ArticleBiophysical journal2007
iRED analysis of TAR RNA reveals motional coupling, long-range correlations, and a dynamical hinge.
Article in Biophysical journal, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Identifying small-molecules binding sites in RNA conformational ensembles with SHAMAN.Nature communications · 2024Article
- Exposing Hidden High-Affinity RNA Conformational States.Journal of the American Chemical Society · 2020Article
- Insights into the mechanisms of RNA secondary structure destabilization by the HIV-1 nucleocapsid protein.RNA (New York, N.Y.) · 2016Article
- Rapid Exchange Between Free and Bound States in RNA-Dendrimer Polyplexes: Implications on the Mechanism of Delivery and Release.Biomacromolecules · 2016Article
- NMR studies of nucleic acid dynamics.Journal of magnetic resonance (San Diego, Calif. : 1997) · 2013Article
- MD simulations of the dsRBP DGCR8 reveal correlated motions that may aid pri-miRNA binding.Biophysical journal · 2010Article
- Referencing strategy for the direct comparison of nuclear magnetic resonance and molecular dynamics motional parameters in RNA.The journal of physical chemistry. B · 2010Article
- Domain-elongation NMR spectroscopy yields new insights into RNA dynamics and adaptive recognition.RNA (New York, N.Y.) · 2009Review
- Constructing atomic-resolution RNA structural ensembles using MD and motionally decoupled NMR RDCs.Methods (San Diego, Calif.) · 2009Article
- Preparation, resonance assignment, and preliminary dynamics characterization of residue specific 13C/15N-labeled elongated DNA for the study of sequence-directed dynamics by NMR.Journal of biomolecular NMR · 2009Article
- Constructing RNA dynamical ensembles by combining MD and motionally decoupled NMR RDCs: new insights into RNA dynamics and adaptive ligand recognition.Nucleic acids research · 2009Article
- Approximate reconstruction of continuous spatially complex domain motions by multialignment NMR residual dipolar couplings.The journal of physical chemistry. B · 2009Article
- Molecular dynamics suggest multifunctionality of an adenine imino group in acid-base catalysis of the hairpin ribozyme.RNA (New York, N.Y.) · 2009Article
- How binding of small molecule and peptide ligands to HIV-1 TAR alters the RNA motional landscape.Nucleic acids research · 2009Article
- Ultrahigh resolution characterization of domain motions and correlations by multialignment and multireference residual dipolar coupling NMR.The journal of physical chemistry. B · 2008Article
- Thermodynamic examination of trinucleotide bulged RNA in the context of HIV-1 TAR RNA.RNA (New York, N.Y.) · 2008Article
- RNA in motion.Current opinion in chemical biology · 2008Review
- Characterizing complex dynamics in the transactivation response element apical loop and motional correlations with the bulge by NMR, molecular dynamics, and mutagenesis.Biophysical journal · 2008Article
- Pressure effects on the ensemble dynamics of ubiquitin inspected with molecular dynamics simulations and isotropic reorientational eigenmode dynamics.Biophysical journal · 2008Article
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3 authors.
Funding
Abstract
The HIV-1 transactivation response RNA element (TAR), which is essential to the lifecycle of the virus, has been suggested, based on NMR and hydrodynamic measurements, to undergo substantial, collective, structural dynamics that are important for its function. To deal with the significant coupling between overall diffusional rotation and internal motion expected to exist in TAR, here we utilize an isotropic reorientational eigenmode dynamics analysis of simulated molecular trajectories to obtain a detailed description of TAR dynamics and an accurately quantified pattern of dynamical correlations. The analysis demonstrates the inseparability of internal and overall motional modes, confirms the existence and reveals the nature of collective domain dynamics, and additionally reveals that the hinge for these motions is centered on residues U23, C24, and C41. Results also indicate the existence of long-range communication between the loop and the core of the RNA, and between the loop and the bulge. Additionally, the isotropic reorientational eigenmode dynamics analysis explains, from a dynamical perspective, several existing biochemical mutational studies and suggests new mutations for future structural dynamics studies.
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