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@INPROCEEDINGS{Bondar:1025183,
      author       = {Bondar, Ana-Nicoleta and Hristova, Kalina and Wimley,
                      William C.},
      title        = {{M}echanism by which water interactions stabilize a
                      p{H}-dependent membrane pore},
      issn         = {0006-3495},
      reportid     = {FZJ-2024-02760},
      year         = {2024},
      abstract     = {Peptides that can form large, stable pores at acidic pH
                      values are of direct interest to deliver cargo to cells and
                      cell compartments with acidic pH. Peptides of the pHD
                      (pH-dependent delivery peptides) have the unique property of
                      forming stable pores with diameters of ∼30–-100 Å at pH
                      below ∼6. Such a pore size could be established with
                      ∼8–30 peptides, and each peptide carries several
                      sidechains that can titrate at the pH of interest.
                      Understanding which protonation states are compatible with
                      stable pore formation is essential, as it could guide
                      rational design of new peptides with pore-forming properties
                      tailored to specific cells and cell compartments. We report
                      on experiment-guided atomistic simulations that probe the
                      protonation-coupled structure and dynamics of pHD pores. To
                      identify interactions that could contribute to the stability
                      of the pores, we used the Bridge/Bridge2 graph algorithm and
                      graphical user interface to compute the hydrogen-bond
                      networks sampled by the peptides, lipid phosphate groups,
                      and water. We identify a complex network of interactions
                      between peptides, lipid headgroups, and water molecules,
                      with water molecules bridging neighboring peptides via
                      dynamic hydrogen bonding. Research was supported in part by
                      the National Institutes of Health award no. 1R01GM151326-01
                      and by the computing time allocation PHDPORES from the
                      JURECA-DC Supercomputing Cluster of the Forschungszentrum
                      Jülich.},
      month         = {Feb},
      date          = {2024-02-10},
      organization  = {Biophysical Society Meeting,
                       Philadelphia (USA), 10 Feb 2024 - 14
                       Feb 2024},
      cin          = {IAS-5 / INM-9},
      ddc          = {570},
      cid          = {I:(DE-Juel1)IAS-5-20120330 / I:(DE-Juel1)INM-9-20140121},
      pnm          = {5241 - Molecular Information Processing in Cellular Systems
                      (POF4-524)},
      pid          = {G:(DE-HGF)POF4-5241},
      typ          = {PUB:(DE-HGF)1},
      doi          = {10.1016/j.bpj.2023.11.2011},
      url          = {https://juser.fz-juelich.de/record/1025183},
}