ArticleNucleic acids research2009
How binding of small molecule and peptide ligands to HIV-1 TAR alters the RNA motional landscape.
Article in Nucleic acids research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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Who cites it
40 citing papers in PubMed, 64 citations in OpenAlex.
- Article
- Three-dimensional structure of the palbociclib-HIV TAR complex.Nucleic acids research · 2026Article
- The kinase inhibitor palbociclib binds to HIV TAR RNA with very low nanomolar affinity and exquisite specificity.Nucleic acids research · 2026Article
- Pharmacophore-Based Discovery of Viral RNA Conformational Modulators.Pharmaceuticals (Basel, Switzerland) · 2022Article
- Targeting Tat-TAR RNA Interaction for HIV-1 Inhibition.Viruses · 2021Article
- Exploring the Druggability of Conserved RNA Regulatory Elements in the SARS-CoV-2 Genome.Angewandte Chemie (International ed. in English) · 2021Article
- Systematically Studying the Effect of Small Molecules Interacting with RNA in Cellular and Preclinical Models.ACS chemical biology · 2021Review
- 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
- Understanding the characteristics of nonspecific binding of drug-like compounds to canonical stem-loop RNAs and their implications for functional cellular assays.RNA (New York, N.Y.) · 2021Article
- Understanding the Contributions of Conformational Changes, Thermodynamics, and Kinetics of RNA-Small Molecule Interactions.ACS chemical biology · 2019Review
- Visualizing RNA Conformational Changes via Pattern Recognition of RNA by Small Molecules.Journal of the American Chemical Society · 2019Article
- An ultra-high affinity ligand of HIV-1 TAR reveals the RNA structure recognized by P-TEFb.Nucleic acids research · 2019Article
- Design of RNA-targeting macrocyclic peptides.Methods in enzymology · 2019Article
- In cell mutational interference mapping experiment (in cell MIME) identifies the 5' polyadenylation signal as a dual regulator of HIV-1 genomic RNA production and packaging.Nucleic acids research · 2018Article
- RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.Chemical reviews · 2018Review
- Ultraslow Domain Motions in HIV-1 TAR RNA Revealed by Solid-State Deuterium NMR.The journal of physical chemistry. B · 2017Article
- Development of Small Molecules with a Noncanonical Binding Mode to HIV-1 Trans Activation Response (TAR) RNA.Journal of medicinal chemistry · 2016Article
- Structure of a low-population binding intermediate in protein-RNA recognition.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Dynamic motions of the HIV-1 frameshift site RNA.Biophysical journal · 2015Article
- Molecular dynamics simulations identify time scale of conformational changes responsible for conformational selection in molecular recognition of HIV-1 transactivation responsive RNA.Journal of the American Chemical Society · 2014Article
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
Abstract
The HIV-1 TAR RNA represents a well-known paradigm to study the role of dynamics and conformational change in RNA function. This regulatory RNA changes conformation in response to binding of Tat protein and of a variety of peptidic and small molecule ligands, indicating that its conformational flexibility and intrinsic dynamics play important roles in molecular recognition. We have used (13)C NMR relaxation experiments to examine changes in the motional landscape of HIV-1 TAR in the presence of three ligands of different affinity and specificity. The ligands are argininamide, a linear peptide mimic of the Tat basic domain and a cyclic peptide that potently inhibits Tat-dependent activation of transcription. All three molecules induce the same motional characteristics within the three nucleotides bulge that represents the Tat-binding site. However, the cyclic peptide has a unique motional signature in the apical loop, which represents a binding site for the essential host co-factor cyclin T1. These results suggest that all peptidic mimics of Tat induce the same dynamics in TAR within this protein binding site. However, the new cyclic peptide mimic of Tat represents a new class of ligands with a unique effect on the dynamics and the structure of the apical loop.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.