ArticleBiophysical journal2006
Conformational dynamics of RNA-peptide binding: a molecular dynamics simulation study.
Article in Biophysical journal, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed, 38 citations in OpenAlex.
- Using Short Molecular Dynamics Simulations to Determine the Important Features of Interactions in Antibody-Protein Complexes.Proteins · 2025Article
- Structural and computational studies of HIV-1 RNA.RNA biology · 2024Review
- Role of salt-bridging interactions in recognition of viral RNA by arginine-rich peptides.Biophysical journal · 2021Article
- RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.Chemical reviews · 2018Review
- Article
- On the Applicability of Elastic Network Models for the Study of RNA CUG Trinucleotide Repeat Overexpansion.PloS one · 2016Article
- Methods to enable the design of bioactive small molecules targeting RNA.Organic & biomolecular chemistry · 2014Review
- Target Flexibility in RNA-Ligand Docking Modeled by Elastic Potential Grids.ACS medicinal chemistry letters · 2011Article
- Binding of the bacteriophage P22 N-peptide to the boxB RNA motif studied by molecular dynamics simulations.Biophysical journal · 2009Article
- Molecular dynamics simulation study of the binding of purine bases to the aptamer domain of the guanine sensing riboswitch.Nucleic acids research · 2009Article
- Dynamics of tRNA at different levels of hydration.Biophysical journal · 2009Article
- The concept of template-based de novo design from drug-derived molecular fragments and its application to TAR RNA.Journal of computer-aided molecular design · 2008Article
- Conformations of flanking bases in HIV-1 RNA DIS kissing complexes studied by molecular dynamics.Biophysical journal · 2007Article
- iRED analysis of TAR RNA reveals motional coupling, long-range correlations, and a dynamical hinge.Biophysical journal · 2007Article
- Article
- Review
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Authors and funding
2 authors at 2 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Molecular dynamics simulations of the binding of the heterochiral tripeptide KkN to the transactivation responsive (TAR) RNA of HIV-1 is presented, using an all-atom force field with explicit water. To obtain starting structures for the TAR-KkN complex, semirigid docking calculations were performed that employ an NMR structure of free TAR RNA. The molecular dynamics simulations show that the starting structures in which KkN binds to the major groove of TAR (as it is the case for the Tat-TAR complex of HIV-1) are unstable. On the other hand, the minor-groove starting structures are found to lead to several binding modes, which are stabilized by a complex interplay of stacking, hydrogen bonding, and electrostatic interactions. Although the ligand does not occupy the binding position of Tat protein, it is shown to hinder the interhelical motion of free TAR RNA. The latter is presumably necessary to achieve the conformational change of TAR RNA to bind Tat protein. Considering the time evolution of the trajectories, the binding process is found to be ligand-induced and cooperative. That is, the conformational rearrangement only occurs in the presence of the ligand and the concerted motion of the ligand and a large part of the RNA binding site is necessary to achieve the final low-energy binding state.
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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.