Browsing by Affiliation "Duquesne University"

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  • Research Data
    NMR structure and dynamics of the stem loop II motif (s2m) from the Omicron variant of SARS-CoV-2
    2025-04-30
    Matzel, Tobias 
    Joseph A. Makowski
    Adam Kensinger
    Andreas Oxenfarth
    Wirtz Martin, Maria Alexandra 
    Jeffrey Evanseck
    Schwalbe, Harald Jochen 
    The stem-loop-II motif (s2m) is a conserved viral RNA element located in the 3’UTR of different viruses including SARS-CoV-2. High resolution 3D structural data for s2m is only available for the fundamentally different SCoV-1 version and difficult to access for SARS-CoV-2 due to the highly dynamic nature of the RNA element. With the omicron variant a large deletion occurred for s2m resulting in a relatively short hairpin with an apical pentaloop. We attempted to determine the NMR solution structure of s2m_omicron by including CCRs and J-coupling derived dihedral restraints in addition to NOE distance restraints. Surprisingly, relatively high 1H,13C heteronuclear NOE values, averaged ribose 3JHH-couplings (H1’H2’; H3’H4’) and dipole(H1’-C1’) dipole(H6/8-C6/8)-CCRs hinted towards significant dynamics for the small pentaloop making structure calculations solely relying on NMR data insufficient. To address this problem, we performed MD-simulations with the NMR structure bundle as a starting point and applied BME reweighting to refine the ensemble with the 3J-coupling data. Our results provide a detailed view of the conformational dynamics of the omicron variant of s2m characterized by different stacking patterns, ribose repuckering and overall heterogeneity of the torsion angles for the loop nucleotides. Strikingly, despite the deletion of the initial nonaloop, as present in the Wuhan and Delta variants of s2m, a dynamic UAC triplet is conserved at the tip of the pentaloop hinting towards a possible connection to the still unknown function of the RNA element.
      18  7
  • Research Data
    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
    2025-02-28
    Wirtz Martin, Maria Alexandra 
    Makowski, Joseph A.
    Matzel, Tobias 
    Herr, Alexander
    Kensinger, Adam H.
    Richter, Christian 
    Evanseck, Jeffrey D.
    Jonker, Hendrik R. A.
    Wacker, Anna
    Schwalbe, Harald Jochen 
    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.
      34  3