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@ARTICLE{Barz:150966,
      author       = {Barz, Bogdan and Wales, David J. and Strodel, Birgit},
      title        = {{A} {K}inetic {A}pproach to the {S}equence–{A}ggregation
                      {R}elationship in {D}isease-related {P}rotein {A}ssembly},
      journal      = {The journal of physical chemistry / B},
      volume       = {118},
      number       = {4},
      issn         = {1520-5207},
      address      = {Washington, DC},
      publisher    = {Soc.},
      reportid     = {FZJ-2014-00997},
      pages        = {1003 - 1011},
      year         = {2014},
      abstract     = {It is generally accepted that oligomers of aggregating
                      proteins play an important role in the onset of
                      neurodegenerative diseases. While in silico aggregation
                      studies of full length amyloidogenic proteins are
                      computationally expensive, the assembly of short protein
                      fragments derived from these proteins with similar
                      aggregating properties has been extensively studied. In the
                      present work, molecular dynamics simulations are performed
                      to follow peptide aggregation on the microsecond time scale.
                      By defining aggregation states, we identify transition
                      networks, disconnectivity graphs, and first passage time
                      distributions to describe the kinetics of the assembly
                      process. This approach unravels differences in the
                      aggregation into hexamers of two peptides with different
                      primary structures. The first is GNNQQNY, a hydrophilic
                      fragment from the prion protein Sup35, and the second is
                      KLVFFAE, a fragment from amyloid-β protein, with a
                      hydrophobic core delimited by two charged amino acids. The
                      assembly of GNNQQNY suggests a mechanism of monomer
                      addition, with a bias toward parallel peptide pairs and a
                      gradual increase in the amount of β-strand content. For
                      KLVFFAE, a mechanism involving dimers rather than monomers
                      is revealed, involving a generally higher β-strand content
                      and a transition toward a larger number of antiparallel
                      peptide pairs during the rearrangement of the hexamer. The
                      differences observed for the aggregation of the two peptides
                      suggests the existence of a sequence-aggregation
                      relationship.},
      cin          = {ICS-6},
      ddc          = {530},
      cid          = {I:(DE-Juel1)ICS-6-20110106},
      pnm          = {452 - Structural Biology (POF2-452)},
      pid          = {G:(DE-HGF)POF2-452},
      typ          = {PUB:(DE-HGF)16},
      UT           = {WOS:000330610400016},
      pubmed       = {pmid:24401100},
      doi          = {10.1021/jp412648u},
      url          = {https://juser.fz-juelich.de/record/150966},
}