000020685 001__ 20685
000020685 005__ 20240619091951.0
000020685 0247_ $$2pmid$$apmid:22404933
000020685 0247_ $$2pmc$$apmc:PMC3296038
000020685 0247_ $$2DOI$$a10.1016/j.bpj.2012.01.002
000020685 0247_ $$2WOS$$aWOS:000301280900017
000020685 0247_ $$2MLZ$$aSmolin20121108
000020685 037__ $$aPreJuSER-20685
000020685 041__ $$aeng
000020685 082__ $$a570
000020685 084__ $$2WoS$$aBiophysics
000020685 1001_ $$0P:(DE-HGF)0$$aSmolin, N.$$b0
000020685 245__ $$aFunctional domain motions in proteins on the 1 - 100 ns timescale: Comparison of neutron spin echo spectroscopy of phosphoglycerate kinase with molecular dynamics simulation
000020685 260__ $$aNew York, NY$$bRockefeller Univ. Press$$c2012
000020685 300__ $$a1108 - 1117
000020685 3367_ $$0PUB:(DE-HGF)16$$2PUB:(DE-HGF)$$aJournal Article
000020685 3367_ $$2DataCite$$aOutput Types/Journal article
000020685 3367_ $$00$$2EndNote$$aJournal Article
000020685 3367_ $$2BibTeX$$aARTICLE
000020685 3367_ $$2ORCID$$aJOURNAL_ARTICLE
000020685 3367_ $$2DRIVER$$aarticle
000020685 440_0 $$0882$$aBiophysical Journal$$v102$$x0006-3495$$y5
000020685 500__ $$aThe research was sponsored by the Laboratory Directed Research and Development Program of Oak Ridge National Laboratory, managed by UT-Battelle, LLC, for the U.S. Department of Energy under contract No. DE-AC05-00OR22725. This research used resources of the National Energy Research Scientific Computing Center, which is supported by the Office of Science of the U.S. Department of Energy under contract No. DE-AC02-05CH11231.
000020685 520__ $$aProtein function often requires large-scale domain motion. An exciting new development in the experimental characterization of domain motions in proteins is the application of neutron spin-echo spectroscopy (NSE). NSE directly probes coherent (i.e., pair correlated) scattering on the ~1-100 ns timescale. Here, we report on all-atom molecular-dynamics (MD) simulation of a protein, phosphoglycerate kinase, from which we calculate small-angle neutron scattering (SANS) and NSE scattering properties. The simulation-derived and experimental-solution SANS results are in excellent agreement. The contributions of translational and rotational whole-molecule diffusion to the simulation-derived NSE and potential problems in their estimation are examined. Principal component analysis identifies types of domain motion that dominate the internal motion's contribution to the NSE signal, with the largest being classic hinge bending. The associated free-energy profiles are quasiharmonic and the frictional properties correspond to highly overdamped motion. The amplitudes of the motions derived by MD are smaller than those derived from the experimental analysis, and possible reasons for this difference are discussed. The MD results confirm that a significant component of the NSE arises from internal dynamics. They also demonstrate that the combination of NSE with MD is potentially useful for determining the forms, potentials of mean force, and time dependence of functional domain motions in proteins.
000020685 536__ $$0G:(DE-Juel1)FUEK505$$2G:(DE-HGF)$$aBioSoft: Makromolekulare Systeme und biologische Informationsverarbeitung (FUEK505)$$cFUEK505$$x0
000020685 536__ $$0G:(DE-HGF)POF2-544$$a544 - In-house Research with PNI (POF2-544)$$cPOF2-544$$fPOF II$$x1
000020685 588__ $$aDataset connected to Web of Science, Pubmed
000020685 650_2 $$2MeSH$$aDiffusion
000020685 650_2 $$2MeSH$$aMolecular Dynamics Simulation
000020685 650_2 $$2MeSH$$aMovement
000020685 650_2 $$2MeSH$$aNeutron Diffraction: methods
000020685 650_2 $$2MeSH$$aPhosphoglycerate Kinase: chemistry
000020685 650_2 $$2MeSH$$aPhosphoglycerate Kinase: metabolism
000020685 650_2 $$2MeSH$$aProtein Structure, Tertiary
000020685 650_2 $$2MeSH$$aRotation
000020685 650_2 $$2MeSH$$aSaccharomyces cerevisiae: enzymology
000020685 650_2 $$2MeSH$$aScattering, Small Angle
000020685 650_2 $$2MeSH$$aTime Factors
000020685 650_7 $$0EC 2.7.2.3$$2NLM Chemicals$$aPhosphoglycerate Kinase
000020685 650_7 $$2WoSType$$aJ
000020685 693__ $$0EXP:(DE-MLZ)KWS2-20140101$$1EXP:(DE-MLZ)FRMII-20140101$$5EXP:(DE-MLZ)KWS2-20140101$$6EXP:(DE-MLZ)NL3ao-20140101$$aForschungs-Neutronenquelle Heinz Maier-Leibnitz$$eKWS-2: Small angle scattering diffractometer$$fNL3ao$$x0
000020685 7001_ $$0P:(DE-Juel1)130542$$aBiehl, R.$$b1$$uFZJ
000020685 7001_ $$0P:(DE-HGF)0$$aKneller, G.B.$$b2
000020685 7001_ $$0P:(DE-Juel1)130917$$aRichter, D.$$b3$$uFZJ
000020685 7001_ $$0P:(DE-HGF)0$$aSmith, J.C.$$b4
000020685 773__ $$0PERI:(DE-600)1477214-0$$a10.1016/j.bpj.2012.01.002$$gVol. 102, p. 1108 - 1117$$p1108 - 1117$$q102<1108 - 1117$$tBiophysical journal$$v102$$x0006-3495$$y2012
000020685 8567_ $$2Pubmed Central$$uhttp://www.ncbi.nlm.nih.gov/pmc/articles/PMC3296038
000020685 909CO $$ooai:juser.fz-juelich.de:20685$$pVDB
000020685 915__ $$0StatID:(DE-HGF)0010$$2StatID$$aJCR/ISI refereed
000020685 915__ $$0StatID:(DE-HGF)0100$$2StatID$$aJCR
000020685 915__ $$0StatID:(DE-HGF)0110$$2StatID$$aWoS$$bScience Citation Index
000020685 915__ $$0StatID:(DE-HGF)0111$$2StatID$$aWoS$$bScience Citation Index Expanded
000020685 915__ $$0StatID:(DE-HGF)0150$$2StatID$$aDBCoverage$$bWeb of Science Core Collection
000020685 915__ $$0StatID:(DE-HGF)0199$$2StatID$$aDBCoverage$$bThomson Reuters Master Journal List
000020685 915__ $$0StatID:(DE-HGF)0200$$2StatID$$aDBCoverage$$bSCOPUS
000020685 915__ $$0StatID:(DE-HGF)0300$$2StatID$$aDBCoverage$$bMedline
000020685 915__ $$0StatID:(DE-HGF)0310$$2StatID$$aDBCoverage$$bNCBI Molecular Biology Database
000020685 915__ $$0StatID:(DE-HGF)1030$$2StatID$$aDBCoverage$$bCurrent Contents - Life Sciences
000020685 915__ $$0StatID:(DE-HGF)1050$$2StatID$$aDBCoverage$$bBIOSIS Previews
000020685 9141_ $$y2012
000020685 9132_ $$0G:(DE-HGF)POF3-552$$1G:(DE-HGF)POF3-550$$2G:(DE-HGF)POF3-500$$aDE-HGF$$bKey Technologies$$lBioSoft  Fundamentals for future Technologies in the fields of Soft Matter and Life Sciences$$vEngineering Cell Function$$x0
000020685 9132_ $$0G:(DE-HGF)POF3-623$$1G:(DE-HGF)POF3-620$$2G:(DE-HGF)POF3-600$$aDE-HGF$$bForschungsbereich Materie$$lIn-house research on the structure, dynamics and function of matter$$vNeutrons for Research on Condensed Matter$$x1
000020685 9131_ $$0G:(DE-HGF)POF2-544$$1G:(DE-HGF)POF2-540$$2G:(DE-HGF)POF2-500$$3G:(DE-HGF)POF2$$4G:(DE-HGF)POF$$aDE-HGF$$bStruktur der Materie$$lForschung mit Photonen, Neutronen, Ionen$$vIn-house Research with PNI$$x0
000020685 9201_ $$0I:(DE-Juel1)ICS-1-20110106$$gICS$$kICS-1$$lNeutronenstreuung$$x0
000020685 9201_ $$0I:(DE-Juel1)JCNS-1-20110106$$gJCNS$$kJCNS-1$$lNeutronenstreuung$$x1
000020685 970__ $$aVDB:(DE-Juel1)136331
000020685 980__ $$aVDB
000020685 980__ $$aConvertedRecord
000020685 980__ $$ajournal
000020685 980__ $$aI:(DE-Juel1)ICS-1-20110106
000020685 980__ $$aI:(DE-Juel1)JCNS-1-20110106
000020685 980__ $$aUNRESTRICTED
000020685 981__ $$aI:(DE-Juel1)IBI-8-20200312
000020685 981__ $$aI:(DE-Juel1)JCNS-1-20110106