ArticleNucleic acids research2000
Molecular dynamics studies of the HIV-1 TAR and its complex with argininamide.
Article in Nucleic acids research, 2000. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 51 citations in OpenAlex.
- Structural and computational studies of HIV-1 RNA.RNA biology · 2024Review
- Role of Mutations in Differential Recognition of Viral RNA Molecules by Peptides.Journal of chemical information and modeling · 2022Article
- Role of salt-bridging interactions in recognition of viral RNA by arginine-rich peptides.Biophysical journal · 2021Article
- Conformational dynamics and energetics of viral RNA recognition by lab-evolved proteins.Physical chemistry chemical physics : PCCP · 2021Article
- Targeting structural features of viral genomes with a nano-sized supramolecular drug.Chemical science · 2021Article
- Impact of Genetic Variations in HIV-1 Tat on LTR-Mediated Transcription via TAR RNA Interaction.Frontiers in microbiology · 2017Article
- 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
- Target Flexibility in RNA-Ligand Docking Modeled by Elastic Potential Grids.ACS medicinal chemistry letters · 2011Article
- Inhibition of Tat-mediated HIV-1 replication and neurotoxicity by novel GSK3-beta inhibitors.Virology · 2011Article
- 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
- Analyzing the flexibility of RNA structures by constraint counting.Biophysical journal · 2008Article
- iRED analysis of TAR RNA reveals motional coupling, long-range correlations, and a dynamical hinge.Biophysical journal · 2007Article
- Conformational dynamics of RNA-peptide binding: a molecular dynamics simulation study.Biophysical journal · 2006Article
- Evidence for a base triple in the free HIV-1 TAR RNA.RNA (New York, N.Y.) · 2004Article
- Molecular dynamics reveals the stabilizing role of loop closing residues in kissing interactions: comparison between TAR-TAR* and TAR-aptamer.Nucleic acids research · 2003Article
- The bulge region of HIV-1 TAR RNA binds metal ions in solution.Nucleic acids research · 2002Article
- Factors governing loss and rescue of DNA binding upon single and double mutations in the p53 core domain.Nucleic acids research · 2002Article
- Molecular dynamics and binding specificity analysis of the bovine immunodeficiency virus BIV Tat-TAR complex.Biophysical journal · 2001Article
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
The dynamic behavior of HIV-1 TAR and its complex with argininamide is investigated by means of molecular dynamics simulations starting from NMR structures, with explicit inclusion of water and periodic boundary conditions particle mesh Ewald representation of the electrostatic energy. During simulations of free and argininamide-bound TAR, local structural patterns, as determined by NMR experiments, were reproduced. An interdomain motion was observed in the simulations of free TAR, which is absent in the case of bound TAR, leading to the conclusion that the free conformation of TAR is intrinsically more flexible than the bound conformation. In particular, in the bound conformation the TAR-argininamide interface is very well ordered, as a result of the formation of a U.A.U base triple, which imposes structural constraints on the global conformation of the molecule. Free energy analysis, which includes solvation contributions, was used to evaluate the influence of van der Waals and electrostatic terms on formation of the complex and on the conformational rearrangement from free to bound TAR.
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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.