Peptide and Protein Engineering: From Concepts to Biotechnological Applications

293 Pages·2020·7.651 MB·English

by  Olga Iranzo, Ana Cecília Roque

Olga Iranzo
Ana Cecília Roque Editors
Peptide
and Protein
Engineering
From Concepts to
Biotechnological Applications
S P H
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Peptide and Protein Engineering
From Concepts to Biotechnological Applications
Edited by
Olga Iranzo
iSm2 UMR CNRS 7313, Aix-Marseille Université, Marseille, France
Ana Cecília Roque
UCIBIO, Chemistry Department, School of Science and Technology, NOVA University of Lisbon, Caparica,
Portugal
Editors
OlgaIranzo AnaCec´ıliaRoque
iSm2UMRCNRS7313 UCIBIO,ChemistryDepartment
Aix-MarseilleUniversite´ SchoolofScienceandTechnology
Marseille,France NOVAUniversityofLisbon
Caparica,Portugal
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Preface
Peptides and proteins are one of the major families of biomolecules in life. Most cellular
eventsareregulatedbyprotein-mediatedinteractionsandreactions,turningthedesignand
engineeringofpeptidesandproteinsintoanimportanttooltocontrolandmediatecellular
functions, with important applications in the biomedical field. Furthermore, engineered
peptides and proteins are also relevant for technical applications, one of the best examples
beingtheuseofenzymesandantibodiesforinvitrodiagnosticdevicesortheuseofenzymes
in the manufacturing of chemicals or as additives in food and cleaning agents. The wide
implementationofpeptidesandproteinsinourlifehasonlybeenpossibleduetoadvancesin
their production following chemical routes or recombinant DNA technologies, as well as
advances in molecular engineering tools to improve (or create) structure and function.
Peptide and protein engineering is indeed a great scientific challenge that indeed entails a
fascinating interplay among a variety of economic, social, governance, and regulatory
institutions.
The aim of this book from the series of Springer Protocols Handbooks is to present the
methodsthatenabledthesuccessofpeptidesandproteinsinawidevarietyofapplications,
which are covered at the biannual workshop PepperSchool. Peptide and Protein Engineer-
ing: From Concepts to Biotechnological Applications is divided in two sections. The first
section comprises a collection of chapters that deal with chemical tools applied to the
production or engineering of peptides and proteins. It starts with the contribution of
Agouridas, Melnyk et al. describing how the bis(2-sulfanylethyl)amido (SEA) ligation, a
chemoselectivepeptidebond-formingreactioncomplementarytothenativechemicalliga-
tion,canbeoptimizedatmildlyacidicpHallowingamoreefficientproteintotalsynthesis.
Subsequently and using the chemical synthesis of SUMO-2 and 3 proteins as examples,
Melnyketal.nicelydescribehowtominimizeaspartimideformationduringSEAligation.In
the next chapter, Agouridas et al. introduce the Protein Chemical Synthesis DataBase
(http://pcs-db.fr), an accessible interactive tool with a user-friendly interface that collects
theinformationaboutthechemicalsynthesisofproteins,usingchemoselectiveamide-bond-
formingreactions,since1994.Thebookcontinueswithtwochaptersfocusedonmethods
usingazide–alkynecycloadditionstoselectivelymodifybiopolymersandproteins.Martins,
Gomes et al. describe the immobilization of arginine-rich peptides onto amine-
functionalized chitosan using the copper(I)-catalyzed azide–alkyne cycloaddition, while
Boutureira et al. report the synthesis of fluoroglycoproteins employing a metal-free proto-
col,i.e.,astrain-promotedazide–alkynecycloaddition.Thelasttwochaptersinthissection
cover protocols describing the production of peptide-based multivalent materials. Subra
etal.reportthesynthesisofhybridsilylatedpeptides,bothinsolutionandonsolidsupport,
and their subsequent use in the preparation of hybrid materials, either by a bottom-up
strategy or by straightforward grafting of these hybrid silylated peptides on the surface of
different materials. Finally, Pulido et al. present their approach to obtain peptide-
oligoethylene glycol conjugates containing different functional groups and their use to
create multivalentnanomaterials, either by means of dendritic platforms or by monovalent
conjugatesthatactasbuildingblocksofothersupramolecularstructures.
The second section focuses on biological approaches used to engineer structure and
function in peptides and proteins. It begins with a report from Urvoas, Minard, and
v
vi Preface
Soumillionthatpresentsawidevarietyofproteinsthatcanbeengineeredbyphagedisplay,
furtherdescribingmethodsforgeneratingandpanninghighlydiversephagelibraries.Be´har
et al. then focus on an alternative method—ribosome display—describing in particular a
methodtoperformribosomedisplayselectionsagainsttargetsatthesurfaceoflivebacterial
cells. Dias finally shows how CIS display can be applied for the discovery of biological
therapeutics detailing an improved protocol to streamline selections using this display
method, thus accelerating the therapeutic discovery of novel biological drugs. Dorrazehi
etal.presenttwomethodsforbuildinggenelibrariesinthechromosomeofGram-negative
and Gram-positive bacteria yielding chromosomal gene libraries with high diversity. Three
more chapters are finally presented, which deal with the design and production of protein
variantsfordistinctapplications.Klehretal.introducetheconceptofartificialcofactors,in
particularthoseemployedtodevelopstreptavidin-basedartificialmetalloenzymes.Delivoria
andSkretasreportahigh-throughputsystemforidentifyingmacrocyclicrescuersofprotein
misfolding. Genetically engineered bacterial cells can simultaneously perform the produc-
tion of combinatorial libraries of cyclic oligopeptides and the identification of bioactive
cyclic peptides that inhibit protein aggregation. Finally, Tugel, Galindo, and Wiltschi
provide a protocol for the site-specific incorporation of a noncanonical amino acid with
reactivesidechain,asaverypowerfultoolfor thedirectchemicalmodificationofproteins.
This volume on Peptide and Protein Engineering: From Concepts to Biotechnological
Applicationswasonlypossibleduetothecontributionsfromallauthors.Itattemptstocover
theemergingprinciplesandmethodologiesinpeptideandproteinengineering,anditisour
hope that the current volume shall be of use to scientists in academia and in industry,
working in areas as diverse as medicine, biology, biotechnology, diagnostics and therapeu-
tics,andbiocatalysis.
Marseille,France OlgaIranzo
Caparica,Portugal AnaCecı´liaRoque
Contents
Preface ..................................................................... v
Contributors................................................................. ix
1 SEA-MediatedLigationIsAcceleratedatMildlyAcidicpH:
ApplicationtotheFormationofDifficultPeptideJunctions.................. 1
MarineCargo¨et,VincentDiemer,LaurentRaibaut,ElizabethLissy,
BenoıˆtSnella,VangelisAgouridas,andOlegMelnyk
2 TheProblemofAspartimideFormationDuringProtein
ChemicalSynthesisUsingSEA-MediatedLigation.......................... 13
JenniferBouchenna,MagalieSe´ne´chal,Herve´Drobecq,Je´roˆmeVicogne,
andOlegMelnyk
3 UsingtheInteractiveTooloftheProteinChemicalSynthesisDatabase........ 29
VangelisAgouridasandOlegMelnyk
4 Onlya“Click”Away:DevelopmentofArginine-RichPeptide-Based
MaterialsUsingClickChemistry.......................................... 37
MarianaBarbosa,Fabı´olaCosta,Ca´tiaTeixeira,M.CristinaL.Martins,
andPaulaGomes
5 FluoroglycoproteinsbyCopper-FreeStrain-Promoted
Azide–AlkyneCycloaddition ............................................. 53
PedroM.S.D.Cal,Gonc¸aloJ.L.Bernardes,andOmarBoutureira
6 HybridSilylatedPeptidesfor theDesignofBio-functionalizedMaterials ...... 69
TitouanMontheil,Ce´cileEchalier,JeanMartinez,AhmadMehdi,
andGillesSubra
7 SynthesisofPeptide-OligoethyleneGlycol(OEG)Conjugates
forMultivalentModificationofNanomaterials ............................. 93
DanielPulidoandMiriamRoyo
8 PhageDisplayMethodologies ............................................ 125
AgatheUrvoas,PhilippeMinard,andPatriceSoumillion
9 Whole-BacteriumRibosomeDisplaySelectionforIsolation
ofAntibacterialAffitins .................................................. 153
GhislaineBe´har,StanimirKambarev,JenniferJazat,
BarbaraMouratou,andFre´de´ricPecorari
10 CISDisplay:DNA-BasedTechnologyasaPlatformforDiscovery
ofTherapeuticBiologics................................................. 173
AnaMargaridaGonc¸alvesCarvalhoDias
11 BuildingScarlessGeneLibrariesintheChromosomeofBacteria ............. 189
GolMohammadDorrazehi,SebastianWorms,JasonBabyChirakadavil,
JohannMignolet,PascalHols,andPatriceSoumillion
vii
viii Contents
12 Streptavidin(Sav)-BasedArtificialMetalloenzymes:Cofactor
DesignConsiderationsandLarge-ScaleExpressionofHost
ProteinVariants ........................................................ 213
JulianeKlehr,JingmingZhao,AmandaSantosKron,ThomasR.Ward,
andValentinK¨ohler
13 IntegratedBacterialProductionandFunctionalScreeningofExpanded
CyclicPeptideLibrariesforIdentifyingChemicalRescuers
ofPathogenicProteinMisfoldingandAggregation ......................... 237
DafniC.DelivoriaandGeorgiosSkretas
14 Site-SpecificIncorporationofNon-canonicalAminoAcids
byAmberStopCodonSuppressioninEscherichiacoli....................... 267
UchralbayarTugel,MeritxellGalindoCasas,andBirgitWiltschi
Index ...................................................................... 283
Contributors
VANGELISAGOURIDAS (cid:129) Univ.Lille,CNRS,Inserm,CHULille,InstitutPasteurdeLille,
U1019-UMR9017-CIIL-Centred’Infectionetd’Immunite´deLille,Lille,France
MARIANA BARBOSA (cid:129) LAQV-REQUIMTE,DepartamentodeQuı´micaeBioquı´mica,
FaculdadedeCieˆncias,UniversityofPorto,Porto,Portugal;i3S,InstitutodeInvestigac¸a˜o
eInovac¸a˜oemSau´de,UniversityofPorto,Porto,Portugal;INEB,InstitutodeEngenharia
Biome´dica,UniversityofPorto,Porto,Portugal;FaculdadedeEngenharia,Universityof
Porto,Porto,Portugal
GHISLAINEBE´HAR (cid:129) CRCINA,INSERM,CNRS,Universite´d’Angers,Universite´de
Nantes,Nantes,France
GONC¸ALOJ.L.BERNARDES (cid:129) DepartmentofChemistry,UniversityofCambridge,
Cambridge,UK;InstitutodeMedicinaMolecular,UniversidadedeLisboa,Lisboa,
Portugal
JENNIFERBOUCHENNA (cid:129) Univ.Lille,CNRS,Inserm,CHULille,InstitutPasteurdeLille,
U1019-UMR9017-CIIL-Center forInfectionandImmunityofLille,Lille,France
OMARBOUTUREIRA (cid:129) DepartamentdeQuı´micaAnalı´ticaiQuı´micaOrg`anica,Universitat
RoviraiVirgili,Tarragona,Spain
PEDROM.S.D.CAL (cid:129) DepartmentofChemistry,UniversityofCambridge,Cambridge,UK;
InstitutodeMedicinaMolecular,UniversidadedeLisboa,Lisboa,Portugal
MARINECARGOE¨T (cid:129) Univ.Lille,CNRS,Inserm,CHULille,InstitutPasteurdeLille,
U1019-UMR9017-CIIL-Centred’Infectionetd’Immunite´deLille,Lille,France
MERITXELL GALINDOCASAS (cid:129) AustrianCentreofIndustrialBiotechnology(acibGmbH),
Graz,Austria;GrazUniversityofTechnology,Graz,Austria
JASONBABYCHIRAKADAVIL (cid:129) BiochemistryandGeneticsofMicroorganisms,LouvainInstitute
ofBiomolecularScienceandTechnology,Universite´catholiquedeLouvain,Louvain-la-
Neuve,Belgium
FABI´OLACOSTA (cid:129) i3S,InstitutodeInvestigac¸a˜oeInovac¸a˜oemSau´de,UniversityofPorto,
Porto,Portugal;INEB,InstitutodeEngenhariaBiome´dica,UniversityofPorto,Porto,
Portugal
DAFNIC.DELIVORIA (cid:129) InstituteofChemicalBiology,NationalHellenicResearch
Foundation,Athens,Greece
ANAMARGARIDAGONC¸ALVESCARVALHODIAS (cid:129) UCIBIO,ChemistryDepartment,NOVA
SchoolofScienceandTechnology,Caparica,Portugal;Isogenica,LLC,Cambridge,UK
VINCENTDIEMER (cid:129) Univ.Lille,CNRS,Inserm,CHULille,InstitutPasteurdeLille,U1019-
UMR9017-CIIL-Centred’Infectionetd’Immunite´deLille,Lille,France
GOLMOHAMMADDORRAZEHI (cid:129) BiochemistryandGeneticsofMicroorganisms,Louvain
InstituteofBiomolecularScienceandTechnology,Universite´catholiquedeLouvain,
Louvain-la-Neuve,Belgium
HERVE´ DROBECQ (cid:129) Univ.Lille,CNRS,Inserm,CHULille,InstitutPasteurdeLille,U1019-
UMR9017-CIIL-Center forInfectionandImmunityofLille,Lille,France
CE´CILEECHALIER (cid:129) IBMMUniv.Montpellier,CNRS,ENSCM,Montpellier,France;ICGM
Univ.Montpellier,CNRS,ENSCM,Montpellier,France
PAULA GOMES (cid:129) LAQV-REQUIMTE,DepartamentodeQuı´micaeBioquı´mica,Faculdade
deCieˆncias,UniversityofPorto,Porto,Portugal
ix