3D modeling of ribosomal RNA using cryo-electron microscopy density maps [Elektronische Ressource] / Alexander Jarasch. Betreuer: Roland Beckmann

Alexander Jarasch

Sujets

• Biologie

Informations

• Publié par: ludwig-maximilians-universitat_munchen
• Publié le: 01 janvier 2011
• Nombre de lectures: 22
• Poids de l'ouvrage: 19 Mo

Extrait

AlexanderErkl?VrungGutachter:DieseHilfeDissertationGutachter:wurdeHopfnerimwurdeSinneM?nchen,voneingereicht?13.Abs..325.05bzw.Diese4ohnederrbPromotionso31.03rdnunraschg31.03.2011vomD29.BeckmannJanuaDrrl-P1998Pr?fung(inrtlichederersicherungFDissertationassunselbst?ndig,gunerlaubtedereravieeitet.rtenam?nderungssatzung.2011vomJa26Dissertation.am:Novemb1.erProf.2004)rvonRolandHerrn2.Prof.Prof.Dr.rRolandKaBeckmanneterbM?ndlicheetreut.am:Ehrenw.2011?MielkPdingaMandonrtsaofT,thisS,thesisote-sphaveS,bwithineenbapublished:eThomasM,BeckBeckmanne5.5-?r,10Jean-PcaulR.Armache,xitAlexanderJPJaSchultenrasceasth4;326(5958):1369-73.,MielkAndreasO,Anger,sthofElizabofethpVilla,ofBasmaosome.Ab2010delHalicMotaal,JaThoO,rstenolypMielkthee,MaOttoraschBerninghausenS,andeRolandE,BStructureecomplexesckmannosome.StructureenbofrqueztheT,No-GoemRNAB,decaWyWilsoncomplexLoDoam34/Hbs1ribbinoundo-EMto80SaoticstalledUSA.80S16;107(46):19754-9.rib25.osomertmannNSMB,AracceptedJPArmacheAJP*T,andDN,JanascentraschchainsA*regionsandosomalAngerNSMBAM*,BeckVillaS,E,,BeckFerF,T,J,BhushanBerninghausenS,WJossinetreF,BeckmannHabmonomericeckmammalianM,withDindangr2009G,ranckFergranckMaenbV,ergeS,ThommMaBrquezrninghausenV,BeatrixMielkS?eJ,T,eThommE,M,DN,BR.ecalizationrninghauseneukO,ryBeatrixecicB,osomalS?roteinsdingaJ,cryWmapethesthofeukE,ryWilsonribDN,PNASBeckmann20R.NovCryEpubo-EMOctstruBhushanctureGaandM,rRNAM,momadehel,ofrascha,translatingeeukBerninghausenaWilsonryBeckmannoticalpha-Helical80Spribeptideosomevisualizedatdistinct5.5-?ofresolution.ribPNASeUSA.tunnel.20201010r;17(3):313-317Nover16;107(46):19748-53.BhushanEpubJa2010AOctArmache27.,ArmacheunesJP*JossinetandGumJartraschMielkA*T,andO,AngerK,AM*,esthofVillaGilmoE,R,BeckEC,erR.T,ofBhushanyS,andJossinetSec61F,interactingHabthecktranslatiM,ribDindaScience.rDecG,F2[BC]
,thesisF.haveop(Switzerlandresented,atctherRNAfolloAnnualwingJean-PinternationalWconferences:tunnelTrgesealks:andRNArticipant:2010,maps15thRNAAnnualJaMeetingJossinet,ofJ.theBeckmannRNAySoEMBOcietRNAyJa,er,Seattledelling(USA)o-EMAlexanderComputationalJayrasch2008,andofJecietan-P(Germany)aulhArmache,Armache,AndreasBeckAnger,TElizabeding,ethandVilla,rT.ofBeckriber,exitF.CourseJossinet,mpJ.2008,Sorance)eding,hE.T.WWesthof,BeckmannDanielribWilsonhigh-resolutionandPRolandaBeckmannConference,Thecrstructureo-EMofRNAa13thtrMeetinganslatingtheeukSoayryBerlinoticAlexander80Srascrib,osomeaulatF.5.5T.?er(invitedM.spopf,eakSoer)E.Pesthofosters:RolandISMB/ECCBMolecula20m09,delStotheckholmeast(Swosomaleden)andAlexandersiteJaPracticalraonscho,utationalF.biologyJossinet,CaE.(FVilla,AlexanderT.rascBeck,er,Jossinet,K.BeckSchulten,E.E.esthofWRolandesthofMoandofRolandosomalBeckmannusing3DcrymomapsdelingathisrtsofP-of2008ribBaselosomalBiologyRNABaselbased)on.Contents.I.1Intro.duction.10.1.structureRib.osomes.11.1.1..Rib.osome.structureso-electron...organization.2.3............T.............this...........database.............2.3.4...........11.1.1.1..Structure.of.th.e.bacterialssmall.riboosomal.sub.unit...........................11.1.1.2..StructureA-minorof.th.e.ar.chaeeral.large.rib.osomal.subunit..................34.........in12.1.1.3..Structures.of.bactedelingri.a.l370S3.1.rib.osomes..............39...........2.2..RNA..............13structural1.1.4..Studies.of.euk.ary.otic.80S.rib.osomes2.3.1..................31...................Rib....14.1.1.5..RNA.expansion.segmen.ts.a.n.d.v.ariable.re.gion.s......33.op.................Pseudoknots......16.1.1.6..Rib.osomal.p.ro2.4.tein.s..............2.5..and.............3..y.o-EM.particle.............3.2..cry..........18.1.2..F.unctionalAimsite41of.rib.osomes..............26.Structural.of.............................28.RNA.motifs........18.1.2.1..The.deco.di.ng.site............30.SCOR...................................2.3.2..motif............18.1.2.2..P.eptidyl.transferase.cen.ter........3.2.3.3..ose-Zipp...................................32.Kink-turn....21.1.2.3..The.rib.oso.mal.tunnel.and.tunn.el.exit.site..........2.3.5..etralo.motifs......................22.1.2.4..T.ransl.a.ti2.3.6.o.n.factor.binding.site..........................34.RNA-protein.teractions....................23.1.3..Ev.olution.of.rib35osomalRNARNAprediction.mo.........................6.Cry.microscop.38.Cry.and.ingle.analysis..................24.2..RNA.26382.1.LimitationsBasefpo-EMairing................................4..of.study.5..ContenttseII.I.motifsMaterials.and.Methoandds.42.5..CryMoo-Electronthemicroscopsegmeny.43.6..Tlaemplates.and.sequen.ces.44.6.1..Ribcryosomal.RNA.sequences................fo.RNA.......Deducing...Homology...novo.........iae.reconstruction.......60.core.euk....44ES36.2..T73emplates.for.the.large.rib.osomal.s.ubunit....W.l.RNA.........8.1.1........mo.......stru.....55....44.6.3..T8.3.emplatesoffor.the.small.ribaestivumosomalosomessubunit58.........complete.80S.....mo.otic...tomic.rib.ES1................45(h16,6.4..T.emplate.forStRNA......77...7.4..analysis.............I.51.rko.mo.and.g.52.mo.................sequence...........5445homolog6.5..T.emplates.for.structural.motifs..55.deling.tu...........RNA.deling.................t.le.............57.of45S.7.riMoondelingEM46Cry7.1..RNA.homology.mo.deling........9.2..del.ary.b.........A.of.k.osomal.tructure...9.2.2..dels.ote-sp.RNA.69.(h6)...............7346(h9,7.1.1..Structure-based.sequence.alignmen.t......ES5...............9.2.2.4.....................46.7.1.2.48S2SVisualization.structure...........................50.I.Results.8..o.w.r.de.ing.tting.r.e.molecules.8.1..homology.deling..................47.7.2..De.novo.mo.deling.of53RNAStructure-based.alignmen.......................8.1.2..the.y.del.........................8.1.3..mo.of47c7.2.1.ralSecondary.structure.p.rediction.of.RNA..........8.2..de.mo..........................47.7.2.2..T.ertiary55structureRenemenmoanddelingexibofttingRNARNA.........................9..del.T..and.cerevis.80S.b.based.high-resolution47o-7.2.3.structuresAssem9.1.bleo-EM.................................58.Near.mo.of.euk.otic.ri.osome.................9.2.1..tomic.del.the48u7.3.aryFittingribandRNArenemenst.of.RNA.mo68delsA.mo.for.ary.ecic.osomal.expansion.ts.9.2.2.1..S..............................48.7.3.1.9.2.2.2.AssemSbleh10)renemen.t..........................9.2.2.3..S.h17)...........................75.ES648(h21)7.3.2..Molecular.Dynamics.Flexib.le.Fitting.(MDFF)..................6.L L
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osomal...........functional.Mo.discussion...............the...(H98)79E9.2.2.6.bES8theS.(h33)..c...site.114.............103.............and.........In...et.Motion...10..80S..80.9.2.2.7..ES9.SThe(h39)....rib...osomal...........r.........9.2.2.23..................S......110......81of9.2.2.8..ES10.S.(h41)S.....111.T............r.euk.10.1..........ding...................e....82.9.2.2.9.teractionES12tS.(h44)euk.......10.3.1..and.....123.eli.tting.E.................S39...............107..83.9.2.2.10..ES.3.../.ES49.3..w(H9,erH10)aestivum.........Comparison.o-EM...........9.3.2..segmen...........110.of.ES6....84.9.2.2.11..E.S5Comparison.een.(H15,andH16-H18)evisiae.112.ES27...............r.retation.of.ry.osome.deco.the...............The86.9.2.2.12..E.S7...of.T..aestivum..114...................115.of.ary.tunnel...........10.2.1..the.with.hains....8810.3.9.2.2.13.oticESexit7...of.S..c.er.evisiaeteraction.c.............Conclusion.11..e.deling.130.9.2.2.22..S31.(H79)..................90.9.2.2.14..ES.9...(H31,105H28-H30)E.................................9.2.2.24..S41(H101)..............92.9.2.2.15..ES.10.../.ES12..109(H38)Comparison.et.een.c.evisiae.T....................9.3.1..of.cry.densities............94.9.2.2.16..ES.15.(h26)110(H45)Comparison.expansion.ts.......................9.3.2.1..teraction.ES3.and.S.....................9.3.2.2.96b9.2.2.17.wEES7S19inSaestivum(H52)S..er.....9.3.2.3..of.L...........................113.Molecula.inte.p.of.sites.the.a.otic.rib971149.2.2.18.TheEdingS20andES7PTC/.ES26.9.2.2.5..(H54,.H55)....................10.1.1..deco.site..................98.9.2.2.19..E.S24.ts.(H59)....10.1.2..PTC.....................................10.2..del.th.euk.otic.osomal....99.9.2.2.20..E.S27.ten.of.T..aestivum....116.In.of.rib.tunnel.nascen.c...........116.The.ary.rib.tunnel.site..........100.9.2.2.21..E.S27.Con.the.exit120.In.of10.4.protein-conductingThannelfactorsitetunnelofsiteS..c121erCanonicalevisiaeranslation.binding.........................IV..and.129.Pip.n.fo.mo.and.RNA.7.EvConnnelten.ts.12..Molecula.rsitemo.del.of.the.80S.rib.osome.134.12.1..Ev.a.l.uation80Sof.RNAdingmo.dels12.3.2.for.the144euk.a.ry.otic.rib.osome......Summa.......unctional.......143.d......135otic12.1.1..Comparison.to.thearyRNA.mo.del.oftranslationthe.mammalian.80S12.4.rib.osome........osomes..135.12.1.2..Comparison.to.the.RNA.mo.del.of.the.Thermomyc12.3.esonlanuginosusosome80S.ri-.b.osome......The.a.PTC.............euk.osomal.............The.tunnel.............12.3.4..binding...........olution....135.12.1.3..Comparison.to.the.X-ra.y.structure147ofofthe.S..c.er.evisiae.80S.ri.b.osome148at1504.5.?.138.12.2..The.rib.osomal.expan.sion.segmen.ts.and.v.ariabl142eFregionssites.the.rib..........................14012.3.1.12.2.1.decoInsiteteractionnbtheet.w.een.ES3.S.and.ES6.S..........143.The.ary.rib.tu........................14012.3.3.12.2.2.eukExpansionoticsegmenexitt.ES6.S....................146.Canonical.factor.site...................147.Co-ev......141.12.2.3..Expansion.segmen.t.ES7.L......................12.5..olution.rib............................142.12.2.4..Expansion.segmen13.tryES278L 98%
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