ArticleBiophysical journal2003
Non-Watson-Crick basepairing and hydration in RNA motifs: molecular dynamics of 5S rRNA loop E.
Article in Biophysical journal, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 49 papers.
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Who cites it
49 citing papers in PubMed.
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- Dynamics and Function of sRNA/mRNAs Under the Scrutiny of Computational Simulation Methods.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Translation Fidelity and Respiration Deficits in CLPP-Deficient Tissues: Mechanistic Insights from Mitochondrial Complexome Profiling.International journal of molecular sciences · 2023Article
- Sensitivity of the RNA Structure to Ion Conditions as Probed by Molecular Dynamics Simulations of Common Canonical RNA Duplexes.Journal of chemical information and modeling · 2023Article
- RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.Chemical reviews · 2018Review
- Ligand-mediated and tertiary interactions cooperatively stabilize the P1 region in the guanine-sensing riboswitch.PloS one · 2017Article
- G4IPDB: A database for G-quadruplex structure forming nucleic acid interacting proteins.Scientific reports · 2016Article
- The RNA 3D Motif Atlas: Computational methods for extraction, organization and evaluation of RNA motifs.Methods (San Diego, Calif.) · 2016Review
- Extended molecular dynamics of a c-kit promoter quadruplex.Nucleic acids research · 2015Article
- Stacking in RNA: NMR of Four Tetramers Benchmark Molecular Dynamics.Journal of chemical theory and computation · 2015Article
- Isosteric and nonisosteric base pairs in RNA motifs: molecular dynamics and bioinformatics study of the sarcin-ricin internal loop.The journal of physical chemistry. B · 2013Article
- Molecular mechanism of preQ1 riboswitch action: a molecular dynamics study.The journal of physical chemistry. B · 2012Article
- Molecular dynamics re-refinement of two different small RNA loop structures using the original NMR data suggest a common structure.Journal of biomolecular NMR · 2012Article
- Molecular dynamics simulations of G-DNA and perspectives on the simulation of nucleic acid structures.Methods (San Diego, Calif.) · 2012Review
- Examinations of tRNA Range of Motion Using Simulations of Cryo-EM Microscopy and X-Ray Data.Journal of biophysics (Hindawi Publishing Corporation : Online) · 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
- Molecular dynamics simulations suggest that RNA three-way junctions can act as flexible RNA structural elements in the ribosome.Nucleic acids research · 2010Article
- Thermodynamics of RNA melting, one base pair at a time.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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7 authors.
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Abstract
Explicit solvent and counterion molecular dynamics simulations have been carried out for a total of >80 ns on the bacterial and spinach chloroplast 5S rRNA Loop E motifs. The Loop E sequences form unique duplex architectures composed of seven consecutive non-Watson-Crick basepairs. The starting structure of spinach chloroplast Loop E was modeled using isostericity principles, and the simulations refined the geometries of the three non-Watson-Crick basepairs that differ from the consensus bacterial sequence. The deep groove of Loop E motifs provides unique sites for cation binding. Binding of Mg(2+) rigidifies Loop E and stabilizes its major groove at an intermediate width. In the absence of Mg(2+), the Loop E motifs show an unprecedented degree of inner-shell binding of monovalent cations that, in contrast to Mg(2+), penetrate into the most negative regions inside the deep groove. The spinach chloroplast Loop E shows a marked tendency to compress its deep groove compared with the bacterial consensus. Structures with a narrow deep groove essentially collapse around a string of Na(+) cations with long coordination times. The Loop E non-Watson-Crick basepairing is complemented by highly specific hydration sites ranging from water bridges to hydration pockets hosting 2 to 3 long-residing waters. The ordered hydration is intimately connected with RNA local conformational variations.
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