Journal Article

PUBDB-2025-02339

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Structural 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. (Corresponding author) ; Evanseck, J. D. (Corresponding author) ; Schwalbe, H. (Corresponding author)Extern*

2025
Oxford Univ. Press Oxford

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Please use a persistent id in citations: doi:10.1093/nar/gkaf552  doi:10.3204/PUBDB-2025-02339

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.

Note: ISSN 1362-4962 not unique: **2 hits**.

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Contributing Institute(s):

1. EMBL-User (EMBL-User)

Research Program(s):

1. 6G3 - PETRA III (DESY) (POF4-6G3) (POF4-6G3)
2. DFG project G:(GEPRIS)495006306 - SARS-CoV-2-RNA: Untersuchungen der Architektur der RNA von SARS-CoV-2 (495006306) (495006306)
3. DFG project G:(GEPRIS)537258662 - Verbesserung der Qualität von NMR-Strukturen von RNA und DNA (537258662) (537258662)

Experiment(s):

1. PETRA Beamline P12 (PETRA III)

Appears in the scientific report 2025

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