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@ARTICLE{Denschlag:20192,
      author       = {Denschlag, R. and Schreier, W.J. and Rieff, B. and
                      Schrader, T.E. and Koller, F.O. and Moroder, L. and Zinth,
                      W. and Tavan, P.},
      title        = {{R}elaxation time prediction for a light switchable peptide
                      by molecular dynamics},
      journal      = {Physical Chemistry Chemical Physics},
      volume       = {12},
      issn         = {1463-9076},
      address      = {Cambridge},
      publisher    = {RSC Publ.},
      reportid     = {PreJuSER-20192},
      pages        = {6204 - 6218},
      year         = {2010},
      note         = {This work was supported by the Deutsche
                      Forschungsgemeinschaft (Grants SFB 533/C1, SFB 749/A5/C4,
                      Forschergruppe 526). Computer time provided by Leibniz
                      Rechenzentrum (project uh408) is gratefully acknowledged.},
      abstract     = {We study a monocyclic peptide called cAPB, whose
                      conformations are light switchable due to the covalent
                      integration of an azobenzene dye. Molecular dynamics (MD)
                      simulations using the CHARMM22 force field and its CMAP
                      extension serve us to sample the two distinct conformational
                      ensembles of cAPB, which belong to the cis and trans isomers
                      of the dye, at room temperature. For gaining sufficient
                      statistics we apply a novel replica exchange technique. We
                      find that the well-known NMR distance restraints are much
                      better described by CMAP than by CHARMM22. In cAPB, the
                      ultrafast cis/trans photoisomerization of the dye elicits a
                      relaxation dynamics of the peptide backbone. Experimentally,
                      we probe this relaxation at picosecond time resolution by IR
                      spectroscopy in the amide I range up to 3 ns after the
                      UV/vis pump flash. We interpret the spectroscopically
                      identified decay kinetics using ensembles of non-equilibrium
                      MD simulations, which provide kinetic data on conformational
                      transitions well matching the observed kinetics. Whereas
                      spectroscopy solely indicates that the relaxation toward the
                      equilibrium trans ensemble is by no means complete after 3
                      ns, the 20 ns MD simulations of the process predict,
                      independently of the applied force field, that the final
                      relaxation into the trans-ensemble proceeds on a time scale
                      of 23 ns. Overall our explicit solvent simulations cover
                      more than 6 micros.},
      keywords     = {Aminobenzoic Acids: chemistry / Azo Compounds: chemistry /
                      Isomerism / Light / Magnetic Resonance Spectroscopy /
                      Molecular Dynamics Simulation / Peptides, Cyclic: chemistry
                      / Temperature / Time Factors / (4-amino)phenylazobenzoic
                      acid (NLM Chemicals) / Aminobenzoic Acids (NLM Chemicals) /
                      Azo Compounds (NLM Chemicals) / Peptides, Cyclic (NLM
                      Chemicals) / J (WoSType)},
      cin          = {ICS-1 / JCNS (München) ; Jülich Centre for Neutron
                      Science JCNS (München) ; JCNS-FRM-II / JCNS-1},
      ddc          = {540},
      cid          = {I:(DE-Juel1)ICS-1-20110106 /
                      I:(DE-Juel1)JCNS-FRM-II-20110218 /
                      I:(DE-Juel1)JCNS-1-20110106},
      pnm          = {BioSoft: Makromolekulare Systeme und biologische
                      Informationsverarbeitung / Großgeräte für die Forschung
                      mit Photonen, Neutronen und Ionen (PNI)},
      pid          = {G:(DE-Juel1)FUEK505 / G:(DE-Juel1)FUEK415},
      experiment   = {EXP:(DE-MLZ)NOSPEC-20140101},
      shelfmark    = {Chemistry, Physical / Physics, Atomic, Molecular $\&$
                      Chemical},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {pmid:20390205},
      UT           = {WOS:000278364600030},
      doi          = {10.1039/b921803c},
      url          = {https://juser.fz-juelich.de/record/20192},
}