalytic RNA: molecular dynamics of the hepatitis delta virus ribozyme.Biophysical journal · 2006Article
- Molecular dynamics simulations of sarcin-ricin rRNA motif.Nucleic acids research · 2006Article
- Solution probing of metal ion binding by helix 27 from Escherichia coli 16S rRNA.RNA (New York, N.Y.) · 2005Article
- Hinge-like motions in RNA kink-turns: the role of the second a-minor motif and nominally unpaired bases.Biophysical journal · 2005Article
- The snRNP 15.5K protein folds its cognate K-turn RNA: a combined theoretical and biochemical study.RNA (New York, N.Y.) · 2005Article
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5 authors.
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Abstract
Molecular dynamics simulations of RNA-protein complex between Escherichia coli loop E/helix IV (LE/HeIV) rRNA and L25 protein reveal a qualitative agreement between the experimental and simulated structures. The major groove of LE is a prominent rRNA cation-binding site. Divalent cations rigidify the LE major groove geometry whereas in the absence of divalent cations LE extensively interacts with monovalent cations via inner-shell binding. The HeIV region shows bistability of its major groove explaining the observed differences between x-ray and NMR structures. In agreement with the experiments, the simulations suggest that helix-alpha1 of L25 is the least stable part of the protein. Inclusion of Mg2+ cations into the simulations causes perturbation of basepairing at the LE/HeIV junction, which does not, however, affect the protein binding. The rRNA-protein complex is mediated by a number of highly specific hydration sites with long-residing water molecules and two of them are bound throughout the entire 24-ns simulation. Long-residing water molecules are seen also outside the RNA-protein contact areas with water-binding times substantially enhanced compared to simulations of free RNA. Long-residency hydration sites thus represent important elements of the three-dimensional structure of rRNA.
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