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Browsing by Affiliation "Faculty of Biochemistry, Chemistry and Pharmacy"

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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.
      47  11
  • Research Data
    Single-molecule dynamics reveals ATP binding alone powers substrate translocation by an ABC transporter
    2025-07-25
    Christoph Nocker
    Matija Pečak (DataCollector)
    Tobias Nocker (DataCollector)
    Amin Fahim (DataCollector)
    Lukas Susac (DataCollector)
    Robert Tampé (ContactPerson)
    ATP-binding cassette (ABC) transporters are molecular machines that are involved in a wide range of physiological processes, including antigen presentation by TAP, a key player in adaptive immunity. TAP and its bacterial homolog TmrAB use ATP to translocate peptides across membranes. To elucidate the mechanism of substrate transport, we employed a single-molecule FRET sensor to visualize single-translocation events by individual ABC transporters, overcoming the limitations of ensemble averaging. Using this approach, we tracked the membrane translocation of single peptides driven by a conformational switch from the inward- to the outward-facing state. In a slow-turnover TmrAB variant, even in the absence of Mg2+, we show that ATP binding alone is sufficient to drive peptide translocation. Structural analyses via cryogenic electron microscopy reveal that ATP binding induces an outward-facing conformation in both wild-type and mutant TmrAB, even without Mg2+. In wild-type TmrAB, this was sufficient for a single peptide translocation. However, Mg2+ was essential for the later stages of ATP hydrolysis and transporter resetting. Together, these results reveal a direct mechanistic link between ATP binding and substrate translocation at single-molecule resolution, providing new insights into the catalytic cycle of ABC transporters.
      22  5
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