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000020192 0247_ $$2pmid$$apmid:20390205
000020192 0247_ $$2DOI$$a10.1039/b921803c
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000020192 0247_ $$2ISSN$$a1463-9076
000020192 0247_ $$2MLZ$$aDenschlag:20192
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000020192 041__ $$aeng
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000020192 084__ $$2WoS$$aChemistry, Physical
000020192 084__ $$2WoS$$aPhysics, Atomic, Molecular & Chemical
000020192 1001_ $$0P:(DE-HGF)0$$aDenschlag, R.$$b0
000020192 245__ $$aRelaxation time prediction for a light switchable peptide by molecular dynamics
000020192 260__ $$aCambridge$$bRSC Publ.$$c2010
000020192 300__ $$a6204 - 6218
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000020192 440_0 $$025363$$aPhysical Chemistry Chemical Physics$$v12$$y23
000020192 500__ $$aThis 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.
000020192 520__ $$aWe study a monocyclic peptide called cAPB, whose conformations are light switchable due to the covalent integration of an azobenzene dye. Molecular dynamics (MD) simulations using the CHARMM22 force field and its CMAP extension serve us to sample the two distinct conformational ensembles of cAPB, which belong to the cis and trans isomers of the dye, at room temperature. For gaining sufficient statistics we apply a novel replica exchange technique. We find that the well-known NMR distance restraints are much better described by CMAP than by CHARMM22. In cAPB, the ultrafast cis/trans photoisomerization of the dye elicits a relaxation dynamics of the peptide backbone. Experimentally, we probe this relaxation at picosecond time resolution by IR spectroscopy in the amide I range up to 3 ns after the UV/vis pump flash. We interpret the spectroscopically identified decay kinetics using ensembles of non-equilibrium MD simulations, which provide kinetic data on conformational transitions well matching the observed kinetics. Whereas spectroscopy solely indicates that the relaxation toward the equilibrium trans ensemble is by no means complete after 3 ns, the 20 ns MD simulations of the process predict, independently of the applied force field, that the final relaxation into the trans-ensemble proceeds on a time scale of 23 ns. Overall our explicit solvent simulations cover more than 6 micros.
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000020192 650_2 $$2MeSH$$aAminobenzoic Acids: chemistry
000020192 650_2 $$2MeSH$$aAzo Compounds: chemistry
000020192 650_2 $$2MeSH$$aIsomerism
000020192 650_2 $$2MeSH$$aLight
000020192 650_2 $$2MeSH$$aMagnetic Resonance Spectroscopy
000020192 650_2 $$2MeSH$$aMolecular Dynamics Simulation
000020192 650_2 $$2MeSH$$aPeptides, Cyclic: chemistry
000020192 650_2 $$2MeSH$$aTemperature
000020192 650_2 $$2MeSH$$aTime Factors
000020192 650_7 $$00$$2NLM Chemicals$$a(4-amino)phenylazobenzoic acid
000020192 650_7 $$00$$2NLM Chemicals$$aAminobenzoic Acids
000020192 650_7 $$00$$2NLM Chemicals$$aAzo Compounds
000020192 650_7 $$00$$2NLM Chemicals$$aPeptides, Cyclic
000020192 650_7 $$2WoSType$$aJ
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000020192 7001_ $$0P:(DE-HGF)0$$aSchreier, W.J.$$b1
000020192 7001_ $$0P:(DE-HGF)0$$aRieff, B.$$b2
000020192 7001_ $$0P:(DE-Juel1)138266$$aSchrader, T.E.$$b3$$uFZJ
000020192 7001_ $$0P:(DE-HGF)0$$aKoller, F.O.$$b4
000020192 7001_ $$0P:(DE-HGF)0$$aMoroder, L.$$b5
000020192 7001_ $$0P:(DE-HGF)0$$aZinth, W.$$b6
000020192 7001_ $$0P:(DE-HGF)0$$aTavan, P.$$b7
000020192 773__ $$0PERI:(DE-600)1476244-4$$a10.1039/b921803c$$gVol. 12, p. 6204 - 6218$$p6204 - 6218$$q12<6204 - 6218$$tPhysical Chemistry Chemical Physics$$v12$$x1463-9076$$y2010
000020192 8567_ $$uhttp://dx.doi.org/10.1039/b921803c
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