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@ARTICLE{Strodel:134967,
      author       = {Strodel, Birgit and Whittleston, Chris S and Wales, David
                      J},
      title        = {{T}hermodynamics and kinetics of aggregation for the
                      {GNNQQNY} peptide.},
      journal      = {Journal of the American Chemical Society},
      volume       = {129},
      number       = {51},
      issn         = {1520-5126},
      address      = {Washington, DC},
      publisher    = {American Chemical Society},
      reportid     = {FZJ-2013-02982},
      pages        = {16005 - 16014},
      year         = {2007},
      abstract     = {The energy landscape of the monomer and dimer are explored
                      for the amyloidogenic heptapeptide GNNQQNY from the
                      N-terminal prion-determining domain of the yeast protein
                      Sup35. The peptide is modeled by a united-atom potential and
                      an implicit solvent representation. Replica exchange
                      molecular dynamics is used to explore the conformational
                      space, and discrete path sampling is employed to investigate
                      the pathways that interconvert the most populated minima on
                      the free energy surfaces. For the monomer, we find a rapid
                      fluctuation between four different conformations, where a
                      geometry intermediate between compact and extended
                      structures is the most thermodynamically favorable. The
                      GNNQQNY dimer forms three stable sheet structures, namely
                      in-register parallel, off-register parallel, and
                      antiparallel. The antiparallel dimer is stabilized by strong
                      electrostatic interactions resulting from interpeptide
                      hydrogen bonds, which restrict its conformational
                      flexibility. The in-register parallel dimer, which is close
                      to the amyloid beta-sheet structure, has fewer interpeptide
                      hydrogen bonds, making hydrophobic interactions more
                      important and increasing the conformational entropy compared
                      to the antiparallel sheet. The estimated two-state rate
                      constants indicate that the formation of dimers from
                      monomers is fast and that the dimers are kinetically stable
                      against dissociation at room temperature. Interconversions
                      between the different dimers are feasible processes and are
                      more likely than dissociation.},
      keywords     = {Oligopeptides (NLM Chemicals)},
      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},
      pubmed       = {pmid:18052168},
      UT           = {WOS:000251974000051},
      doi          = {10.1021/ja075346p},
      url          = {https://juser.fz-juelich.de/record/134967},
}