Enzyme-Mediated Ligation Methods

369 Pages·2019·9.145 MB·English

by  Timo Nuijens, Marcel Schmidt

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
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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