protein surface functionalisation as a general strategy ... · details of the proteins, their...
TRANSCRIPT
Supportinginformationfor:
ProteinsurfacefunctionalisationasageneralstrategyforfacilitatingbiomimeticmineralisationofZIF-8
NatashaK.Maddigana,AndrewTarziaa,DavidM.Huanga,ChristopherJ.Sumbya,StephenG.Bella*,PaoloFalcaroab*andChristian.J.Doonana*
a.DepartmentofChemistryandtheCentreforAdvancedNanomaterials,TheUniversityofAdelaide,Adelaide,SouthAustralia5005,Australia.Email:[email protected].
b.InstituteofPhysicalandTheoreticalChemistry,GrazUniversityofTechnology,Stremayrgasse9,Graz8010,Austria.
Electronic Supplementary Material (ESI) for Chemical Science.This journal is © The Royal Society of Chemistry 2018
Contents
1. Materials 3
2. Proteinsurfacemodificationreactions 3
3. Timecoursebiomimeticmineralisationstudies 4
4. PowderX-raydiffraction(PXRD)data 6
5. Scanningelectronmicroscopy 8
6. UV-visiblespectra 9
7. Additionalcomputationalmethods 10
8. Additionalcomputationalresults 11
9. References 16
1. Materials
TableS1.Detailsoftheproteins,theirsources,productcodesandtheProteinDataBank(PDB)codesfortheproteinsinvestigatedinthisresearch.
Protein Source ProductCode PDBFileUseda
Pepsin Porcinegastricmucosa
P6887 4pep1
Bovineserumalbumin(BSA) Bovine A9418 4f5s2Lipase,CandidaantarcticaLipaseB(CALB)
Aspergillusoryzae 62288 1tca3
Catalase BovineLiver C9322 3re84Peroxidasefromhorseradish(HRP)
Horseradish 77332 1w4w5
Myoglobin Equineskeletalmuscle
M0630 2frf6
Haemoglobin Human H7379 2dn27Trypsin Porcinepancreas T4799 1s818Lysozyme Eggwhite AstralScientific
(LDB0308)2vb19
aProteinstructuresarefromthesameorganismfromwhichtheproteinsampleissourced.
2.Proteinsurfacemodificationreactions
SchemeS1.Surfacemodificationreactions.SuccinylationandacetylationreactionslowerthepIofaproteinbymodificationofexposedaminegroups.Aminationreactionscapcarboxylgroupswithafreeamine,thusincreasingthepI.
3. Timecoursebiomimeticmineralisationstudies
Haemoglobin
HaemoglobinSuccinylated
HaemoglobinAcetylated
Myoglobin
MyoglobinSuccinylated
MyoglobinAcetylated
Figure S1. Sequential photographs of Haemoglobin (Hb), succinylated haemoglobin (HbSucc),acetylatedhaemoglobin(HbAc),myoglobin(Mb),succinylatedmyoglobin(MbSucc),andacetylatedmyoglobin(MbAc)samples(2mgprotein)immediatelyaftermixingofthemIM(160mM)andzincsolutions (40mM) (T=0) until immediately prior to centrifugation andwashing (T=16 hours). Theunmodifiedhaemoglobinandmyoglobinsamplesremainclearuponadditionofthezincsolution,bothyieldingminimalproductafter16hours.ThesuccinylatedandacetylatedformsofbothproteinscauseimmediateprecipitationofZIF.
BSA
Pepsin
BSAAminated
PepsinAminated
FigureS2.Sequentialphotographsofunmodifiedandaminatedbovineserumalbumin(BSA)andpepsin(2mgprotein)immediatelyaftermixingofthemIM(160mM)andzincsolutions(40mM)(T=0)untilimmediatelypriortocentrifugationandwashing(T=16hours).TheunmodifiedBSAandpepsinsamplesgaveimmediatebiomineralizationuponadditionofthezincsolution.TheaminatedBSAandpepsinsamplesshowadramaticreductioninprecipitationyieldingonlyminimalproductafter16hours.
4. PowderX-raydiffraction(PXRD)data
FigureS3.PowderX-raydiffractionpatternsofbiomimeticallymineralisedZIFsamplesofunmodifiedproteinsmadeunderstandardconditions(4:1mIM:Zn2+).Datacollectedondriedsamplesafterwasheswithwaterandethanol.Unmodifiedhaemoglobin,myoglobin,lysozyme,andtrypsindidnotyieldsufficientproductforPXRDanalysis.ThesimulatedpatternrelatestoZIF-8.
FigureS4.PowderX-raydiffractionpatternsofbiomimeticallymineralisedZIFsamplesofHbSuccandMbSucc(top)andHbAcandMbAc(bottom)madeunderstandardconditions(4:1mIM:Zn2+).Datacollectedondriedsamplesafterwasheswithwaterandethanol.AminatedBSAandpepsin,didnotyieldsufficientproductforPXRDanalysis.ThesimulatedpatternrelatestoZIF-8.
5. Scanningelectronmicroscopy
FigureS5.HbSucc@ZIF-8(left)andMbSucc@ZIF-8(right)after16hoursfromthebeginningofthebiomimeticmineralizationreaction;therhombicdodecahedralmorphologycanbeobserved.
1µm 1µm
6. UV-visiblespectra
FigureS6.UV-visiblespectraofthesupernatantremovedaftercentrifugationofthebiocompositesampleswheretheproteinwasmyoglobin(Mb),succinylatedmyoglobin(MbSucc),andacetylatedmyoglobin(MbAc)(left)andhaemoglobin(Hb),succinylatedhaemoglobin(HbSucc),andacetylatedhaemoglobin(HbAc)(right).UnmodifiedhaemoglobinandmyoglobinformedminimalproductandthereforeshowalargeSoretabsorbanceintheremovedsolution,indicatingthattheproteinhasnotbeenimmobilised.Inboththesuccinylatedandacetylatedvariants,theabsorbancehasdecreasedthusindicatingthattheproteinhasbeenremovedfromsolutionandincorporatedintoZIF-8asitformed.
FigureS7.UV-visiblespectraofthewashingsofsuccinylatedhaemoglobinZIF-8samples.Thesupernatant(red)wasobtainedaftercentrifugationoftheproductandshowsnoevidenceofproteinremaininginsolution.SDSwashes1(blue)and2(pink)showtheappearanceofthehaemoglobinabsorbancepeak,indicatingthatsomeproteinwassurfaceboundhadbeenwashedoff.AftertheSDSwashestoremovesurfaceboundproteinshowednofurtherprotein,theZIF-8samplewasdissolvedincitricacidbuffer(pH6)containingEDTA(20mM)andtheabsorbancewasmeasuredtoshowpresenceofencapsulatedprotein.
7. Additionalcomputationalmethods
7.1. Calculationoftheaveragehydropathicindex
Thehydropathicindexisameasureofanaminoacidsequenceshydropathicity.Negativevaluesimplyan overall hydrophilic protein,whereas positive values imply an overall hydrophobic protein. ThehydropathicindexforaproteinsequencewascalculatedusingtheKyteandDoolittlescaleofresiduehydropathicity,10whichquantifiesthehydropathicityofeachresidue,andtheBiopythonmodule.11,12Asinglevalueisreported,whichisthesumofthehydropathicindicesofallresiduesdividedbythelengthofthesequence.7.2. PreparationofPDBfilesandcalculationofproteinchargestate
CrystalstructureswereobtainedfromtheProteinDataBank13foreachprotein(PDBaccessioncodesgiveninTableS1).Whereavailableaproteinstructureassociatedwiththesameorganismastheexperimentalsourcewasobtained.EachPDBfilecomeswithoneormorepeptidechain,whereeachchainrepresentsaseparatesequenceofaminoacidsinthecrystalstructure.ForBSA,onlythefirstpolypeptidechaininthePDBfilewasusedbecausethisproteinisexpectedtoexistasamonomerinsolution.InallothercasesallchainsinthePDBfilewereused.Heteroatoms(non-naturalaminoacidresiduesorligands),boundionsorwatermoleculesintheproteinstructureswereremoved.
PROPKA3.014,15wasusedtoestimatethepKaofeachionisableresidueineachproteinstructureusingahighlyefficient,empiricalmethod.PROPKAuseseffectivepotentialstocalculatethetotalenvironmentalperturbationtothefreeenergyofprotonationduetomovingtheionisableresiduefromwaterintothe3Denvironmentoftheprotein.TheresultantfreeenergywasusedtodeterminetheshiftintheknownpKaofeachresidueduetotheproteinenvironment.WehaveconfirmedthatsimilarresultsareobtainedforthecalculatedpKa’susingthemoresophisticatedDELPHIPKA16toassignatomchargesandprotonationstates(resultsnotshown).DELPHIPKAusesavariabledielectriccoefficientwithintheproteinandthefreeenergydifferencebetweentheprotonatedanddeprotonatedstateofeachionisableresiduewithinthe3Dstructure(usingaPoisson–Boltzmann-basedapproachtocalculatethefreeenergydifference)toobtainthepKaforeachresidue.ThecalculatedpKaofeachionisableresidue,givenbyPROPKA,wasthenusedtocalculatethe3DmodelpIofeachproteinusingtheHenderson–Hasselbachequation.
Beforeanalysingeachcrystalstructure,thePDB2PQRsoftware17,18wasusedtoaddmissingheavyatoms,tomakesuretherewerenooverlappingatomsinthestructure,toprotonatethestructurebasedonthepKa’scalculatedbyPROPKAandthegivenpH(wherearesidueisprotonatedifitspKaisgreaterthanthegivenpH)andtoassignchargesandradiifromtheAMBER19forcefieldtoeachatom.WenotethattheAMBERforcefieldincludedwithPDB2PQRdoesnotcontainchargeparametersforresiduesincertainprotonationstatesderivedbyPROPKA(forexample,aneutralN-terminusstateisnotsupportedbytheforcefieldprovidedbyPDB2PQR)andthereforesomeresidueswillalwaysexistintheirpH7state.
8. Additionalcomputationalresults
8.1. Proteinmetrics
InFigureS8weshowthecalculatedaveragehydropathicindexofthesequenceofeachprotein.TheresultsindicatethattheproteinsthatseedZIF-8growthhavehydropathicitiesthatoverlapcompletelywithproteinsthatdonotseedZIF-8growth.ThisfindingfurthersupportsthedominantnatureofelectrostaticinteractionsindeterminingZIF-8formation,whichallowsfortheuseofsuchsimplifiedscreeningmethods.
FigureS8.Categoricalscatterplotoftheaveragehydropathicityofthepeptidesequencesforallproteins.ClosedcirclesareproteinsthatformZIF-8andopencirclesareproteinsthatdonotformZIF-8.
8.2. ComparisonofpIfromsequencemodels,3Dmodelsandexperiments
FigureS9showscategoricalscatterplotsofthecalculatedpIsfromthe3Dstructure(obtainedfromPROPKA3.0)andpeptidesequence(obtainedfromBiopython)ofeachprotein,whichshowsthatbothcalculationmethodspredictZIF-8growthreasonablyaccurately.ParityplotsofthepIsobtainedfrombothcalculationmethodsaswellasacomparisonbetweenthepIscalculatedfromthe3DproteinstructureandthereportedpIs(Table1)arealsoshown.Importantly,reasonableagreementbetweenthetwocalculationmethodswasobtained,indicatingthatthemuchsimplersequence-basedmodelcanbeusedwithoutadverselyaffectingpredictionaccuracy.WenotethatsomeexperimentalpIsarereportedasarangeofvalues,andsoerrorbarsareincludedinFigureS9d,forwhichtheuncertaintyencompassesthereportedrangeandthepIisthemeanofthereportedrange.
FigureS9.CategoricalscatterplotsofthecalculatedpI(a)fromthe3Dmodeland(b)sequencemodelofallproteins.ParityplotscomparingthecalculatedpIfromthe3Dmodeland(c)thesequencemodeland(d)thereportedpIvalues(they=xlineisshown).ErrorbarsrepresentrangesofpIvaluesreportedfromexperiments.ClosedcirclesareproteinsthatformZIF-8andopencirclesareproteinsthatdonotformZIF-8.
8.3. Experimentalzincionenhancement
FigureS10showsacategoricalscatterplotoftheenhancementofzincionscalculatedfromtheexperimentalzetapotentialsinTable1usingEquation4.Experimentalzetapotentialsgivereasonableapproximationsofthesurfaceelectrostaticpotentialofeachproteininsolutionand,therefore,aproteinsabilitytoenhancezincionconcentrationsnearthesurfaceand,hence,seedZIF-8growth.BasedonFigureS10,asurfacezincionenhancementof>10,whichisazincionconcentrationof0.4M,leadstoZIF-8formationunderexperimentalconditions.
FigureS10.CategoricalscatterplotsofthezincionenhancementscalculatedfromtheexperimentalzetapotentialsatpH11forallproteins.ClosedcirclesareproteinsthatformZIF-8andopencirclesareproteinsthatdonotformZIF-8.
8.4. Zincionenhancementfrom3Dmodel
Thecalculatedaveragesurfacepotentialsfromthe3Dmodelofeachproteinshowreasonableagreementwiththeexperimentalzetapotentials(FigureS11).Themaindiscrepanciesaretheoverestimationoftheaveragesurfacepotentialcomparedwithexperimentalzetapotentialsforveryhighlychargedproteins,suchasBSA,catalaseandpepsin.Thisresultisnotunexpected,giventheuseofthelinearisedPoisson–Boltzmannequation,whichbreaksdowninregimesofhighzeta
potential(|𝜁| > %B'()*
≈ 12mV).Theunderestimationoftheaveragesurfacepotentialcompared
withexperimentalzetapotentialsforlipaseandHRPislikelyaresultofexperimentalimpurities.Bothproteinsareexpectedtobeglycosylated,20,21whichisknowntoaffectzetapotentialmeasurements,22whereasthecalculationsusednon-glycosylatedstructures.Additionally,HRPcouldbeamixtureofdifferentiso-enzymeswithvastlydifferentelectrostaticproperties.23WenotethatbothproteinshavereportedpIsthatspanabroadrangeofvalues(Table1),indicatingabroadrangeofelectrostaticpropertiesfordifferentsamples.
Ourcalculationmethodologyusedstatic3DstructuresofeachproteinobtainedfromX-raycrystallography,whichareunlikelytoberepresentativeoftheproteinstructureinsolutionatapHof11.AthighpHs,thepresenceofhigh-chargeregionswouldleadtorepulsionandadegreeofunfolding,whichsuchasimplemodelcouldnottakeintoaccount.Wealsonotethatithasbeenshownpreviouslythattheinteriorofaproteinhasahighlyvariabledielectriccoefficientandassumingaconstantdielectriccoefficient,aswehave,cangiverisetoerrorsnearthesurfaceofproteins.24Furthermore,bytakingtheaveragesurfacepotentialtobeequaltotheexperimentalzetapotentialforaheterogenousproteinsurfaceweassumedthattheelectricdoublelayersurroundingtheproteinisthincomparedwiththesizeoftheproteinandthatthelinearisedPoisson–Boltzmannequationapplies,whichmaynotalwaysbethecaseforthesystemsstudied(discussedabove).25Thesemi-quantitativeagreementwithexperimentinmostcasesisveryencouraging,consideringtheapproximationsinthecalculations.
FigureS11.Parityplotscomparingthecalculatedsurfacepotentialfromour3Dmodelandexperimentalzetapotentialsat(a)pH7and(b)pH11forallproteins(they=xlineisshown).ClosedcirclesareproteinsthatformZIF-8andopencirclesareproteinsthatdonotformZIF-8.
FigureS12showsacategoricalscatterplotofthecalculatedaveragesurfacepotentialsatpH9andpH11forallproteins.Theseresultssupporttheexperimentalfindingsandshowareasonableabilitytopredictaprotein’spropensitytoseedZIF-8formation.ResultsatpH9andpH11areshownastheinitialsolution(beforezincionsareadded)isatapproximatelypH11,butuponzincionaddition,thepHquicklydecreases toaround9, likelybecauseof ZIFnucleation.26 Finally, FigureS13 shows thevariationinthesurfacepotentialaroundallproteinsatpH11calculatedfromour3Dmodel.
FigureS12.Categoricalscatterplotsofthecalculatedsurfacepotentialfromthe3Dmodel(a)atpH9and(b)pH11forallproteins.ClosedcirclesareproteinsthatformZIF-8andopencirclesareproteinsthatdonotformZIF-8.TheshadedregionhighlightstheapproximateboundaryofthezetapotentialintheexperimentsforproteinsthatdoanddonotseedZIF-8growth.
FigureS13.Surfacepotentialsurroundingallproteinscalculatedfromour3DmodelatpH11.LipaseandHRPareoutliersbasedonouranalysis.
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