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@ARTICLE{Ilie:280486,
      author       = {Ilie, I. and den Otter, W. K. and Briels, Willem},
      title        = {{A} coarse grained protein model with internal degrees of
                      freedom. {A}pplication to α-synuclein aggregation},
      journal      = {The journal of chemical physics},
      volume       = {144},
      number       = {8},
      issn         = {1089-7690},
      address      = {Melville, NY},
      publisher    = {American Institute of Physics},
      reportid     = {FZJ-2016-00256},
      pages        = {085103},
      year         = {2016},
      abstract     = {Particles in simulations are traditionally endowed with
                      fixed interactions. While this is appropriate for particles
                      representing atoms or molecules, objects with significant
                      internal dynamics—like sequences of amino acids or even an
                      entire protein—are poorly modelled by invariable
                      particles. We develop a highly coarse grained polymorph
                      patchy particle with the ultimate aim of simulating proteins
                      as chains of particles at the secondary structure level.
                      Conformational changes, e.g., a transition between
                      disordered and β-sheet states, are accommodated by internal
                      coordinates that determine the shape and interaction
                      characteristics of the particles. The internal coordinates,
                      as well as the particle positions and orientations, are
                      propagated by Brownian Dynamics in response to their local
                      environment. As an example of the potential offered by
                      polymorph particles, we model the amyloidogenic
                      intrinsically disordered proteinα-synuclein, involved in
                      Parkinson’s disease, as a single particle with two
                      internal states. The simulations yield oligomers of
                      particles in the disordered state and fibrils of particles
                      in the “misfolded” cross-β-sheet state. The
                      aggregationdynamics is complex, as aggregates can form by a
                      direct nucleation-and-growth mechanism and by
                      two-step-nucleation through conversions between the two
                      cluster types. The aggregationdynamics is complex, with
                      fibrils formed by direct nucleation-and-growth, by
                      two-step-nucleation through the conversion of an oligomer
                      and by auto-catalysis of this conversion.},
      cin          = {ICS-3},
      ddc          = {540},
      cid          = {I:(DE-Juel1)ICS-3-20110106},
      pnm          = {551 - Functional Macromolecules and Complexes (POF3-551)},
      pid          = {G:(DE-HGF)POF3-551},
      typ          = {PUB:(DE-HGF)16},
      UT           = {WOS:000371618800056},
      pubmed       = {pmid:26931727},
      doi          = {10.1063/1.4942115},
      url          = {https://juser.fz-juelich.de/record/280486},
}