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外文翻译-- The Morphology Prediction of Lysozyme Crystals Deduced from the BFDH Law and.PDF

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外文翻译-- The Morphology Prediction of Lysozyme Crystals Deduced from the BFDH Law and.PDF

TheMorphologyPredictionofLysozymeCrystalsDeducedfromtheBFDHLawandAttachmentEnergyModelBasedontheIntermolecularInteractionZhanzhongWang,PingpingJiangSchoolofAgricultureandBioengineeringTianjinUniversityTianjin300072,PeoplesRepublicofChinawzz7698tju.edu.cnLepingDangSchoolofChemicalEngineeringandTechnologyTianjinUniversityTianjin300072,PeoplesRepublicofChinadlepinghotmail.comAbstractThecrystalmorphologyoforthorhombiclysozymeispredictedusingtheBravaisFriedelDonnayHarkerBFDHandtheattachmentenergyAEmodelsofmolecularsimulationsoftwareCerius2invacuo.Themorphologypredictedbytwomodelsisapproximatelyconsistent.ThemorphologypredictedbyAEmodelisingoodagreementwiththemorphologyofcrystalsgrownfromsolutionatpH6.5.Themaincrystalfaces{011},{101}and{110}areobservedinmorphologypredictedbyAEmodel.BycleavingrevealablecrystalfacesinmorphologypredictedbyAEmodel,surfacechemistryvisualizationandtheoreticalanalysisbasedoninteractionofinintramoleculesorintermoleculesfortheimportantmorphologicalformsareperformed.TheresultshowsthatsterichindranceandHbandinteractionplayscriticalrolefortheplatelikemorphologyoforthorhombiclysozyme.KeywordslysozymemorphologypredcitionmodelingIntermolecularInteractionINTRODUCTIONTheshapeofacrystalisgovernedbytherelativegrowthratesofeachofthecrystalfacespresent.Themostprominentfaceofacrystalistheslowestgrowing,whilethesmallestfaceisthefastestgrowing.Thus,themorphologicalimportanceofaparticularfaceisinverselyproportionaltothegrowthrateofcrystalface.Identificationofpossiblegrowthdirectionsorfacesisthefirstpartofmorphologyprediction1.EarlyworkincrystalmorphologypredictionwasundertakenbyGibbsin1875inwhichheproposedthattheshapeofacrystalwillbeonetominimizethetotalfreeenergyassociatedwiththesurfaceenergiesofthegrowncrystal.LaterBravais,Friedel,andDannayandHarker1,2proposedmorphologicalsimulationsbasedmerelyoncrystallatticegeometry.TheBFDHlaw,substantiatedbyempiricalobservation,proposedthatthecrystalwillbeformedbyfacesboundingthedirectionsofthegreatestinterplanarspacingofthecrystallattice.Accordingtothislaw,thelargertheinterplanardistancedhklis,thelargerthemorphologicalimportanceMIofthecorrespondinghklfaceis.Thus,basedonunitcellparameters,spacegroupandhence,extinctioncondition,andthereciprocaloftheinterplanardistances1/dhkl,usedasthedistancesfromthecentreofthecrystaltotherespectivehklsurfaces,onemayobtainatheoreticalBFDHmorphology.TheBFDHmethodestimatesthemorphologyfromthecrystalsymmetryandthelatticeparameterswithouttakingintoaccountthechemicalnatureandpackingoftheatomsormoleculesthatformthecrystalandneglectingthepossibilityofspecificenergeticinteractionsbetweenthesurfaceatomsinfluencingthecrystalmorphology.Itmaybeusedasaquickscreeningtooltoestimatethehabitofacrystal.In1955,HartmanandPerdokproposedperiodicbondchainPBCtheorytoaccountforenergyinteractionsbetweencrystallizingspeciesinthederivationofcrystalmorphology.LaterthistheorywasfurtherdevelopedbyHartmanandHartmanandBennema3.APBCisastrongbondbetweenmoleculesrunningparalleltoacrystallographicdirection.AcrystalismadeofanetworkofPBCshavingdifferentenergiesdependingonthebondenergybetweenthemoleculestheycontain.Consequently,itispossibletoclassifythePBCsasafunctionoftheirenergyanddistinguishstrongPBCsfromweakPBCs4.Growthrateisrelatedtodirectionofbondchainandthefastestdirectionofcrystalgrowthisthatofthestrongestchemicalbond.In1980,basedonPBCmodel,HartmanandPerdokproposedattachmentenergymodel.Buildonincorporatingenergytermsinthecalculationofthetheoreticalcrystalmorphology,advancesinmorphologypredictionwererealizedwhencrystalgrowthwasviewedastheattachmentofslicesorlayersoforderedmoleculestoanexistingcrystalface1.Thisconcept,knownastheattatchmentenergyAEmethod,requiresthedeterminationofthelatticeandsliceenergiesforcalculationoftheattachmentenergyineachimportantcrystallographicdirection.Thisattachmentenergydirectlyinfluencesthemacroscopicshapeofthecrystal4.Thelatticeenergyistheenergycalculatedbysummingpairinteractionsfortheentire,perfectcrystal.Theenergyreleasedontheformationofagrowthsliceofthickness,dhkl,isthesliceenergy,whiletheenergyreleasedontheattachmentofagrowthslicetothecrystalsurfaceistheattachmentenergy.Thetermofinterestformorphologicalpredictionsistheattachmentenergyofeachcrystalface.Subtractingthesliceenergyforeachfacefromthelatticeenergyprovidestheattachmentenergyforeachofthefaces.Therelativegrowthrateforeachfacewastakentobeproportionaltoattachmentenergyandhencefaceswiththelowestattachmentenergieswerepredictedtobetheslowestgrowingsurfacesandhencetohavethehighestmorphologicalimportance5.Thenamecrystallogenesisarosewhenitbecameevidentthatthefieldofcrystallizationofproteinsandotherbiologicalmacromoleculeswasnotrestrictedsimplytocrystalproductionfordiffractionstudies,butitencompassed,infact,allphasesofstructuralbiology,fromproteinexpressionandpurification,torecordingofdiffractiondata.Withregardto9781424447138/10/25.00©2010IEEEbiologicalmacromolecule,Xraycrystallographyhasplayedafundamentalroleinconnectingthedotsbetweengenomicdataandbiologicalfunctionbyprovidingaccuratestructuralinformationtoresolveseveralsignificantresearchproblems.TheearliestXraydiffractionstudiesofthestructuresofbiologicalmacromoleculesbeganintheearlypartofthe20thcentury,verylittleprogresshasbeenmadeinourunderstandingofhowtofacilitatetheprocessofcrystallizingsuchmacromoleculesforstructuralanalyses.Asaresult,obtaininghighqualitymacromolecularcrystalsremainsdifficult,unpredictable,andfrustratingandbecomespersistentbottlenecktothegreaterapplicationofXraycrystallographyinstructuralbiology6,7.SolvingproteinstructuresbyXraycrystallographyiscontingentupontheavailabilityofordered,diffractionqualitycrystals8.Inthefieldofcrystalgrowth,inordertoobtainhighqualitylaboratorygrowncrystals,theresearcherwhoisinterestedincrystalmorphologyoftenneedstovisualizeacrystalhabitresultingfromasetofobservedorcalculateddata,suchasgrowthrates,surfaceenergiesandhabitcontrollingfactors.Crystallizationiseffectedviamolecularrecognitionattheinterfacebetweenthegrowingcrystalanditsmotherphase.Sucheffectshavelongbeenobservedandhavebeenrelatedtogrowthsolutionthermodynamics,specificfacestructureandgrowthmechanism,andmolecularrecognitionprocessatspecificplanes9.Increasedunderstandingofcrystalgrowthfromsolutioncanenhancetheperformanceoftheseparationandpurificationprocessesinmanyindustries.Althoughthecrystalgrowthhabitdiffersfromthetheoreticalmorphologyduetotheinfluenceofcrystalgrowthenvironment,thecrystalmorphologyisverymuchconnectedwiththecrystalstructure.Crystalmorphologyhasbeenthefocusofnumerousresearchefforts1012.Crystallizationofheneggwhitelysozymehasalreadybeenstudiedforsomeyearssinceitisanidealmodelsystemforcrystallizationofproteinsingeneral.Otherkindsoflysozymecrystalshaveseldombeenused,exceptforthetheorthorhombicform13.Themorphologyanalysisoftheorthorhombiclysozymecrystalsmayincreaseourknowledgeofcrystalgrowthoflysozymetoinstructtoobtainhighqualitycrystals,whichcanbeappliedstructuralanlysistoprovideaccurateinformationforgenomicdataandbiologicalfunction.Theaimofthepresentresearchiswastoapplyadvancedmolecularmodellingtechniquestosimulatethetheoreticalcrystalmorphologyoforthorhombiclysozyme,andcomparesthetheoreticalmorphologywithactualhabitoflysozymecrystalgrowninanaqueoussolution.Inthecourseofrefiningthemodel,valuableinformationconcerningmolecularinteractionswithinthelysozymecrystalwasextractedfromthesimulation.EXPERIMENTALANDCOMPUTATIONALMOLECULARMODELINGMETHODOLOGYMaterialsHeneggwhitelysozyme,recrystallizedandlyopholizedwaspurchasedfromSigmaandusedwithoutfurtherpurification.Itsmolecularweightwasassumedtobe14.3kgmol1.Otherchemicalreagentswereanalyticalpurity.DistilleddeionizedwaterofHPLCgradewasused.Crystallizationexperimentandmicroscopymeasurement.Proteinwaterstocksolutionswithproteinconcentrationof1020wereprepared,andtheirmeasuredpHwas6.5orslightlyhigher.Ifnecessary,pHwasloweredto6.5bysmalladditionsofHClaqueoussolutions.Supersaturatedsolutionswereobtainedbymixingproteinwaterstocksolutionswithconcentratedsaltwaterstocksolutions.Astocksolutionofsodiumacetatebuffercontaining0.02sodiumazidewasalsoaddedtominimizepossiblepHchanges.Thesupersaturatedsolutionswerethenleftat4°C315daysdependingonsamplesupersaturationtoproducecrystals.Amicroscopicobservationofthecrystalmorphologywascarriedouttakingadvantageofelectronicmicroscopy.DigitalimagesanalysiswasperformedusingaPanasonicLumixDMCFZ20systemoperatingthePanasonicimageanalysisconnectedtoa3CCDcolorvisioncameramountedonanOlympusBH2opticalmicroscope.Cerius2modelingCrystalstructuresdataoforthorhombiclysozymewasachievedbyProteinDataBanktocalculatetheoreticalmorphology.Experimentalmorphologywasusedtocomparewiththeresultofthesimulatedtheoreticalmorphology.CrystalMorphologyPredictionUsingBFDHandAEmodelClassicmolecularmechanicsanddynamicssimulationswerecarriedoutusingtheCerius2softwarepackage.Thecrystalbuilder,molecularmechanics,andmorphologypredictionmoduleswereemployedtoaccomplishthemodelinggoalsofthisresearch.Universalforcefieldwasused.RESULTSANDDISCUSSIONStructureanalysisThecrystalstructureoflysozymereportedincludedorthorhombic,monoclinic,tetragonalandtriclinicforms,whichhasbeenresolvedusingXraydiffractionstudies.Inoursimulations,thecrystalstructureoftheorthorhombiclysozymewasobtainedfromtheProteinDataBank14.ThesterestructureoflysozymemoleculeisshowninFigure1.Theunitcellofitscrystalstructureareasfollowsa30.47,b59.39,c68.78,αβγ90°,andspacegroupisP212121,whichisshowninFigure2.Figure1.Thesterestructureoflysozymemoleculeballandstickstyleleft,stickstylerightFigure2.TheunitcelloforthorhombiclysozymeMorphologypredictionbyBFDHmodelStructureanalysisThethreefaces{110},{002},{011},{101}dominatedthecrystalhabitasrevealedfromtheBFDHmorphologicalprediction.TheresultsaresummarizedinTableⅠ.AccordingtoBFDHlaw,thelargertheinterplanardistancedhklis,thelargerthemorphologicalimportanceMIofthecorrespondinghklfaceis.FromtheTable1,itcanbeseenthatdhklof{011}faceisthelargestanditsfacetareais63.49oftotalfacetarea,whichmeans{011}faceownsthelargestthemorphologicalimportanceMI.Thedhklof{101}faceisslightlylargerthan{110}faceanddhklof{002}isthesmallest.CrystalmorphologypredictedbyBFDHmodelcanbededucedandwasshowninFigure3a,revealingallfaceswhichbelongtothecrystallographiczones{110},{002},{011},and{101},respectively.FromFigure3a,thereisawellagreementwithcalculationresultinTable1.The{011}facewasfoundtobethelargestinarea,subsequently{101}face,{110}faceand{002}face.TABLEⅠ.CALCUTIONRESULTSOFBFDHMODELhklMultiplicitydhklTotalfacetareaTotalfacetarea/{011}444.9590.9763.49{002}234.399.0406.309{101}427.8626.8718.75{110}427.1116.4111.45MorphologypredictionbyAEmodelTheresultsofattachmentenergycalculationswerereportedinTableⅡ.Basedonattachmentenergymodel,theMIsequenceisbasedontheassumptionthatthegrowthratesoffacesareproportionaltoattachmentenergy.Hence,thegreaterattachmentenergy,thefasterthecorrespondingfacegrowsandthesmalleritsmorphologicalimportance.Oncetherelativegrowthratesofthesignificantfacesareknown,amacroscopicimageofthecrystalmorphologycanbepostulated.CrystalmorphologypredictedbyAEmodelcanbededucedandwasshowninFigure3b.ThemorphologyFigure3apredictedbyBFDHmodelisapproximatelyconsistentwiththatpredictedAEmodel.Themaindifferencesexistindisappearanceof{002}faceinAEmodel.FromTableⅡandFigure3b,itcanbeseenthatthereisagoodcorrelationbetweengrowthfaceareaandtheattachmentenergyofthedominantface.Themorphologypredictedisplatelike,suggestingthatasinglefaceisindeeddominatingtheoverallcrystalgrowth.Inthesecases,themostdominantfacehasanattachmentenergywhoseabsolutevalueismuchlowerthanthatfortheotherfaces,andtherelativegrowthrateisnotablysmaller.Hence,onefacedominatesthecrystalgrowth.TABLEⅡ.CALCULATIONRESULTSOFAEMODELhklMultiplicitydhklEatttotalTotalfacetareaTotalfacetarea/Å/kcal/mol/Å2/Å2{011}444.9574.1116130076.80{101}427.8148.74285020.40{110}427.11167.758782.799abFigure3.PredictedcrystalmorphologyaBFDHmodel,bAEmodelComparisonofpredictedmorphologywithexperimentalgrowthcrystalThemorphologicalsimulationswereconfrontedwithexperimentaldataobtainedfromsolutiongrowncrystals.Thecrystalmorphologywasassessedbyopticalmicroscopy.MorphologicalsketchwasshowninFigure4.Figure4.ExperimentalcrystalmorphologyThepredictedmorphologybasedupontheAEmodelandBFDHmodelcomparesfavorablywiththeexperimentalmorphology.Themaindifferencebetweentheexperimentalmorphologyandpredictedmorphologyisthat{002}facedisappearsintheexperimentalmorphology,whichismoreconsistentwiththemorphologypredictedbyAEmodelthanbyBFDHmodel.Despitedifferencebetweenpredictedandexperimentalmorphology,itshouldberememberedthat,overall,thepredictedandsolutiongrownmorphologyarerathercomparable.Byfurtheranalyzingmorphologypredictedbytwomodelsandexperimentalmorphology,itcanbeseenthat{011}faceisthemostdominantinarea.Thiswasperhapsduetothefactthatthisfacehadsmallergrowthpromotinghydrogenbondingcomponentinvolvedintheintermolecularinteractionsinvolvedinitsattachmentenergy,incontrasttothoseonthe{110},{002},{101}faces.SurfacechemistryvisualizationfortheimportantmorphologicalformsThesurfacechemistryofthethreemainsurfaceswasinvestigatedtoprovidebetterunderstandingtointeractionandrecognitionamonglysozymethethreefaces{011},{101},and{110}expecteddominatethecrystalhabitasrevealedfromtheAEmorphologicalprediction.a011b101c110Figure5.Cleavagestructureofmainexposurecrystalplanea{011},b{101},c{110}TheresultsaresummarizedinFigure5.The{011}surfaceFigure5awasfoundtoberoughonthemolecularlevel.Incontrastto{101}crystalface,chemicalgrouprevealingisbigger,whichcanbringaboutagreatersterichindrancetoholdbackpackingoflysozymemoleculeinsolutionin{011}face.Asaresult,thegrowthrateof{011}crystalfaceiscomparativeslow,showinghighmorphologicalimportance.Examinationofthe{101}surfaceFigure5brevealsasmoothersurfacecomparedwith{011}faceonthemolecularlevel.Thechemicalgrouprevealingissmall,whichallowslysozymemoleculeeasilytopackin{101}surface,leadingto{101}surfacehaverapidgrowthrate.The{110}surfaceFigure5cwasfoundtobeveryopenandroughonthemolecularlevelrevealingadiagonalpatterndownthroughthesurfacewithalternatingorientationsofthelysozymemolecule.Thepatternproducedwasdiagonalinnaturewithhydrogenbondinganddonororacceptoratomswereactiveonthesurfaceforbindingoncomingmolecules.Inaddition,withthissurface,bothaminogroupandhydroxylcomponentsoflysozymemoleculewerefoundtoberevealabletopossiblebindingwithappropriatemolecules.Asaresult,thegrowthrateof{110}surfaceisthegreatest,showingthesmallestmorphologicalimportance.CONCLUSIONSThecrystalmorphologyoforthorhombiclysozymeispredictedusingAEmodelinconjunctionwithBFDHmodel.Accuratemodelingandmorphologypredictionofthiscrystalareachieved.Themorphologypredictedbytwomodelsisapproximatelyconsistent.ThemorphologypredictedbyAEmodelismoreconsistentwiththemorphologyofcrystalsgrownfromsolutionthanBFDHmodel.Themaincrystalfaces{011},{101}and{110}areobservedanddominantinmorphologypredictedbyAEmodel.Bycleavingthesedominantcrystalfaces,surfacechemistryvisualizationandtheoreticalanalysisbasedoninteractioninintramoleculesorintermoleculesfortheimportantmorphologicalformsareperformed.TheresultindicatesthatsterichindranceeffectandHbandinteractionplayscriticalrolefortheplatelikemorphologyoforthorhombiclysozyme,whichprovidesaimportantinstructioninmolecularlevelforpreparationofhighqualitylysozymecrystal.ACKNOWLEDGMENTThisworkwasfundedbytheNationalNaturalScienceFoundationofChinaNo.20806053,DoctoralFundofMinistryofEducationofChinaNo.200800561029andChinaPostdoctoralScienceFoundationNo.20080440677REFERENCES1J.C.Givand,R.W.Rousseau,P.J.Ludovice,CharacterizationofLisoleucinecrystalmorphologyfrommolecularmodeling,J.Cryst.Growth,vol.194,pp.228–238,1998.2J.Prywer,ExplanationofsomepeculiaritiesofcrystalmorphologydeducedfromtheBFDHlaw,J.Cryst.Growth,vol.270,pp.699–710,2004.3G.Pfefer,R.Boistelle,Theoreticalmorphologyofadipicacidcrystals,J.Cryst.Growth,vol.208,pp.615–622,2000.4P.Hartman,TheattachmentenergyasahabitcontrollingfactorI.Theoreticalconsiderations,J.Cryst.Growth,vol.49,pp.145–156,1980.5S.David,C.Coombes,A.Richard,CalculationofAttachmentEnergiesandRelativeVolumeGrowthRatesasanAidtoPolymorphPrediction,Cryst.GrowthDes,vol.5,pp.879–885,2005.6C.M.Li,K.L.Kirkwood,G.D.Brayer,TheBiologicalCrystallizationResourceFacilitatingKnowledgeBasedProteinCrystallizations,Cryst.GrowthDes,vol.7,pp.2147–2152,2007.7S.X.Lin,A.McPherson,R.Giegé,GoodCrystals,StillaChallengeforStructuralBiology,J.Cryst.Growth,vol.7,pp.2124–2125,2007.8A.Warke,C.Momany,AddressingtheProteinCrystallizationBottleneckByCocrystallization,J.Cryst.Growth,vol.7,pp.2219–2225,2007.9M.W.Elaine,J.R.Kevin,J.M.Stephen,AMolecularDynamicsStudyofSolventandImpurityInteractionontheCrystalHabitSurfacesofεCaprolactam,Langmuir,vol.14,pp.5620–5630,1998.10N.Kubota,J.W.Mullin,Akineticmodelforcrystalgrowthfromaqueoussolutioninthepresenceofimpurity,J.Cryst.Growth,vol.152,pp.203–208,1995.11H.C.Koolman,R.W.Rousseau,EffectsofisomorphiccompoundsonthepurityandmorphologyofLisoleucinecrystals,AIChEJournal,vol.42,pp.147–153,1996.12J.Z.Chen,N.F.Zhuang,S.K.Lin,Theoreticalmorphologyandgrowthhabitofrubidiumhydrogenselenatecrystals,J.Cryst.Growth,vol.205,pp.584–589,1999.13Y.Matsuzukia,T.Kubotab,X.Y.Liua,AFMobservationofthesurfacemorphologyandimpurityeffectsonorthorhombicheneggwhitelysozymecrystals,J.Cryst.Growth,vol.242,pp.199–208,2002.14http//www.rcsb.org/pdb/home/home.do

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