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  6. Integrated NMR/MD investigation reveals differences after reweighting in conformational ensembles of the GAAG and GCAA tetraloops
 
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Title(s)
TitleLanguage
Integrated NMR/MD investigation reveals differences after reweighting in conformational ensembles of the GAAG and GCAA tetraloops
en
 
Author(s)
NameORCIDGNDAffiliation
David Leopold
0000-0003-3250-3043
Organic Chemistry and Chemical Biology 
Oxenfarth, Andreas
0000-0001-6859-6849
Organic Chemistry and Chemical Biology 
Thomasen, F. Emil
0000-0002-2096-4873
University of Copenhagen
Kümmerer, Felix
0000-0002-4697-4658
University of Copenhagen
Schnieders, Robbin
Organic Chemistry and Chemical Biology 
Pinter, György
0000-0001-6769-7277
Organic Chemistry and Chemical Biology 
Wacker, Anna
0000-0001-5892-5661
Max Planck Institute for Terrestrial Microbiology
Jonker, Hendrik R. A.
0000-0002-5582-3931
Organic Chemistry and Chemical Biology 
Fürtig, Boris
0000-0001-6443-7656
Goethe University Frankfurt 
Richter, Christian 
0000-0002-5420-2826
Goethe University Frankfurt 
Lindorff-Larsen, Kresten
0000-0002-4750-6039
University of Copenhagen
Schwalbe, Harald Jochen 
0000-0001-5693-7909
Goethe-Universität Frankfurt am Main, Goethe-Universität Frankfurt am Main Fachbereich 14 Biochemie Chemie und Pharmazie, Instruct-ERIC, Massachusetts Institute of Technology, University of Oxford
 
Faculty
14 Biochemistry, Chemistry and Pharmacy
 
DFG-Subject
201-01 Biochemistry
 
Date Issued
08 May 2026
 
Publisher(s)
Goethe-Universität Frankfurt
 
Handle
https://gude.uni-frankfurt.de/handle/gude/776
 
DOI
10.25716/gude.0kmt-q1xh
 

Type(s) of data
Dataset
Software
 
Language(s)
en
 
Subject Keyword(s)
  • Nuclear magnetic reso...

  • Molecular dynamics

  • RNA

  • RNA tetraloop

  • Basyesian/Maximum Ent...

 
Abstract(s)
AbstractLanguage
While the GNRA tetraloops are an extensively studied and common folding motif, their dynamic NMR structures in solution integrating state-of-the-art NMR parameters such as residual dipolar couplings (RDC) and cross correlated relaxation rates (CCR) have previously not been determined. Given their dominant occurrence among tetraloops in the PDB and the advance of experimentally reweighted MD simulations, the present work aims at investigating the entire conformational space of two literature known GNRA tetraloops sequences by an extensive NMR investigation of NOEs, J-couplings constants, RDCs and CCRs as rich experimental base for MD Bayesian/maximum entropy reweighting, as classical structure calculation proofed insufficient for the more dynamic tetraloop. The resulting ensembles were clustered and compared to classically restrained structure calculations, structures from the PDB and models predicted by the prediction algorithms FarFar and Alphafold 3. Our results show that GNRA tetraloops can vary in dynamic sampling of conformational space. They highlight the importance of individual experimental validation of computationally obtained dynamic ensembles and model predictions.
 

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All rights reserved
 

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Acquisition Date
May 22, 2026
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Acquisition Date
May 22, 2026
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