ArticlePhysical chemistry chemical physics : PCCP2016
Inter-helical conformational preferences of HIV-1 TAR-RNA from maximum occurrence analysis of NMR data and molecular dynamics simulations.
Article in Physical chemistry chemical physics : PCCP, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Integrated NMR and MD structure and dynamics of the stem-loop-II motif (s2m) from the Omicron variant of SARS-CoV-2.RNA (New York, N.Y.) · 2025Article
- Targeting RNA with small molecules, from RNA structures to precision medicines: IUPHAR review: 40.British journal of pharmacology · 2024Review
- Structural and computational studies of HIV-1 RNA.RNA biology · 2024Review
- DNA-Encoded Library Screening To Inform Design of a Ribonuclease Targeting Chimera (RiboTAC).Journal of the American Chemical Society · 2022Article
- Characterizing conformational ensembles of multi-domain proteins using anisotropic paramagnetic NMR restraints.Biophysical reviews · 2022Review
- RNA Dynamics by NMR Spectroscopy.Chembiochem : a European journal of chemical biology · 2019Review
- RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.Chemical reviews · 2018Review
- Determination of the conformational ensemble of the TAR RNA by X-ray scattering interferometry.Nucleic acids research · 2017Article
- Identification of productive and futile encounters in an electron transfer protein complex.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
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Authors and funding
6 authors.
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Abstract
Detecting conformational heterogeneity in biological macromolecules is a key for the understanding of their biological function. We here provide a comparison between two independent approaches to assess conformational heterogeneity: molecular dynamics simulations, performed without inclusion of any experimental data, and maximum occurrence (MaxOcc) distribution over the topologically available conformational space. The latter only reflects the extent of the averaging and identifies regions which are most compliant with the experimentally measured NMR Residual Dipolar Couplings (RDCs). The analysis was performed for the HIV-1 TAR RNA, consisting of two helical domains connected by a flexible bulge junction, for which four sets of RDCs were available as well as an 8.2 μs all-atom molecular dynamics simulation. A sample and select approach was previously applied to extract from the molecular dynamics trajectory conformational ensembles in agreement with the four sets of RDCs. The MaxOcc analysis performed here identifies the most likely sampled region in the conformational space of the system which, strikingly, overlaps well with the structures independently sampled in the molecular dynamics calculations and even better with the RDC selected ensemble.
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