Download MendeleyStructural heterogeneity and dynamics in the apical stem loop of s2m from SARS-CoV-2 Delta by an integrative NMR spectroscopy and MD simulation approach.
Wirtz Martin, M.A., Makowski, J.A., Matzel, T., Kensinger, A.H., Herr, A., Richter, C., Jonker, H.R.A., Wacker, A., Evanseck, J.D., Schwalbe, H.(2025) Nucleic Acids Res 53
- PubMed: 40586311
- DOI: https://doi.org/10.1093/nar/gkaf552
- Primary Citation of Related Structures:
9FM4 - PubMed Abstract:
In structured RNAs, helical elements are often capped by apical loops that are integral structural elements, ranging from 3 to >20 nts of size on average, and display a highly heterogeneous energy landscape profile, rendering structural characterization particularly challenging. We here provide a characterization of the SARS-CoV-2 Delta s2m element containing a highly dynamic nonaloop using an integrative approach of nuclear magnetic resonance spectroscopy (NMR), small angle X-ray scattering (SAXS), and molecular dynamics simulations (MD). We further explored the conformational space in the s2m nonaloop and its transient closing 5'-G-U-3' base pair by MD simulations weighted by experimental NMR observables, leading to a comprehensive representation of the s2m nonaloop motif. Our deconvolution of the ensemble into conformations and dynamics provides a basis for future ensemble-functional characterization of RNA structures featuring dynamic motifs.
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438 Frankfurt, Germany.
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