Faculty of Biochemistry, Chemistry and Pharmacy: Research Data

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Browsing Faculty of Biochemistry, Chemistry and Pharmacy: Research Data by Subject "Basyesian/Maximum Entropy Reweighting"

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  • Research Data
    Integrated NMR/MD investigation reveals differences after reweighting in conformational ensembles of the GAAG and GCAA tetraloops
    2026-05-08
    David Leopold
    Oxenfarth, Andreas
    Thomasen, F. Emil
    Kümmerer, Felix
    Schnieders, Robbin
    Pinter, György
    Wacker, Anna
    Jonker, Hendrik R. A.
    Fürtig, Boris
    Richter, Christian 
    Lindorff-Larsen, Kresten
    Schwalbe, Harald Jochen 
    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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