Hauptseite > Publikationsdatenbank > Relaxation time prediction for a light switchable peptide by molecular dynamics > print

001     20192
005     20240619091940.0
024 7 _ |2 pmid
|a pmid:20390205
024 7 _ |2 DOI
|a 10.1039/b921803c
024 7 _ |2 WOS
|a WOS:000278364600030
024 7 _ |2 ISSN
|a 1463-9076
024 7 _ |2 MLZ
|a Denschlag:20192
037 _ _ |a PreJuSER-20192
041 _ _ |a eng
082 _ _ |a 540
084 _ _ |2 WoS
|a Chemistry, Physical
084 _ _ |2 WoS
|a Physics, Atomic, Molecular & Chemical
100 1 _ |0 P:(DE-HGF)0
|a Denschlag, R.
|b 0
245 _ _ |a Relaxation time prediction for a light switchable peptide by molecular dynamics
260 _ _ |a Cambridge
|b RSC Publ.
|c 2010
300 _ _ |a 6204 - 6218
336 7 _ |a Journal Article
|0 PUB:(DE-HGF)16
|2 PUB:(DE-HGF)
336 7 _ |a Output Types/Journal article
|2 DataCite
336 7 _ |a Journal Article
|0 0
|2 EndNote
336 7 _ |a ARTICLE
|2 BibTeX
336 7 _ |a JOURNAL_ARTICLE
|2 ORCID
336 7 _ |a article
|2 DRIVER
440 _ 0 |0 25363
|a Physical Chemistry Chemical Physics
|v 12
|y 23
500 _ _ |a 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.
520 _ _ |a 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.
536 _ _ |0 G:(DE-Juel1)FUEK505
|2 G:(DE-HGF)
|a BioSoft: Makromolekulare Systeme und biologische Informationsverarbeitung
|c P45
|x 0
536 _ _ |0 G:(DE-Juel1)FUEK415
|2 G:(DE-HGF)
|a Großgeräte für die Forschung mit Photonen, Neutronen und Ionen (PNI)
|c P55
|x 1
588 _ _ |a Dataset connected to Web of Science, Pubmed
650 _ 2 |2 MeSH
|a Aminobenzoic Acids: chemistry
650 _ 2 |2 MeSH
|a Azo Compounds: chemistry
650 _ 2 |2 MeSH
|a Isomerism
650 _ 2 |2 MeSH
|a Light
650 _ 2 |2 MeSH
|a Magnetic Resonance Spectroscopy
650 _ 2 |2 MeSH
|a Molecular Dynamics Simulation
650 _ 2 |2 MeSH
|a Peptides, Cyclic: chemistry
650 _ 2 |2 MeSH
|a Temperature
650 _ 2 |2 MeSH
|a Time Factors
650 _ 7 |0 0
|2 NLM Chemicals
|a (4-amino)phenylazobenzoic acid
650 _ 7 |0 0
|2 NLM Chemicals
|a Aminobenzoic Acids
650 _ 7 |0 0
|2 NLM Chemicals
|a Azo Compounds
650 _ 7 |0 0
|2 NLM Chemicals
|a Peptides, Cyclic
650 _ 7 |2 WoSType
|a J
693 _ _ |0 EXP:(DE-MLZ)NOSPEC-20140101
|5 EXP:(DE-MLZ)NOSPEC-20140101
|e No specific instrument
|x 0
700 1 _ |0 P:(DE-HGF)0
|a Schreier, W.J.
|b 1
700 1 _ |0 P:(DE-HGF)0
|a Rieff, B.
|b 2
700 1 _ |0 P:(DE-Juel1)138266
|a Schrader, T.E.
|b 3
|u FZJ
700 1 _ |0 P:(DE-HGF)0
|a Koller, F.O.
|b 4
700 1 _ |0 P:(DE-HGF)0
|a Moroder, L.
|b 5
700 1 _ |0 P:(DE-HGF)0
|a Zinth, W.
|b 6
700 1 _ |0 P:(DE-HGF)0
|a Tavan, P.
|b 7
773 _ _ |0 PERI:(DE-600)1476244-4
|a 10.1039/b921803c
|g Vol. 12, p. 6204 - 6218
|p 6204 - 6218
|q 12<6204 - 6218
|t Physical Chemistry Chemical Physics
|v 12
|x 1463-9076
|y 2010
856 7 _ |u http://dx.doi.org/10.1039/b921803c
909 C O |o oai:juser.fz-juelich.de:20192
|p VDB:MLZ
|p VDB
913 1 _ |0 G:(DE-Juel1)FUEK505
|a DE-HGF
|b Schlüsseltechnologien
|k P45
|l Biologische Informationsverarbeitung
|v BioSoft: Makromolekulare Systeme und biologische Informationsverarbeitung
|x 0
913 1 _ |0 G:(DE-Juel1)FUEK415
|a DE-HGF
|b Struktur der Materie
|k P55
|l Großgeräteforschung mit Photonen, Neutronen und Ionen
|v Großgeräte für die Forschung mit Photonen, Neutronen und Ionen (PNI)
|x 1
913 2 _ |0 G:(DE-HGF)POF3-623
|1 G:(DE-HGF)POF3-620
|2 G:(DE-HGF)POF3-600
|a DE-HGF
|b Forschungsbereich Materie
|l In-house research on the structure, dynamics and function of matter
|v Neutrons for Research on Condensed Matter
|x 0
914 1 _ |y 2010
915 _ _ |0 StatID:(DE-HGF)0010
|2 StatID
|a JCR/ISI refereed
915 _ _ |0 StatID:(DE-HGF)0100
|2 StatID
|a JCR
915 _ _ |0 StatID:(DE-HGF)0111
|2 StatID
|a WoS
|b Science Citation Index Expanded
915 _ _ |0 StatID:(DE-HGF)0150
|2 StatID
|a DBCoverage
|b Web of Science Core Collection
915 _ _ |0 StatID:(DE-HGF)0199
|2 StatID
|a DBCoverage
|b Thomson Reuters Master Journal List
915 _ _ |0 StatID:(DE-HGF)0300
|2 StatID
|a DBCoverage
|b Medline
920 1 _ |0 I:(DE-Juel1)ICS-1-20110106
|g ICS
|k ICS-1
|l Neutronenstreuung
|x 0
920 1 _ |0 I:(DE-Juel1)JCNS-FRM-II-20110218
|k JCNS (München) ; Jülich Centre for Neutron Science JCNS (München) ; JCNS-FRM-II
|l JCNS-FRM-II
|x 1
920 1 _ |0 I:(DE-Juel1)JCNS-1-20110106
|g JCNS
|k JCNS-1
|l Neutronenstreuung
|x 2
970 _ _ |a VDB:(DE-Juel1)135310
980 _ _ |a VDB
980 _ _ |a ConvertedRecord
980 _ _ |a journal
980 _ _ |a I:(DE-Juel1)ICS-1-20110106
980 _ _ |a I:(DE-Juel1)JCNS-FRM-II-20110218
980 _ _ |a I:(DE-Juel1)JCNS-1-20110106
980 _ _ |a UNRESTRICTED
981 _ _ |a I:(DE-Juel1)IBI-8-20200312
981 _ _ |a I:(DE-Juel1)JCNS-1-20110106
981 _ _ |a I:(DE-Juel1)JCNS-FRM-II-20110218

LibraryCollectionCLSMajorCLSMinorLanguageAuthor
Marc 21