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@ARTICLE{Samantray:889721,
      author       = {Samantray, Suman and Yin, Feng and Kav, Batuhan and
                      Strodel, Birgit},
      title        = {{D}ifferent {F}orce {F}ields {G}ive {R}ise to {D}ifferent
                      {A}myloid {A}ggregation {P}athways in {M}olecular {D}ynamics
                      {S}imulations},
      journal      = {Journal of chemical information and modeling},
      volume       = {60},
      number       = {12},
      issn         = {1549-960X},
      address      = {Washington, DC},
      publisher    = {American Chemical Society64160},
      reportid     = {FZJ-2021-00343},
      pages        = {6462 - 6475},
      year         = {2020},
      abstract     = {The progress toward understanding the molecularbasis of
                      Alzheimers’s disease is strongly connected to
                      elucidatingthe early aggregation events of the amyloid-β
                      (Aβ) peptide.Molecular dynamics (MD) simulations provide a
                      viable techniqueto study the aggregation of Aβ into
                      oligomers with high spatial andtemporal resolution. However,
                      the results of an MD simulation canonly be as good as the
                      underlying force field. A recent study by ourgroup showed
                      that none of the common force fields can distinguishbetween
                      aggregation-prone and nonaggregating peptide sequences,
                      producing a similar and in most cases too fast
                      aggregationkinetics for all peptides. Since then, new force
                      fields specially designed for intrinsically disordered
                      proteins such as Aβ weredeveloped. Here, we assess the
                      applicability of these new force fields to studying peptide
                      aggregation using the Aβ16−22 peptide andmutations of it
                      as test case. We investigate their performance in modeling
                      the monomeric state, the aggregation into oligomers, andthe
                      stability of the aggregation end product, i.e., the
                      fibrillar state. A main finding is that changing the force
                      field has a stronger effecton the simulated aggregation
                      pathway than changing the peptide sequence. Also the new
                      force fields are not able to reproduce theexperimental
                      aggregation propensity order of the peptides. Dissecting the
                      various energy contributions shows that
                      AMBER99SB-dispoverestimates the interactions between the
                      peptides and water, thereby inhibiting peptide aggregation.
                      More promising results areobtained with CHARMM36m and
                      especially its version with increased protein−water
                      interactions. It is thus recommended to usethis force field
                      for peptide aggregation simulations and base future
                      reparameterizations on it.},
      cin          = {IBI-7},
      ddc          = {540},
      cid          = {I:(DE-Juel1)IBI-7-20200312},
      pnm          = {553 - Physical Basis of Diseases (POF3-553)},
      pid          = {G:(DE-HGF)POF3-553},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {33174726},
      UT           = {WOS:000608875100080},
      doi          = {10.1021/acs.jcim.0c01063},
      url          = {https://juser.fz-juelich.de/record/889721},
}