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 reveal ATP binding alone powers substrate translocation by an ABC transporter
    2025-07-25
    Christoph Nocker
    Pečak, Matija (DataCollector)
    Nocker, Tobias (DataCollector)
    Amin Fahim (DataCollector)
    Susac, Lukas (DataCollector)
    Tampé, Robert  (ContactPerson)
    ATP-binding cassette (ABC) transporters are molecular machines involved in diverse physiological processes, including antigen processing by TAP, a key component of adaptive immunity. TAP and its bacterial homolog TmrAB use ATP to translocate peptides across membranes, yet the precise mechanism linking ATP binding to substrate movement remains unclear. Here, we employ a single-molecule FRET sensor to visualize single translocation events by individual ABC transporters, overcoming the limitations of ensemble averaging. This approach reveals that substrate transport is driven by a conformational switch from the inward- to the outward-facing state. Using a slow-turnover TmrAB variant, we demonstrate that ATP binding alone, even in the absence of Mg2+, is sufficient to drive a single round of peptide translocation. Cryo-EM structures of wild-type and slow-turnover TmrAB show that ATP binding induces the outward-facing conformation without Mg2+. In wild-type TmrAB, this conformational transition supports a single translocation event, whereas Mg2+-dependent ATP hydrolysis is required to reset the transporter. These findings establish a direct mechanistic link between ATP binding and substrate translocation at single-molecule resolution, providing new insights into the catalytic cycle of ABC transporters.
      5  2