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@ARTICLE{Bachmann:134961,
      author       = {Bachmann, Michael and Strodel, Birgit and Osborne, Kenneth
                      L.},
      title        = {{T}hermodynamic analysis of structural transitions during
                      {GNNQQNY} aggregation},
      journal      = {Proteins},
      volume       = {81},
      number       = {7},
      issn         = {0887-3585},
      address      = {New York, NY},
      publisher    = {Wiley-Liss},
      reportid     = {FZJ-2013-02976},
      pages        = {1141 - 1155},
      year         = {2013},
      abstract     = {Amyloid protein aggregation characterizes many
                      neurodegenerative disorders, including Alzheimer's,
                      Parkinson's, and Creutzfeldt-Jakob disease. Evidence
                      suggests that amyloid aggregates may share similar
                      aggregation pathways, implying simulation of full-length
                      amyloid proteins is not necessary for understanding amyloid
                      formation. In this study, we simulate GNNQQNY, the
                      N-terminal prion-determining domain of the yeast protein
                      Sup35 to investigate the thermodynamics of structural
                      transitions during aggregation. Utilizing a coarse-grained
                      model permits equilibration on relevant time scales.
                      Replica-exchange molecular dynamics is used to gather
                      simulation statistics at multiple temperatures and clear
                      energy traps that would aversely impact results.
                      Investigating the association of 3-, 6-, and 12-chain
                      GNNQQNY systems by calculating thermodynamic quantities and
                      orientational order parameters, we determine the aggregation
                      pathway by studying aggregation states of GNNQQNY. We find
                      that the aggregation of the hydrophilic GNNQQNY sequence is
                      mainly driven by H-bond formation, leading to the formation
                      of β-sheets from the very beginning of the assembly
                      process. Condensation (aggregation) and ordering take place
                      simultaneously, which is underpinned by the occurrence of a
                      single heat capacity peak.},
      cin          = {ICS-6},
      ddc          = {540},
      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:000320474100005},
      pubmed       = {pmid:23408546},
      doi          = {10.1002/prot.24263},
      url          = {https://juser.fz-juelich.de/record/134961},
}