Journal Article

PreJuSER-20192

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Relaxation time prediction for a light switchable peptide by molecular dynamics

Denschlag, R. ; Schreier, W. J. ; Rieff, B. ; Schrader, T. E.FZJ* ; Koller, F. O. ; Moroder, L. ; Zinth, W. ; Tavan, P.

2010
RSC Publ. Cambridge

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Please use a persistent id in citations: doi:10.1039/b921803c

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.

Keyword(s): Aminobenzoic Acids: chemistry (MeSH) ; Azo Compounds: chemistry (MeSH) ; Isomerism (MeSH) ; Light (MeSH) ; Magnetic Resonance Spectroscopy (MeSH) ; Molecular Dynamics Simulation (MeSH) ; Peptides, Cyclic: chemistry (MeSH) ; Temperature (MeSH) ; Time Factors (MeSH) ; (4-amino)phenylazobenzoic acid ; Aminobenzoic Acids ; Azo Compounds ; Peptides, Cyclic ; J

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.

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Contributing Institute(s):

1. Neutronenstreuung (ICS-1)
2. JCNS-FRM-II (JCNS (München) ; Jülich Centre for Neutron Science JCNS (München) ; JCNS-FRM-II)
3. Neutronenstreuung (JCNS-1)

Research Program(s):

1. BioSoft: Makromolekulare Systeme und biologische Informationsverarbeitung (P45)
2. Großgeräte für die Forschung mit Photonen, Neutronen und Ionen (PNI) (P55)

Experiment(s):

1. No specific instrument

Appears in the scientific report 2010

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Database coverage:
; JCR ; Science Citation Index Expanded ; Thomson Reuters Master Journal List ; Web of Science Core Collection

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