ArticleNucleic acids research2003
Molecular dynamics simulations of RNA kissing-loop motifs reveal structural dynamics and formation of cation-binding pockets.
Article in Nucleic acids research, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed.
- Structural Prediction of Coronavirus s2m Kissing Complexes and Extended Duplexes.ACS physical chemistry Au · 2025Article
- Understanding the Thermodynamics of Magnesium Binding to RNA Structural Motifs.Life (Basel, Switzerland) · 2024Article
- Dynamics and Function of sRNA/mRNAs Under the Scrutiny of Computational Simulation Methods.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Structural and computational studies of HIV-1 RNA.RNA biology · 2024Review
- 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
- Extended molecular dynamics of a c-kit promoter quadruplex.Nucleic acids research · 2015Article
- Direct evidence for RNA-RNA interactions at the 3' end of the Hepatitis C virus genome using surface plasmon resonance.RNA (New York, N.Y.) · 2013Article
- RNA dimerization plays a role in ribosomal frameshifting of the SARS coronavirus.Nucleic acids research · 2013Article
- The role of salt concentration and magnesium binding in HIV-1 subtype-A and subtype-B kissing loop monomer structures.Journal of biomolecular structure & dynamics · 2013Article
- Interactions of cations with RNA loop-loop complexes.Biophysical journal · 2011Article
- Computational exploration of mobile ion distributions around RNA duplex.The journal of physical chemistry. B · 2010Article
- Dynamics of the base of ribosomal A-site finger revealed by molecular dynamics simulations and Cryo-EM.Nucleic acids research · 2010Article
- Theoretical studies of RNA catalysis: hybrid QM/MM methods and their comparison with MD and QM.Methods (San Diego, Calif.) · 2009Review
- Molecular dynamics simulation study of the binding of purine bases to the aptamer domain of the guanine sensing riboswitch.Nucleic acids research · 2009Article
- Molecular simulation studies of monovalent counterion-mediated interactions in a model RNA kissing loop.Journal of molecular biology · 2009Article
- Conformations of flanking bases in HIV-1 RNA DIS kissing complexes studied by molecular dynamics.Biophysical journal · 2007Article
- The conformational landscape of the ribosomal protein S15 and its influence on the protein interaction with 16S RNA.Biophysical journal · 2007Article
- Review
- Resolving fast and slow motions in the internal loop containing stem-loop 1 of HIV-1 that are modulated by Mg2+ binding: role in the kissing-duplex structural transition.Nucleic acids research · 2007Article
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5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Explicit solvent molecular dynamics (MD) simulations were carried out for three RNA kissing-loop complexes. The theoretical structure of two base pairs (2 bp) complex of H3 stem-loop of Moloney murine leukemia virus agrees with the NMR structure with modest violations of few NMR restraints comparable to violations present in the NMR structure. In contrast to the NMR structure, however, MD shows relaxed intermolecular G-C base pairs. The core region of the kissing complex forms a cation-binding pocket with highly negative electrostatic potential. The pocket shows nanosecond-scale breathing motions coupled with oscillations of the whole molecule. Additional simulations were carried out for 6 bp kissing complexes of the DIS HIV-1 subtypes A and B. The simulated structures agree well with the X-ray data. The subtype B forms a novel four-base stack of bulged-out adenines. Both 6 bp kissing complexes have extended cation-binding pockets in their central parts. While the pocket of subtype A interacts with two hexacoordinated Mg2+ ions and one sodium ion, pocket of subtype B is filled with a string of three delocalized Na+ ions with residency times of individual cations 1-2 ns. The 6 bp complexes show breathing motions of the cation-binding pockets and loop major grooves.
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