Methods in Molecular Biology 2012 Timo Nuijens Marcel Schmidt Editors Enzyme-Mediated Ligation Methods M M B ETHODS IN OLECULAR IO LO GY SeriesEditor JohnM.Walker School of Lifeand MedicalSciences University ofHertfordshire Hatfield, Hertfordshire,AL109AB,UK Forfurther volumes: http://www.springer.com/series/7651 Enzyme-Mediated Ligation Methods Edited by Timo Nuijens and Marcel Schmidt EnzyPep B.V., Geleen, The Netherlands Editors TimoNuijens MarcelSchmidt EnzyPepB.V. EnzyPepB.V. Geleen,TheNetherlands Geleen,TheNetherlands ISSN1064-3745 ISSN1940-6029 (electronic) MethodsinMolecularBiology ISBN978-1-4939-9545-5 ISBN978-1-4939-9546-2 (eBook) https://doi.org/10.1007/978-1-4939-9546-2 ©SpringerScience+BusinessMedia,LLC,partofSpringerNature2019 Thisworkissubjecttocopyright.AllrightsarereservedbythePublisher,whetherthewholeorpartofthematerialis concerned,specificallytherightsoftranslation,reprinting,reuseofillustrations,recitation,broadcasting,reproduction onmicrofilmsorinanyotherphysicalway,andtransmissionorinformationstorageandretrieval,electronicadaptation, computersoftware,orbysimilarordissimilarmethodologynowknownorhereafterdeveloped. Theuseofgeneraldescriptivenames,registerednames,trademarks,servicemarks,etc.inthispublicationdoesnotimply, evenintheabsenceofaspecificstatement,thatsuchnamesareexemptfromtherelevantprotectivelawsandregulations andthereforefreeforgeneraluse. Thepublisher,theauthors,andtheeditorsaresafetoassumethattheadviceandinformationinthisbookarebelievedto betrueandaccurateatthedateofpublication.Neitherthepublishernortheauthorsortheeditorsgiveawarranty, expressorimplied,withrespecttothematerialcontainedhereinorforanyerrorsoromissionsthatmayhavebeenmade. Thepublisherremainsneutralwithregardtojurisdictionalclaimsinpublishedmapsandinstitutionalaffiliations. ThisHumanaimprintispublishedbytheregisteredcompanySpringerScience+BusinessMedia,LLC,partofSpringer Nature. Theregisteredcompanyaddressis:233SpringStreet,NewYork,NY10013,U.S.A. Preface Theincreasingunderstandingofbiologicalsystemsprovidesexcitingnovelopportunitiesfor their modulation using a wealth of therapeutic modalities. Whereas drug discovery has traditionally focused on small-molecule drugs, the advances in life science over the past 30 years have led to a significant expansion of this focus toward larger molecules beyond Lipinski’sruleoffive,suchaspeptideorprotein-basedtherapeutics.Theemergenceofthis classoflargerbiologicalmacromoleculesassuccessfultherapeuticshasbeenaccompaniedby acomplementaryneedofmethodologiestoenabletheirsynthesis,derivativesthereof(e.g., containing unnatural moieties), or hybrid-modality conjugates (e.g., antibody-drug con- jugates). Whereas initial efforts to modify peptides and proteins mostly focused on tradi- tional chemical ligation methodologies such as native chemical ligation, alkyne-azide cycloaddition(“click”chemistry),andothers,harnessingthebiocatalyticpowerofnature’s mostdiversetoolkit,namely,enzymes,hasnotbeeninthecenteroffocusinthebeginning. Althoughenzymeshadbeenwidelyusedforthederivatizationofsmallmolecules,theiruse onpeptideandproteinlevelstillhadtobeexplored.However,overthepastyears,enzyme- mediated ligation strategies for the efficient preparation of modified peptides or proteins have been widely recognized as a powerful adjunct to existing chemical methodologies. Consequently, this increased interest resulted in the discovery of novel naturally occurring enzymesandthecreationofoptimizedvariantsthereof.Theavailablesetofligasescomprises enzymes from various classes such as engineered proteases (e.g. subtilisin variants), trans- peptidases (sortases), or lipid transferases (e.g., PPTase). Current applications include the useinlinearpeptidesynthesis,inpeptidemacrocyclization,andinpeptideandprotein(e.g., antibody) derivatization, as a tool both in research and in manufacture. In either environ- ment, the use of enzymes in many cases enables site-specific, efficient ligations under mild conditionsandprovidesanelegantlinkbetweenchemistryandbiology. In this edition of Methods in Molecular Biology, we cover many different enzyme- catalyzed ligation methodologies, and the book is devoted to those students and scientists fromdifferentdisciplines,whoconsider touseenzymaticstrategiesforavarietyofresearch questions. We hope to facilitate the use of enzymes by providing protocols for a variety of chemicaltransformationsandtobreakthe“virtualbarrier”formanypeopletoactivelyand widelyuseenzymesasatoolinacademicresearchaswellasinindustrialsettings. Geleen,TheNetherlands TimoNuijens MarcelSchmidt v Contents Preface ..................................................................... v Contributors................................................................. ix 1 SortaseAEnzyme-MediatedGenerationofSite-Specifically ConjugatedAntibody–DrugConjugates................................... 1 Re´myGe´bleux,ManfredBriendl,UlfGrawunder,andRogerR.Beerli 2 Site-SpecificC-TerminalLabelingofRecombinantProteins withProximity-BasedSortase-MediatedLigation(PBSL).................... 15 HejiaHenryWangandAndrewTsourkas 3 CyclizingDisulfide-RichPeptidesUsingSortaseA.......................... 29 AkelloJ.Agwa,DavidJ.Craik,andChristinaI.Schroeder 4 ChemoenzymaticSynthesisofLinear-andHead-to-TailCyclicPeptides UsingOmniligase-1..................................................... 43 MarcelSchmidtandTimoNuijens 5 Site-SpecificLabelingofProteinsUsingtheFormylglycine-Generating Enzyme(FGE) ......................................................... 63 IgorRupniewskiandDavidRabuka 6 Butelase1-MediatedLigationofPeptidesandProteins...................... 83 XinyaHemu,XiaohongZhang,XiaobaoBi,Chuan-FaLiu, andJamesP.Tam 7 Trypsiligase-CatalyzedPeptideandProteinLigation ........................ 111 SandraLiebscherandFrankBordusa 8 Site-SpecificAntibody–DrugConjugationUsingMicrobial Transglutaminase ....................................................... 135 StephanDickgiesser,LukasDeweid,RolandKellner,HaraldKolmar, andNicolasRasche 9 TailoringActivityandSelectivityofMicrobialTransglutaminase .............. 151 LukasDeweid,OlgaAvrutina,andHaraldKolmar 10 SpyLigase-CatalyzedModificationofAntibodies............................ 171 VanessaSiegmund,BirgitPiater,FrankFischer,andHaraldKolmar 11 PeptideCyclizationCatalyzedbyCyanobactinMacrocyclases ................ 193 WaelE.Houssen 12 InVitroandInPlantaCyclizationofTargetPeptides UsinganAsparaginylEndopeptidasefromOldenlandiaaffinis ............... 211 Karen S.Harris,SimonPoon,PedroQuimbar,andMarilynA.Anderson 13 Site-SpecificAntibodyLabelingUsingPhosphopantetheinyl Transferase-CatalyzedLigation ........................................... 237 JanGru¨newald,AnsgarBrock,andBernhardH.Geierstanger 14 LipoicAcidLigase-PromotedBioorthogonalProteinModification andImmobilization..................................................... 279 JosephG.PlaksandJoelL.Kaar vii viii Contents 15 BioIDasaToolforProtein-ProximityLabelinginLivingCells............... 299 RhiannonM.Sears,DanielleG.May,andKyleJ.Roux 16 N-MyristoylTransferase(NMT)-CatalyzedLabelingofBacterial ProteinsforImaginginFixedandLiveCells ............................... 315 SamuelH.HoandDavidA.Tirrell 17 TubulinTyrosineLigase-MediatedModificationofProteins ................. 327 MarcusGerlach,TinaStoschek,HeinrichLeonhardt, ChristianP.R.Hackenberger,DominikSchumacher,andJonasHelma 18 Inducible,SelectiveLabelingofProteinsviaEnzymatic OxidationofTyrosine................................................... 357 JorickJ.Bruins,CrissvandeWouw,JordiF.Keijzer,BaukeAlbada, andFlorisL.vanDelft Index ...................................................................... 369 Contributors AKELLOJ.AGWA (cid:1) InstituteforMolecularBioscience,TheUniversityofQueensland,Brisbane, QLD,Australia BAUKE ALBADA (cid:1) LaboratoryofOrganicChemistry,WageningenUniversityandResearch, Wageningen,TheNetherlands MARILYNA.ANDERSON (cid:1) HeximaLimited,DepartmentofBiochemistryandGenetics,La TrobeInstituteforMolecularScience,LaTrobeUniversity,Melbourne,VIC,Australia OLGAAVRUTINA (cid:1) Clemens-Scho¨pfInstituteforOrganicChemistryandBiochemistry, TechnischeUniversita€tDarmstadt,Darmstadt,Germany ROGERR.BEERLI (cid:1) NBE-TherapeuticsLtd.,Basel,Switzerland XIAOBAOBI (cid:1) SchoolofBiologicalSciences,NanyangTechnologicalUniversity,Singapore, Singapore FRANKBORDUSA (cid:1) InstituteofBiochemistry/Biotechnology,Charles-Tanford-ProteinCenter, Martin-Luther-UniversityHalle-Wittenberg,Halle,Germany MANFREDBRIENDL (cid:1) NBE-TherapeuticsLtd.,Basel,Switzerland ANSGARBROCK (cid:1) Biotherapeutics,GenomicsInstituteoftheNovartisResearchFoundation, SanDiego,CA,USA JORICKJ.BRUINS (cid:1) LaboratoryofOrganicChemistry,WageningenUniversityandResearch, Wageningen,TheNetherlands DAVIDJ.CRAIK (cid:1) InstituteforMolecularBioscience,TheUniversityofQueensland,Brisbane, QLD,Australia LUKAS DEWEID (cid:1) Clemens-Scho¨pfInstituteforOrganicChemistryandBiochemistry, TechnischeUniversita€tDarmstadt,Darmstadt,Germany STEPHANDICKGIESSER (cid:1) ADCs&TargetedNBETherapeutics,MerckKGaA,Darmstadt, Germany FRANKFISCHER (cid:1) BiomoleculeAnalytics,MerckKGaA,Darmstadt,Germany RE´MYGE´BLEUX (cid:1) NBE-TherapeuticsLtd.,Basel,Switzerland BERNHARDH.GEIERSTANGER (cid:1) Biotherapeutics,GenomicsInstituteoftheNovartisResearch Foundation,SanDiego,CA,USA MARCUS GERLACH (cid:1) DepartmentofBiologyII,LMUMunich,Planegg/Martinsried, Germany JANGRU¨NEWALD (cid:1) Biotherapeutics,GenomicsInstituteoftheNovartisResearchFoundation, SanDiego,CA,USA ULFGRAWUNDER (cid:1) NBE-TherapeuticsLtd.,Basel,Switzerland CHRISTIAN P.R.HACKENBERGER (cid:1) DepartmentofChemical-Biology,Leibniz-Institutfu¨r MolekularePharmakologie(FMP),Berlin,Germany;DepartmentofChemistry,Humboldt Universita€tzuBerlin,Berlin,Germany KARENS.HARRIS (cid:1) HeximaLimited,DepartmentofBiochemistryandGenetics,LaTrobe InstituteforMolecularScience,LaTrobeUniversity,Melbourne,VIC,Australia JONAS HELMA (cid:1) DepartmentofBiologyII,LMUMunich,Planegg/Martinsried,Germany XINYAHEMU (cid:1) SchoolofBiologicalSciences,NanyangTechnologicalUniversity,Singapore, Singapore SAMUELH.HO (cid:1) DivisionofChemistryandChemicalEngineering,CaliforniaInstituteof Technology,Pasadena,CA,USA ix x Contributors WAELE.HOUSSEN (cid:1) MarineBiodiscoveryCentre,ChemistryDepartment,Universityof Aberdeen,Aberdeen,UK;InstituteofMedicalSciences,UniversityofAberdeen,Aberdeen, UK;PharmacognosyDepartment,FacultyofPharmacy,MansouraUniversity,Mansoura, Egypt JOELL.KAAR (cid:1) DepartmentofChemicalandBiologicalEngineering,UniversityofColorado, Boulder,CO,USA JORDIF.KEIJZER (cid:1) LaboratoryofOrganicChemistry,WageningenUniversityandResearch, Wageningen,TheNetherlands ROLAND KELLNER (cid:1) ADCs&TargetedNBETherapeutics,MerckKGaA,Darmstadt, Germany HARALD KOLMAR (cid:1) Clemens-Scho¨pfInstituteforOrganicChemistryandBiochemistry, TechnischeUniversita€tDarmstadt,Darmstadt,Germany HEINRICH LEONHARDT (cid:1) DepartmentofBiologyII,LMUMunich,Planegg/Martinsried, Germany SANDRA LIEBSCHER (cid:1) InstituteofBiochemistry/Biotechnology,Charles-Tanford-Protein Center,Martin-Luther-UniversityHalle-Wittenberg,Halle,Germany CHUAN-FALIU (cid:1) SchoolofBiologicalSciences,NanyangTechnologicalUniversity,Singapore, Singapore DANIELLEG.MAY (cid:1) EnablingTechnologyGroup,SanfordResearch,SiouxFalls,SD,USA TIMONUIJENS (cid:1) EnzyPepB.V.,Geleen,TheNetherlands BIRGITPIATER (cid:1) ADCs&TargetedNBETherapeutics,MerckKGaA,Darmstadt,Germany JOSEPH G.PLAKS (cid:1) DepartmentofChemicalandBiologicalEngineering,Universityof Colorado,Boulder,CO,USA SIMONPOON (cid:1) HeximaLimited,DepartmentofBiochemistryandGenetics,LaTrobe InstituteforMolecularScience,LaTrobeUniversity,Melbourne,VIC,Australia PEDRO QUIMBAR (cid:1) HeximaLimited,DepartmentofBiochemistryandGenetics,LaTrobe InstituteforMolecularScience,LaTrobeUniversity,Melbourne,VIC,Australia DAVIDRABUKA (cid:1) CatalentPharmaSolutions,Richmond,CA,USA NICOLAS RASCHE (cid:1) ADCs&TargetedNBETherapeutics,MerckKGaA,Darmstadt, Germany KYLEJ.ROUX (cid:1) EnablingTechnologyGroup,SanfordResearch,SiouxFalls,SD,USA; DepartmentofPediatrics,SanfordSchoolofMedicine,UniversityofSouthDakota,Sioux Falls,SD,USA IGORRUPNIEWSKI (cid:1) CatalentPharmaSolutions,Richmond,CA,USA MARCELSCHMIDT (cid:1) EnzyPepB.V.,Geleen,TheNetherlands;Van’tHoffInstituteof MolecularSciences,UniversityofAmsterdam,Amsterdam,TheNetherlands CHRISTINAI.SCHROEDER (cid:1) InstituteforMolecularBioscience,TheUniversityofQueensland, Brisbane,QLD,Australia DOMINIK SCHUMACHER (cid:1) DepartmentofBiologyII,LMUMunich,Planegg/Martinsried, Germany;DepartmentofChemical-Biology,Leibniz-Institutfu¨rMolekulare Pharmakologie(FMP),Berlin,Germany RHIANNONM.SEARS (cid:1) EnablingTechnologyGroup,SanfordResearch,SiouxFalls,SD,USA; BasicBiomedicalSciences,SanfordSchoolofMedicine,UniversityofSouthDakota, Vermillion,SD,USA VANESSASIEGMUND (cid:1) ProteinEngineeringandAntibodyTechnologies,MerckKGaA, Darmstadt,Germany TINASTOSCHEK (cid:1) DepartmentofBiologyII,LMUMunich,Planegg/Martinsried,Germany Contributors xi JAMESP.TAM (cid:1) SchoolofBiologicalSciences,NanyangTechnologicalUniversity,Singapore, Singapore DAVIDA.TIRRELL (cid:1) DivisionofChemistryandChemicalEngineering,CaliforniaInstitute ofTechnology,Pasadena,CA,USA ANDREWTSOURKAS (cid:1) DepartmentofBioengineering,SchoolofEngineeringandApplied Science,UniversityofPennsylvania,Philadelphia,PA,USA CRISS VANDEWOUW (cid:1) LaboratoryofOrganicChemistry,WageningenUniversityand Research,Wageningen,TheNetherlands FLORISL.VANDELFT (cid:1) LaboratoryofOrganicChemistry,WageningenUniversityand Research,Wageningen,TheNetherlands HEJIAHENRYWANG (cid:1) BiochemistryandMolecularBiophysicsGraduateGroup,Perelman SchoolofMedicine,UniversityofPennsylvania,Philadelphia,PA,USA XIAOHONGZHANG (cid:1) SchoolofBiologicalSciences,NanyangTechnologicalUniversity, Singapore,Singapore