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@ARTICLE{Mello:639659,
      author       = {Mello, Victor Hugo and Wald, Jiri and Marlovits, Thomas and
                      Sartori, Pablo},
      title        = {{E}lastic analysis bridges structure and dynamics of an
                      {AAA}+ molecular motor},
      journal      = {PLoS Computational Biology},
      volume       = {21},
      number       = {10},
      issn         = {1553-734X},
      address      = {San Francisco, Calif.},
      publisher    = {Public Library of Science},
      reportid     = {PUBDB-2025-04616},
      pages        = {e1013596 -},
      year         = {2025},
      abstract     = {Proteins carry out cellular functions by changing their
                      structure among a few conformations, each characterised by a
                      different energy level. Therefore, structural changes,
                      energy transformations, and protein function are intimately
                      related. Despite its central importance, this relationship
                      remains elusive. For example, while many hexameric ATPase
                      motors are known to function using a hand-over-hand
                      alternation of subunits, how energy transduction throughout
                      the assembly’s structure drives the hand-over-hand
                      mechanism is not known. In this work, we unravel the
                      energetic basis of hand-over-hand in a model AAA+ motor,
                      RuvB. To do so, we develop a general method to compute the
                      residue-scale elastic pseudoenergy due to structure changes
                      and apply it to RuvB structures, recently resolved through
                      cryo-EM. This allows us to quantify how progression through
                      RuvB’s mechanochemical cycle translates into residue-scale
                      energy transduction. In particular, we find that DNA binding
                      is associated with overcoming a high energy barrier. This is
                      possible through inter-subunit transmission of energy, and
                      ultimately driven by nucleotide exchange. Furthermore, we
                      show how this structure-inferred energetic quantification
                      can be integrated into a non-equilibrium model of AAA+
                      assembly dynamics, consistent with single-molecule
                      biophysics measurements. Overall, our work elucidates the
                      energetic basis for the hand-over-hand mechanism in RuvB’s
                      cycle. Besides, it presents a generally applicable
                      methodology for studying the energetics of conformational
                      cycles in other proteins, allowing to quantitatively bridge
                      data from structural biology and single-molecule
                      biophysics.},
      cin          = {CSSB-UKE-TM},
      ddc          = {610},
      cid          = {I:(DE-H253)CSSB-UKE-TM-20210520},
      pnm          = {633 - Life Sciences – Building Blocks of Life: Structure
                      and Function (POF4-633)},
      pid          = {G:(DE-HGF)POF4-633},
      experiment   = {EXP:(DE-MLZ)NOSPEC-20140101},
      typ          = {PUB:(DE-HGF)16},
      doi          = {10.1371/journal.pcbi.1013596},
      url          = {https://bib-pubdb1.desy.de/record/639659},
}