Work

Integrated NMR/MD investigation reveals differences after reweighting in conformational ensembles of the GAAG and GCAA tetraloops

Year: 2026

Type: article

Abstract: While the GNRA tetraloops are an extensively studied and common RNA 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 known tetraloop sequences by an extensive NMR investigation of NOEs, J -couplings constants, RDCs and CCRs. As classical structure calculation proved insufficient for the more dynamic tetraloop, we turned to Bayesian/maximum entropy reweighting of molecular simulations using our rich set of experiments. 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-like 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.

Source: RNA

DOI: 10.1261/rna.081067.126