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Publié par | technische_universitat_dresden |
Publié le | 01 janvier 2009 |
Nombre de lectures | 23 |
Langue | English |
Poids de l'ouvrage | 14 Mo |
Extrait
Investigationofstructuralpropertiesin
biomolecularsystemsusing
synchrotron-basedspectroscopies
Dissertation
zurErlangungdesakademischenGrades
Doctorrerumnaturalium
(Dr.rer.nat.)
vorgelegtderFakulta¨tMathematikundNaturwissenschaftender
TechnischenUniversita¨tDresdenvon
Dipl.-Phys.KurtKummer
geborenam27.Dezember1982inSchwedt/Oder
Eingereichtam25.November2009
DieDissertationwurdeinderZeitvonOktober2007bisNovember2009
amInstitutfu¨rFestko¨rperphysikangefertigt.
Gutachter:
rP.fo
.forP
.rD
.rD
Clemens
Laubschat
Eckhardt
lhu¨R
(UF
UT(
Dresden)
Berlin)
Abstract
Solidstateapproachestostructuralpropertieslikediractionormicroscopytech-
niquesoftencannotbeappliedtobiomolecularsystems,atleastnotwithoutspecialpost-
preparationwhichoftencorruptsthedesiredpropertiesofthepristinesystems.Inthis
workthecapabilitiesofsynchrotron-based,softX-rayspectroscopiesasanalternativeway
tounravelstructuralpropertiesofsuchsystemsaretested.Tothisend,threeexemplary
systemswereinvestigatedeachwiththefocusonanotherfacetandcharacteristiclength
scale.TherstexampleareDNA-alkanethiolself-assembledmonolayers,alsoknownas
DNAmicroarraysorDNAchips,forwhichawaytomonitorandcontrollablytunethe
structuralcompositiononthemesoscopicscaleofmanythousandsofmoleculeswassought
for.Thesecondexamplefocusesonthesingle-moleculeandsubmolecularscaleinmetal-
proteinhybridcompoundswiththeaimtoidentifythebindingsiteofmetalatomsorions
withinproteinmoleculesandtheunderlyinginteractionmechanisms.Themostfundamen-
talstructuralscale,thelevelofsinglebondsandmolecularorbitals,isaddressedinthe
lastexamplewhereitwastriedtoelaborateanapproachtomapthetopologyofmolecular
orbitalsbaseduponX-rayabsorptionproperties.Thisapproachwasputtothepractical
testforthecharacteristic*peptideorbitalsinproteinbackbones.Forallthreeinvestigated
examples,spectroscopiesusingsoftX-raysynchrotronradiationwereabletoextractthe
desiredinformation,thusconrmingthattheymaygrantalternativeaccesstostructural
propertiesofsoft-mattersystemsincaseswherestandardapproachesfail.
Kurzfassung
KlassischeFestko¨rpertechnikenzurStrukturuntersuchung,wieStreu-oderMikrosko-
piemethoden,ko¨nnenha¨ugnichtaufBiomoleku¨lsystemeangewandtwerden,zumindest
nichtohnespeziellePostpra¨paration,diedieurspru¨nglichenEigenschaftendieserSysteme
oftverfa¨lscht.IndieserArbeitsolluntersuchtwerden,inwieweitRo¨ntgenspektroskopien
basierendaufSynchrotronstrahlungeinenalternativenZugangzuStruktureigenschaften
solcherSystemebieten.DazuwurdendreiSystemeexemplarischuntersucht,jeweilsmit
SchwerpunktaufeinenanderenAspektundcharakteristischenLa¨ngenbereich.Fu¨rselbst-
organisierendeDNA-Alkanthiol-Schichten,sogenannteDNA-Chips,wurdenacheineWeg
gesucht,ihrestrukturelleZusammensetzungaufdermesoskopischenEbenevielertausend
Moleku¨lezubestimmenundkontrolliertzumodizieren.MetallisierteProteinstrukturen
wurdenaufEinzelmoleku¨l-bzw.submolekularerEbeneuntersucht,mitdemZiel,dieOrte
derMetallanlagerunginnerhalbdesProteinsunddiezugrundeliegendenWechselwirkungs-
mechanismenzuidentizieren.DieunterstestrukturelleEbene,derBereicheinzelne
BindungenundMoleku¨lorbitale,wurdeadressiertamBeispielder*peptideOrbitaledes
Proteinru¨ckrats.Dafu¨rwurdeeineMethodezurKartographierungeinzelnerOrbitalean-
handvonRo¨ntgenabsorptionseigentschaftenherausgearbeitetundpraktischgetestet.In
allendreiFa¨llenkonntenRo¨ntgenspektroskopiendieno¨tigenInformationenliefernund
damitihrPotentialfu¨rStrukturuntersuchungeninweicherMaterieunterBeweisstellen.
Contents
1Preface
3
2Synchrotron-basedspectroscopiesinthesoftX-rayrange5
2.1Photoelectronspectroscopy..........................5
2.1.1Basicprinciples.............................5
2.1.2Core-levelenergyshiftsinphotoemissionspectra...........7
2.1.3Analysisofcore-levelPEspectra...................10
2.1.4Instrumentation.............................12
2.2X-rayabsorptionspectroscopy.........................15
2.2.1Crosssectionandoscillatorstrength.................15
2.2.2CharacteristicsofX-rayabsorptionspectra..............17
2.2.3DetectionofX-rayabsorptionsignals.................25
3MonitoringandtuningstructuralpropertiesinDNAmicroarrays:Alook
intoself-assembledstructuresofbiomoleculesonthemesoscopicscale29
3.1Introduction...................................29
3.2XPScharacterizationofmercaptohexanolself-assembledmonolayers...31
3.3Core-levelelectronicstructureofDNA....................35
3.4TuningtheprobedensityinmixedDNA-MCHmonolayers.........40
3.5InuenceofthesolventtypeontheDNA-SAM...............45
3.6CompetitiveinterplaybetweenMCHandthiolizedDNA..........47
3.7Summary....................................50
4Modicationofthepeptidebondbyatomicandioniccalcium:Metal
bindingmechanisminproteinstructures51
4.1Introduction...................................51
4.2Bindingsiteofcalciumintheproteinstructure...............53
4.2.1Experimentalresults..........................53
4.2.2Abinitiocalculations..........................59
4.3Evidenceforcalciumpenetrationintotheproteinlayer...........61
4.4Chemicalkineticsofthemetalbindingreaction...............63
4.5Conclusions...................................67
1
5Oscillatorstrengthofthe1s!*X-rayabsorptionresonancesofthe
peptidebond:Anapproachtomappingofindividualmolecularorbitals69
5.1Introduction...................................69
5.2Characterizationandrenementofthebeamlinephotonux........70
5.2.1Beammonochromatization.......................70
5.2.2Photonux...............................73
5.3SpectraldependenceoftheX-rayabsorptionofproteins...........75
5.4Finestructureofthe1sX-rayabsorptionedgesinproteins.........77
5.4.1N1sabsorptionedge..........................77
5.4.2C1sabsorptionedge..........................79
5.4.3O1sabsorptionedge..........................80
5.5AbsoluteX-rayabsorptioncrosssectionsandoscillatorstrengths......82
5.5.1Normalizationtotheabsolutescale..................82
5.5.2Oscillatorstrengthofthepeptidebondresonances..........84
5.6Correlationbetweenoscillatorstrengthsandtheorbitaltopology......87
5.7Conclusions...................................89
6Summary91
Bibliography93
AExperimentaldetails105
A.1Beamlinesandexperimentalend-stations...................105
A.1.1Russian-GermanbeamlineatBESSYII................105
A.1.2BeamlineD1011attheMAX-labfacility...............106
A.2Samplepreparation...............................106
A.2.1Mercaptohexanolself-assembledmonolayers.............106
A.2.2GenomicDNA.............................107
A.2.3DierentMgCl2concentrations....................107
A.2.4Dierenttypesofsolvent........................107
A.2.5SimultaneousDNAimmobilizationandSAMformation.......108
A.2.6BacterialsurfaceproteinlayersonSiOx/Si..............108
Acknowledgments111
Eigensta¨ndigkeitserkla¨rung113
1
Preface
Sinceabout20yearsagowhenbiotechnologyandorganicsemiconductortechnologiesbegan
toriseresearchintoorganicandbiomoleculeshasfoundarenaissanceandhasconstantly
intensiedeversince.Todaythesesystemsaresubjecttooneofthemostlivelybranchesof
materialscienceandtheinexhaustiblefundoforganiccompoundsmakesthemanoceanic
poolfordiversetechnologicalapplicationsspanningvariousimaginableeldsfromorganic
solarcellsandLEDsoverbiosensorstomolecularcomputing.Themainreasonforthis
successisthatthesenewmaterialsdorevealnumerousnewanduniquepropertieswhen
comparedtohithertoemployedinorganiccompounds.
Oneandpossiblythemoststrikingprincipallynewaspectoforganicandbiological
systemsistheircapabilitytoself-organizeintoevenhighlycomplexfunctionalstructures.
Withthatbottom-upfabrication,i.e.theself-assemblyofentiretechnologicalunitsfrom
soluteswithoutexternalsteering,comesintosight.Naturally,thedevelopmentandpur-
posefulapplicationofsuchrevolutionarynewfabricationmethodswouldalwaysrequirea
waytomonitorcompositionandpropertiesoftheresultingnanoscopicstructures.Unfor-
tunately,thosetechniquesthatareroutinelyappliedtocharacterizestructuralproperties
of”classical”,inorganicsystemsareinmanycasesnotwell-suitedforthispurpose.Re-
ciprocalorreal-spaceimaging,i.e.diractionorhigh-resolutionmicroscopytechniques,
reachtheirlimitationswhenitcomestosoftmatterstructures.Microscopicstudiesare
oftennotsuitable,becausetheyarerelativelyslow,notchemicallyselectiveandrequire
specialpost-preparationofthesamples,whichrulesthemoutforinsitumonitoringofthe
formationprocessofsuchstructures.Theabsenceof3-dimensionalcrystallineorder,on
theotherhand,oftenprecludestheuseofdiractionmethods.1
Incertaincasestheapplicationofsynchrotron-basedspectroscopiescouldopenan
alternativepathwaytowardsthedesiredstructuralinformation.Althoughthesespectro-
scopiesaddresstheelectronicratherthanthespatialstructureofmattertheycanalso
providewithsomeinsightintothelatterbecauseoftheclosecorrelationbetweenboth.In
thepresentwork,thecapabilityofspectroscopiesusingsoftX-raysynchrotronradiation
forstructuralcharacterizationofbiomolecularsystemsistestedatthreedistinctexam-
1Notethat,todate,X-raydiractionisthemajortooltoexplorethespatialstructureofproteins.
However,itsapplicationisboundtotheavailabilityofspeci