ArticleJournal of the American Chemical Society2014
Molecular dynamics simulations identify time scale of conformational changes responsible for conformational selection in molecular recognition of HIV-1 transactivation responsive RNA.
Article in Journal of the American Chemical Society, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 36 citations in OpenAlex.
- A Computational Modeling for Reconfigurable Biosensors.BioNanoScience · 2026Article
- Structural and computational studies of HIV-1 RNA.RNA biology · 2024Review
- Differences in ion-RNA binding modes due to charge density variations explain the stability of RNA in monovalent salts.Science advances · 2022Article
- Article
- Role and Perspective of Molecular Simulation-Based Investigation of RNA-Ligand Interaction: From Small Molecules and Peptides to Photoswitchable RNA Binding.Molecules (Basel, Switzerland) · 2021Review
- Targeting structural features of viral genomes with a nano-sized supramolecular drug.Chemical science · 2021Article
- RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.Chemical reviews · 2018Review
- AMOEBA Polarizable Atomic Multipole Force Field for Nucleic Acids.Journal of chemical theory and computation · 2018Article
- NMR Structures and Dynamics in a Prohead RNA Loop that Binds Metal Ions.The journal of physical chemistry letters · 2016Article
- RNA folding pathways in stop motion.Nucleic acids research · 2016Article
- Inter-helical conformational preferences of HIV-1 TAR-RNA from maximum occurrence analysis of NMR data and molecular dynamics simulations.Physical chemistry chemical physics : PCCP · 2016Article
- Elastic network models for RNA: a comparative assessment with molecular dynamics and SHAPE experiments.Nucleic acids research · 2015Article
- Information content of long-range NMR data for the characterization of conformational heterogeneity.Journal of biomolecular NMR · 2015Article
- Slowdown of Interhelical Motions Induces a Glass Transition in RNA.Biophysical journal · 2015Article
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Authors and funding
7 authors at 5 institutions in 3 countries.
Funding
Abstract
The HIV-1 Tat protein and several small molecules bind to HIV-1 transactivation responsive RNA (TAR) by selecting sparsely populated but pre-existing conformations. Thus, a complete characterization of TAR conformational ensemble and dynamics is crucial to understand this paradigmatic system and could facilitate the discovery of new antivirals targeting this essential regulatory element. We show here that molecular dynamics simulations can be effectively used toward this goal by bridging the gap between functionally relevant time scales that are inaccessible to current experimental techniques. Specifically, we have performed several independent microsecond long molecular simulations of TAR based on one of the most advanced force fields available for RNA, the parmbsc0 AMBER. Our simulations are first validated against available experimental data, yielding an excellent agreement with measured residual dipolar couplings and order parameter S(2). This contrast with previous molecular dynamics simulations (Salmon et al., J. Am. Chem. Soc. 2013 135, 5457-5466) based on the CHARMM36 force field, which could achieve only modest accord with the experimental RDC values. Next, we direct the computation toward characterizing the internal dynamics of TAR over the microsecond time scale. We show that the conformational fluctuations observed over this previously elusive time scale have a strong functionally oriented character in that they are primed to sustain and assist ligand binding.
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