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@ARTICLE{Paul:904329,
      author       = {Paul, Arghadwip and Samantray, Suman and Anteghini, Marco
                      and Khaled, Mohammed and Strodel, Birgit},
      title        = {{T}hermodynamics and kinetics of the amyloid-β peptide
                      revealed by {M}arkov state models based on {MD} data in
                      agreement with experiment},
      journal      = {Chemical science},
      volume       = {12},
      number       = {19},
      issn         = {2041-6520},
      address      = {Cambridge},
      publisher    = {RSC},
      reportid     = {FZJ-2021-05899},
      pages        = {6652 - 6669},
      year         = {2021},
      abstract     = {The amlyoid-β peptide (Aβ) is closely linked to the
                      development of Alzheimer's disease. Molecular dynamics (MD)
                      simulations have become an indispensable tool for studying
                      the behavior of this peptide at the atomistic level. General
                      key aspects of MD simulations are the force field used for
                      modeling the peptide and its environment, which is important
                      for accurate modeling of the system of interest, and the
                      length of the simulations, which determines whether or not
                      equilibrium is reached. In this study we address these
                      points by analyzing 30-μs MD simulations acquired for Aβ40
                      using seven different force fields. We assess the
                      convergence of these simulations based on the convergence of
                      various structural properties and of NMR and fluorescence
                      spectroscopic observables. Moreover, we calculate Markov
                      state models for the different MD simulations, which provide
                      an unprecedented view of the thermodynamics and kinetics of
                      the amyloid-β peptide. This further allows us to provide
                      answers for pertinent questions, like: which force fields
                      are suitable for modeling Aβ? (a99SB-UCB and
                      a99SB-ILDN/TIP4P-D); what does Aβ peptide really look like?
                      (mostly extended and disordered) and; how long does it take
                      MD simulations of Aβ to attain equilibrium? (at least
                      20–30 μs). We believe the analyses presented in this
                      study will provide a useful reference guide for important
                      questions relating to the structure and dynamics of Aβ in
                      particular, and by extension other similar disordered
                      proteins.},
      cin          = {IBI-7},
      ddc          = {540},
      cid          = {I:(DE-Juel1)IBI-7-20200312},
      pnm          = {5244 - Information Processing in Neuronal Networks
                      (POF4-524)},
      pid          = {G:(DE-HGF)POF4-5244},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {pmid:34040740},
      UT           = {WOS:000640200800001},
      doi          = {10.1039/D0SC04657D},
      url          = {https://juser.fz-juelich.de/record/904329},
}