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@ARTICLE{Yorke:643130,
      author       = {Yorke, Briony A. and Ginn, Helen},
      title        = {{C}alculation of minimum energy pathways in transport
                      proteins},
      journal      = {Communications chemistry},
      volume       = {8},
      number       = {1},
      issn         = {2399-3669},
      address      = {[London]},
      publisher    = {Macmillan Publishers Limited, part of Springer Nature},
      reportid     = {PUBDB-2026-00028},
      pages        = {377},
      year         = {2025},
      note         = {cc-by},
      abstract     = {Although static structures of protein metastable states are
                      well-studied, the fleeting transitions between these states
                      are difficult to experimentally observe or predict. We
                      present a computationally inexpensive algorithm,
                      “cold-inbetweening”, which generates trajectories
                      between experimentally determined end-states. Here we apply
                      cold-inbetweening to provide mechanistic insight into the
                      ubiquitous alternate access model of operation in three
                      membrane transporter superfamilies. Here, we study DraNramp
                      from Deinococcus radiodurans, MalT from Bacillus cereus, and
                      MATE from Pyrococcus furiosus. In MalT, the trajectory
                      demonstrates elevator transport through unwinding of a
                      supporter arm helix, maintaining adequate space to transport
                      maltose. In DraNramp, outward-gate closure occurs prior to
                      inward-gate opening, in accordance with the alternate access
                      hypothesis. In the MATE transporter, switching conformation
                      involves obligatory rewinding of the N-terminal helix to
                      avoid steric backbone clashes. This concurrently plugs the
                      cavernous ligand-binding site mid-conformational change.
                      Cold-inbetweening can generate hypotheses about large
                      functionally relevant protein conformational changes.},
      cin          = {FS-CFEL-1-DNMX},
      ddc          = {540},
      cid          = {I:(DE-H253)FS-CFEL-1-DNMX-20231108},
      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          = {10.1038/s42004-025-01754-1},
      url          = {https://bib-pubdb1.desy.de/record/643130},
}