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  4. F14 - Faculty of Biochemistry, Chemistry and Pharmacy
  5. Faculty of Biochemistry, Chemistry and Pharmacy: Research Data
  6. 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
 
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Title(s)
TitleLanguage
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
en
 
Author(s)
NameORCIDGNDAffiliation
Wirtz Martin, Maria Alexandra 
0000-0002-0318-7785
Organic Chemistry and Chemical Biology 
Makowski, Joseph A.
0000-0002-2597-8211
Duquesne University 
Matzel, Tobias 
0009-0008-6024-4062
Organic Chemistry and Chemical Biology 
Herr, Alexander
Organic Chemistry and Chemical Biology 
Kensinger, Adam H.
0000-0002-1931-9703
Duquesne University 
Richter, Christian 
0000-0002-5420-2826
Organic Chemistry and Chemical Biology 
Evanseck, Jeffrey D.
0000-0003-2616-7354
Duquesne University 
Jonker, Hendrik R. A.
0000-0002-5582-3931
Organic Chemistry and Chemical Biology 
Wacker, Anna
0000-0001-5892-5661
Organic Chemistry and Chemical Biology 
Schwalbe, Harald Jochen 
0000-0001-5693-7909
Organic Chemistry and Chemical Biology 
 
Faculty
14 Biochemistry, Chemistry and Pharmacy
 
Date Issued
28 February 2025
 
Publisher(s)
Goethe-Universität Frankfurt
 
Handle
https://gude.uni-frankfurt.de/handle/gude/489
 
DOI
10.25716/gude.0pdz-ar7h
 

Type(s) of data
Dataset
 
Language(s)
en
 
Subject Keyword(s)
  • s2m

  • Covid-19

  • NMR Assignment

  • RNA structure

  • NMR dynamics

  • Molecular simulation

 
Abstract(s)
AbstractLanguage
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. This renders their structural characterization particularly challenging. We here provide an example for comprehensive characterization of the SARS-CoV-2 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). As representation of the structure by a single conformation is unsuitable, we here present ensemble of NMR structures in agreement with SAXS data. 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 characterisation of functional RNA structures featuring dynamic motifs.
en
 

License
All rights reserved
 

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Acquisition Date
May 9, 2025
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3
Acquisition Date
May 9, 2025
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