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@ARTICLE{Smorodina:1019568,
      author       = {Smorodina, Eva and Kav, Batuhan and Fatafta, Hebah and
                      Strodel, Birgit},
      title        = {{E}ffects of ion type and concentration on the structure
                      and aggregation of the amyloid peptide {A} β16−22$$
                      {\boldsymbol{\beta}}_{16-22} $$},
      journal      = {Proteins},
      volume       = {93},
      number       = {8},
      issn         = {0887-3585},
      address      = {New York, NY},
      publisher    = {Wiley-Liss},
      reportid     = {FZJ-2023-05505},
      pages        = {1369-1382},
      year         = {2025},
      abstract     = {Among the various factors controlling the amyloid
                      aggregation process, the influences ofions on the
                      aggregation rate and the resultingstructures are important
                      aspects to con-sider, which can be studied by molecular
                      simulations. There is a wide variety of proteinforce fields
                      and ion models, raising the question of which model to use
                      in such studies. Toaddress this question, we perform
                      molecular dynamics simulations of Aβ16–22, a fragmentof
                      the Alzheimer's amyloidβpeptide, using different protein
                      force fields, AMBER99SB-disp (A99-d) and CHARMM36m (C36m),
                      and different ion parameters. The influences ofNaCl and
                      CaCl2at various concentrations are studied and compared with
                      the systemswithout the addition of ions. Our results
                      indicate a sensitivity of the peptide-ion interac-tions to
                      the different ion models. In particular, we observe a strong
                      binding of Ca2+to res-idue E22 with C36m and also with the
                      Åqvist ion model used together with A99-d, whichslightly
                      affects the monomeric Aβ16–22structures and the
                      aggregation rate, but signifi-cantly affects the oligomer
                      structures formedin the aggregation simulations. For
                      example,at high Ca2+concentrations, there was a switch from
                      an antiparallel to a parallelβ-sheet.Such ionic influences
                      are of biological relevance because local ion concentrations
                      canchange in vivo and could help explain thepolymorphism of
                      amyloid fibrils.},
      cin          = {IBI-7},
      ddc          = {570},
      cid          = {I:(DE-Juel1)IBI-7-20200312},
      pnm          = {5241 - Molecular Information Processing in Cellular Systems
                      (POF4-524)},
      pid          = {G:(DE-HGF)POF4-5241},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {37964477},
      UT           = {WOS:001105186900001},
      doi          = {10.1002/prot.26635},
      url          = {https://juser.fz-juelich.de/record/1019568},
}