Cleavable ester-linked magnetic nanoparticles for labeling of 5 solvent-exposed primary amine groups

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12Notes&Tips4Cleavableester-linkedmagneticnanoparticlesforlabelingof

5solvent-exposedprimaryaminegroupsofpeptides/proteins6

7

8UjwalS.Patila,LauraOsornoa,AngelaEllendera,CaseyGrimmb,MatthewA.Tarra,⇑9aDepartmentofChemistry,UniversityofNewOrleans,NewOrleans,LA70148,USA

10bSouthernRegionalResearchCenter,NewOrleans,LA70124,USA

1113articleinfo

14Articlehistory:

15Received5February2015

16Receivedinrevisedform1April2015

17Accepted7May2015

18Availableonlinexxxx

19Keywords:

20Ethyleneglycolbis(succinimidylsuccinate)

21Coreshellmagneticnanoparticles

22Solvent-exposedlysineresidues

23

24abstract25Tostudythesolvent-exposedlysineresiduesofpeptides/proteins,wepreviouslyreported26disulfide-linkedN-hydroxysuccinimideester-modifiedsilica-coatedironoxidemagneticnanoparticles27(NHS–SS–SiO2@Fe3O4MNPs).Thepresenceofadisulfidebondinthelinkerlimitstheuseofdisulfide28reducingagentduringproteindigestionandallowsunwanteddisulfideformationbetweentheMNPs29andprotein.Inthecurrentwork,thedisulfidebondwasreplacedwithacleavableestergrouptosynthe-30sizeNHSester-modifiedSiO2@Fe3O4MNPs.Useofthecleavableestergroupprovidesanimproved31methodforproteinlabelingandallowstheuseofdisulfidereducingagentsduringproteindigestion.32Ó2015ElsevierInc.Allrightsreserved.33

343536Thelabelingofproteinsusingchemicallycleavableamino37acid-specificprobescoupledwithmassspectrometricanalysis38remainsamajorchoicetostudythesolvent-accessiblesurfaceof39proteins.Theaminoacid-specificprobescanspecificallylabelthe40functionalgroupofaminoacids,andacleavablebondassistswith41theisolationandidentificationoflabeledproteins[1].Avarietyof42cleavableaminoacid-specificprobestargetingtheprimaryamine43groupshavebeendevelopedduetoanabundanceoflysineresi-44duesonthesolvent-accessiblesurfaceofproteins[2,3].Thelabel-45ingprobescontainingN-hydroxysuccinimide(NHS)1/sulfo-NHS46groupscancovalentlylabeltheprimaryaminegroupsoflysineresi-47duesinphysiologicalbuffersandatroomtemperaturetoforma48stableamidebond[3].Thedisulfide-linked,lysine-targetingcleav-49ablelabelingreagentsarecommerciallyavailableandhavebeen50widelyusedtoobtainstructuralinformationofproteins.Onlabeling,51proteinsaredigestedusingreducingagents(dithiothreitol[DTT]and52tris(2-carboxyethyl)phosphine[TCEP])thatcleavedisulfidebondsto53unfoldtheproteinstructurethatisrequiredtodenaturetheprotein.54Proteindenaturationunfoldstheproteininordertoachievethe55maximumefficiencyfordownstreamprocessessuchastryptic56digestion.Thepresenceofdisulfidebondsinthecrosslinkermay57limittheuseofreducingagentssuchasDTTandTCEPpriorto58proteindigestion.Theuseofdisulfide-containinglinkersisnotcom-59patiblewithDTT-containingbuffersandmaybeattackedbyfree60thiolgroupsincomplexcellularconditions.Analternativecrosslin-61ker,ethyleneglycolbis(succinimidylsuccinate)(EGS),couldbean62effectivereplacementfordisulfide-containingcrosslinkersthatcan63allowtheuseofdisulfide-cleavingreducingagentsduringprotein64digestion[4].65Onlabelingthefunctionalgroupsofproteins,labeledproteins66areseparatedandpurifiedbyusingconventionalelectrophoretic,67chromatographic,orcentrifugationtechniquesthatcanbe68time-consuming,tedious,anddetrimentaltothestructureofapro-69tein[5].Recently,magneticnanoparticleshaveemergedasan70effectivealternativetoachieverapidandeffectiveseparationfor71samplepreparationinproteomics[6,7].Inourlaboratory,wehave72developeddisulfide-linked,NHSester-modifiedsilica-coatediron73oxidemagneticnanoparticles(SiO2@Fe3O4MNPs)to‘‘label’’the74solvent-exposedlysineresiduesofproteins[8]andyeastcellsur-75faceproteins[9].TheNHS/sulfo-NHSester-modifiedMNPsallowed76labelingoflysineresiduesunderphysiologicalconditionsatroom77temperature.TheMNP-basedlabelingapproachofferedrapidand78softmagneticseparationofconjugatedproteins,whichisadvanta-79geousovertraditionalproteinseparationtechniquessuchascol-80umnchromatographyandgelelectrophoresis.However,the81disulfidebondintheNHS–SS–SiO2@Fe3O4MNPscanbeattacked82bythereducingagentsduringproteindigestion,therebycleaving83thedisulfidebondpriortothemagneticseparationstep.84Moreover,anextrastepofalkylationoffreethiolgroupsneeds85tobeaddedpriortothelabelingprocesstoprotectdisulfidegroups86inthelinker.Inthiswork,wereplacedthecleavabledisulfidebond

http://dx.doi.org/10.1016/j.ab.2015.05.0060003-2697/Ó2015ElsevierInc.Allrightsreserved.

⇑Correspondingauthor.

E-mailaddress:mtarr@uno.edu(M.A.Tarr).1Abbreviationsused:NHS,N-hydroxysuccinimide;DTT,dithiothreitol;TCEP,

tris(2-carboxyethyl)phosphine;EGS,ethyleneglycolbis(succinimidylsuccinate);SiO2@Fe3O4MNPs,silica-coatedironoxidemagneticnanoparticles;TEM,transmis-