Membrane protein structure and function characterization : methods and protocols

421 Pages·2017·13.809 MB·English

by  Lacapère, Jean-Jacques

Methods in
Molecular Biology 1635
Jean-Jacques Lacapere Editor
Membrane
Protein Structure
and Function
Characterization
Methods and Protocols
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
Membrane Protein Structure
and Function Characterization
Methods and Protocols
Edited by
Jean-Jacques Lacapere
Sorbonne Universités—UPMC Univ Paris 06 École Normale Supérieure—PSL Research University
Département de Chimie, CNRS UMR 7203 LBM, Paris, France
Editor
Jean-JacquesLacapere
SorbonneUniversite´s—UPMCUnivParis06,
E´coleNormaleSupe´rieure—PSLResearchUniversity
De´partementdeChimie,CNRSUMR7203LBM
Paris,France
ISSN1064-3745 ISSN1940-6029 (electronic)
MethodsinMolecularBiology
ISBN978-1-4939-7149-7 ISBN978-1-4939-7151-0 (eBook)
DOI10.1007/978-1-4939-7151-0
LibraryofCongressControlNumber:2017943682
©SpringerScience+BusinessMediaLLC2017
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Preface
Membraneproteinsareessentialcomponentsofbiologicalprocessessuchasions,metabolites
or water transport, signal transduction, sensing cell environment, and control of cell-cell
contact. Dysfunction of these proteins induces numerous human pathologies like cystic
fibrosis which originates from a genetic disorder that is linked to the most common case
to the deletion of one amino acid. Many other disorders like cancers and inflammatory
diseases occur through cell-cell communications and involve membrane proteins.
Althoughmanystudieshavebeenperformedtocharacterizemembraneproteins,there
isalackofinformationuponthisclassofproteinsbothintermsofstructuresandfunction.
Oneofthebottlenecksisthelowabundanceoftheseproteinsinnativemembranes,making
difficult the characterization and the study of their function. To overcome this difficulty,
overexpression in various systems has gained increasing interest over the last decades,
leading, in particular, to the production of sufficient amounts for structural studies.
Although thenumberofhighresolution structuresofmembraneproteins hasincreased, it
remainswellbelowthatofsolubleproteins.
Somemembraneproteinshavebeeneasilyoverexpressed,butitisnotacommoncase.
Expression remains challenging especially for mammalian proteins compared to bacterial
ones, the former often requiring molecular chaperones to fold correctly, and post-
translational modifications to befunctional. This volumeaddresses different approaches to
produce membrane proteins, to purify them, to verify their function, to determine their
structure,andtomodeltheminmembrane.Sinceeverymembraneproteinbehavesmostly
inauniqueway,knowledgeofguidelinesandtricksmayhelptoincreasechancestoexpress,
purify,andcharacterizeapeculiarmembraneprotein.Productionofcorrectlyfoldedprotein
remains a challenge.Moreover, getting a functional and stableprotein requires optimizing
membranemimickingenvironmentsthatcanbedetergentorartificialmembranes.Insome
cases,thefindingofthecorrectligandthatwillstabilizethedesiredconformationisneeded.
In other cases, stabilization can be obtained using specific antibodies. This volume also
presentsdifferenttechniquestoanalyzethefunctionalstatusofmembraneproteins.
Recent progresses in structural biology of membrane proteins are described using
examples for the main approaches that are electron microscopy, X-Ray diffraction, nuclear
magnetic resonance (NMR), and bioinformatic computing. The new detector used for
electron microscopes has increased resolution gained from either two-dimensional crystals
or single particles. X-Ray free electron laser has permit to get high resolution structures
using micron-size crystals. Solid-state NMR study gives de novo atomic structure of low
molecular weight membrane proteins reconstituted in liposomes, but only spectral finger-
prints of larger proteins. Recent developments in computing both from computer power
(hardware)andfromalgorithms(software)havemadepossiblemoleculardynamicsoflarger
membraneproteinsattimescalescompatiblewithconformationalchangesinthemillisecond
range. Structure-based drug design is a reality for membrane proteins in a close-to-native
environment.
Paris,France Jean-JacquesLacapere
v
Contents
Preface ..................................................................... v
Contributors................................................................. ix
1 RecombinantOverexpressionofMammalianTSPOIsoforms1and2......... 1
LucileSenicourt,SoriaIatmanen-Harbi,ClaudeHattab,
MarianoAnibalOstuni,Marie-FranceGiraud,andJean-JacquesLacapere
2 FunctionalAssemblyofSolubleandMembraneRecombinantProteins
ofMammalianNADPHOxidaseComplex................................. 27
HajerSouabni,AymenEzzine,TaniaBizouarn,andLauraBaciou
3 DirectExtractionandPurificationofRecombinantMembrane
ProteinsfromPichiapastorisProtoplasts................................... 45
LucieHartmann,EstelleMetzger,Noe´mieOttelard,
andRenaudWagner
4 Cell-FreeExpressionfor theStudyofHydrophobicProteins:
TheExampleofYeastATP-SynthaseSubunits.............................. 57
IsabelleLarrieu,JamesTolchard,CorinneSanchez,EdmondYazoKone,
AlexandreBarras,ClaireStines-Chaumeil,BenoıˆtOdaert,
andMarie-FranceGiraud
5 WheatGermCell-FreeOverexpressionfor theProduction
ofMembraneProteins................................................... 91
Marie-Laure Fogeron,Aure´lieBadillo,Franc¸oisPenin,
andAnjaB¨ockmann
6 Methyl-SpecificIsotopeLabelingStrategiesforNMRStudies
ofMembraneProteins................................................... 109
ViliusKurauskas,PaulSchanda,andRemySounier
7 LabelingofMembraneComplexesforElectronMicroscopy.................. 125
FrancescaGubelliniandRe´miFronzes
8 Expression,Biochemistry,andStabilizationwithCamel
AntibodiesofMembraneProteins:CaseStudy
oftheMouse5-HT3Receptor ........................................... 139
Ghe´riciHassa¨ıne,Ce´dricDeluz,LuiginoGrasso,RomainWyss,
RuudHovius,HenningStahlberg,TakashiTomizaki,AlineDesmyter,
ChristopheMoreau,LuciePeclinovska,SonjaMinniberger,
LamiaMebarki,Xiao-DanLi,HorstVogel,andHuguesNury
9 CharacterizationofNewDetergentsandDetergentMimetics
byScatteringTechniquesforMembraneProteinCrystallization .............. 169
Franc¸oiseBonnete´ andPatrickJ.Loll
10 SecondaryStructureDeterminationbyMeansofATR-FTIRSpectroscopy .... 195
BatoulSrour,StefanBruechert,SusanaL.A.Andrade,
andPetraHellwig
vii
viii Contents
11 NativeMassSpectrometryfor theCharacterizationofStructure
andInteractionsofMembraneProteins.................................... 205
JeroenF.vanDyck,AlbertKonijnenberg,andFrankSobott
12 MassSpectrometryofMitochondrialMembraneProteinComplexes.......... 233
LucNegroni,MichelZivy,andClaireLemaire
13 FunctionalStudiesonMembraneProteinsbyMeans
ofH/DExchangeinInfrared:StructuralChangesinNa+NQR
fromV.choleraeinthePresenceofLipids.................................. 247
YashvinNeehaul,SebastienKriegel,BlancaBarquera,
andPetraHellwig
14 ReconstitutionofMembraneProteinsinLiposomes ........................ 259
AliceVerche`re,IsabelleBroutin,andMartinPicard
15 IonChannelsasReportersofMembraneReceptorFunction:
AutomatedAnalysisinXenopusOocytes................................... 283
MichelVivaudou,ZlatomirTodorov,GinaCatalinaReyes-Mejia,
andChristopheMoreau
16 TheCRACAMRobot:Two-DimensionalCrystallization
ofMembraneProtein ................................................... 303
PhilippeRosier,Fre´de´ricGe´le´bart,NicolasDumesnil,
GauthierEsnot,ManuelaDezi,MarcMorand,
andCatherineVe´nien-Bryan
17 ReconstitutionofMembraneProteinsintoNanodiscs
forSingle-ParticleElectronMicroscopy ................................... 317
LaetitiaDaury,Jean-ChristopheTaveau,DimitriSalvador,
MarieGlavier,andOlivierLambert
18 Solid-StateNMRofMembraneProteinReconstituted
inProteoliposomes,theCaseofTSPO .................................... 329
LucileSenicourt,LuminitaDuma,VassiliosPapadopoulos,
andJean-JacquesLacapere
19 SamplePreparationforMembraneProteinStructural
StudiesbySolid-StateNMR.............................................. 345
DenisLacabanne,BrittaKunert,CaroleGardiennet,
BeatH.Meier,andAnjaB¨ockmann
20 SimulationofLigandBindingtoMembraneProteins ....................... 359
SamuelMurail
21 MolecularModelingofTransporters:FromLow
ResolutionCryo-ElectronMicroscopyMaptoConformational
Exploration.TheExampleofTSPO....................................... 383
AuroreVaitinadapouleandCatherineEtchebest
Index...................................................................... 417
Contributors
SUSANAL.A.ANDRADE (cid:1) BIOSSCentreforBiologicalSignallingStudies,Freiburg,Germany;
Institutfu€rBiochemie,Albert-Ludwigs-Universita€tFreiburg,Freiburg,Germany
LAURA BACIOU (cid:1) LaboratoiredeChimiePhysique,UMR8000CNRSUniversite´ ParisSud,
Universite´ ParisSaclay,Orsaycedex,France
AURE´LIE BADILLO (cid:1) InstitutdeBiologieetChimiedesProte´ines,MolecularMicrobiologyand
StructuralBiochemistry,LabexEcofect,UMR5086CNRS,Universite´ deLyon,Lyon,
France
BLANCABARQUERA (cid:1) DepartmentofBiologicalSciences,Center forBiotechnology
andInterdisciplinaryStudies,RensselaerPolytechnicInstitute,Troy,NY,USA
ALEXANDREBARRAS (cid:1) SysTEMM,IBGC,CNRS,UMR5095,IBGC,Bordeaux,France;
CNRS,UMR5248,CBMN,Universite´ deBordeaux,Pessac,France
TANIABIZOUARN (cid:1) LaboratoiredeChimiePhysique,UMR8000CNRSUniversite´ParisSud,
Universite´ ParisSaclay,Orsaycedex,France
ANJABO¨CKMANN (cid:1) InstitutdeBiologieetChimiedesProte´ines,MolecularMicrobiology
andStructuralBiochemistry,LabexEcofect,UMR5086CNRS,Universite´ deLyon,
Lyon,France
FRANC¸OISE BONNETE (cid:1) IBMMUMR5247CNRS-UM-ENSCM,ChimieBioOrganique
etSystemesAmphiphiles,Universited’Avignon,Avignon,France
ISABELLEBROUTIN (cid:1) LaboratoiredeCristallographieetRMNBiologiques,Faculte´ de
pharmacie,UMR8015CentreNationaldelaRechercheScientifique,Universite´ Paris
Descartes,Paris,France
STEFANBRUECHERT (cid:1) Institutfu€rBiochemie,Albert-Ludwigs-Universita€tFreiburg,
Freiburg,Germany
LAETITIADAURY (cid:1) CBMN,UMRCNRS5248,Universite´ deBordeaux,Pessac,France
CE´DRICDELUZ (cid:1) LaboratoryofPhysicalChemistryofPolymersandMembranes,Ecole
PolytechniqueFe´de´raledeLausanne,Lausanne,Switzerland
ALINE DESMYTER (cid:1) ArchitectureetFonctiondesMacromole´culesBiologiques,Unite´ Mixtede
Recherche7257CentreNationaldelaRechercheScientifique,Aix-Marseille,France
MANUELA DEZI (cid:1) IMPMC,UMR7590,UPMC-MNHN-IRD,Paris,France
LUMINITADUMA (cid:1) CNRSEnzymeandCellEngineeringLaboratory,SorbonneUniversite´s,
Universite´ deTechnologiedeCompie`gne,Compie`gneCedex,France
NICOLAS DUMESNIL (cid:1) IMPMC,UMR7590,UPMC-MNHN-IRD,Paris,France
JEROENF.VANDYCK (cid:1) BiomolecularandAnalyticalMassSpectrometryGroup,Chemistry
Department,UniversityofAntwerp,Antwerp,Belgium
GAUTHIERESNOT (cid:1) IMPMC,UMR7590,UPMC-MNHN-IRD,Paris,France
CATHERINEETCHEBEST (cid:1) Unite´ INSERMUMRS1134,InstitutNationaldelaTransfusion
Sanguine,Universite´ Paris7DenisDiderot,Paris,France
AYMEN EZZINE (cid:1) LaboratoiredeChimiePhysique,UMR8000CNRSUniversite´ ParisSud,
Universite´ ParisSaclay,Orsaycedex,France
MARIE-LAUREFOGERON (cid:1) InstitutdeBiologieetChimiedesProte´ines,MolecularMicrobiology
andStructuralBiochemistry,LabexEcofect,UMR5086CNRS,Universite´deLyon,Lyon,
France
ix
x Contributors
RE´MIFRONZES (cid:1) Unite´G5Biologiestructuraledelase´cre´tionbacte´rienne,InstitutPasteur,
Paris,France;UMR3528,CNRS,InstitutPasteur,Paris,France;EuropeanInstituteof
ChemistryandBiology,UniversityofBordeaux,Pessac,France;CNRSUMR5234
MicrobiologieFondamentaleetPathoge´nicite,Paris,France
CAROLEGARDIENNET (cid:1) MolecularMicrobiologyandStructuralBiochemistry,LabexEcofect,
UMR5086CNRS–Universite´ deLyon,Lyon,France;CRM2,UMR7036,CNRS,
Universite´ deLorraine,Vandoeuvre-le`s-Nancy,France
FRE´DE´RIC GE´LE´BART (cid:1) IMPMC,UMR7590,UPMC-MNHN-IRD,Paris,France
MARIE-FRANCE GIRAUD (cid:1) SysTEMM,IBGC,CNRS,UMR5095,Bordeaux,France;
Universite´ deBordeaux,Bordeaux,France
MARIEGLAVIER (cid:1) CBMN,UMRCNRS5248,Universite´ deBordeaux,Pessac,France
LUIGINOGRASSO (cid:1) LaboratoryofPhysicalChemistryofPolymersandMembranes,Ecole
PolytechniqueFe´de´raledeLausanne,Lausanne,Switzerland
FRANCESCAGUBELLINI (cid:1) Unite´ G5Biologiestructuraledelase´cre´tionbacte´rienne,
UMR3528CNRS,InstitutPasteur,Paris,France;UMR3528,CNRS,InstitutPasteur,
Paris,France;Unite´ deMicrobiologieStructurale,InstitutPasteur,Paris,France
LUCIE HARTMANN (cid:1) BiotechnologyandCellSignalling,IMPReSsProteinFacility,
UMR7242CNRS-UniversityofStrasbourg,Illkirch,France
GHE´RICIHASSA¨INE (cid:1) Theranyx,Marseille,France
CLAUDEHATTAB (cid:1) UMR-S1134,IntegratedBiologyofRedBloodCells,Inserm,Universite´
ParisDiderot,SorbonneParisCite´,InstitutNationaldelaTransfusionSanguine,
Laboratoired’ExcellenceGR-Ex,Paris,France
PETRA HELLWIG (cid:1) LaboratoiredeBioe´lectrochimieetSpectroscopie,UMR7140CNRS,
ChimiedelaMatie`reComplexe,Universite´ deStrasbourg,Strasbourg,France
RUUDHOVIUS (cid:1) LaboratoryofPhysicalChemistryofPolymersandMembranes,
EcolePolytechniqueFe´de´raledeLausanne,Lausanne,Switzerland
SORIAIATMANEN-HARBI (cid:1) SorbonneUniversite´s—UPMCUnivParis06,E´coleNormale
Supe´rieure—PSLResearchUniversity,De´partementdeChimie,CNRSUMR7203LBM,
Paris,France
ALBERTKONIJNENBERG (cid:1) BiomolecularandAnalyticalMassSpectrometryGroup,Chemistry
Department,UniversityofAntwerp,Antwerp,Belgium
SEBASTIENKRIEGEL (cid:1) LaboratoiredeBioe´lectrochimieetSpectroscopie,UMR7140CNRS,
Chimiedelamatie`recomplexe,Universite´ deStrasbourg,Strasbourg,France
BRITTAKUNERT (cid:1) MolecularMicrobiologyandStructuralBiochemistry,LabexEcofect,
UMR5086CNRS,Universite´ deLyon,Lyon,France
VILIUSKURAUSKAS (cid:1) Universite´ GrenobleAlpes,InstitutdeBiologieStructurale(IBS),
Grenoble,France;CNRS,IBS,Grenoble,France;CEA,IBS,Grenoble,France
DENIS LACABANNE (cid:1) MolecularMicrobiologyandStructuralBiochemistry,LabexEcofect,
UMR5086CNRS,Universite´ deLyon,Lyon,France
JEAN-JACQUESLACAPERE (cid:1) SorbonneUniversite´s—UPMCUnivParis06,E´coleNormale
Supe´rieure—PSLResearchUniversity,De´partementdeChimie,CNRSUMR7203LBM,
Paris,France
OLIVIER LAMBERT (cid:1) CBMN,UMRCNRS5248,Universite´ deBordeaux,Pessac,France
ISABELLELARRIEU (cid:1) SysTEMM,CNRS,UMR5095,IBGC,Bordeaux,France;Universite´ de
Bordeaux,Bordeaux,France
CLAIRELEMAIRE (cid:1) CNRS-UMR9198,CEA-IBITECS,Universite´ Paris-Sud,I2BC,
Gif-sur-Yvette,France
Contributors xi
XIAO-DANLI (cid:1) LaboratoryofBiomolecularResearch,PaulScherrerInstitute,
Villigen,Switzerland
PATRICKJ.LOLL (cid:1) DepartmentofBiochemistryandMolecularBiology,DrexelUniversity
CollegeofMedicine,Philadelphia,PA,USA
LAMIA MEBARKI (cid:1) Theranyx,Marseille,France
BEATH.MEIER (cid:1) PhysicalChemistry,ETHZurich,Zurich,Switzerland
ESTELLEMETZGER (cid:1) BiotechnologyandCellSignalling,IMPReSsProteinFacility,
UMR7242CNRS-UniversityofStrasbourg,Illkirch,France
SONJAMINNIBERGER (cid:1) Universite´ GrenobleAlpes,CNRS,CEA,CNRS,IBS,Grenoble,
France
MARCMORAND (cid:1) IMPMC,UMR7590,UPMC-MNHN-IRD,Paris,France
CHRISTOPHEMOREAU (cid:1) Univ.GrenobleAlpes,CNRS,CEA,CNRS,IBS,Grenoble,France
SAMUELMURAIL (cid:1) LaboratoiredeBiochimieThe´orique,CNRS,UPR9080,UniversityParis
Diderot,SorbonneParisCite´,Paris,France;AirLiquide,CentredeRecherchesParis-
Saclay,Jouy-en-Josas,France
YASHVINNEEHAUL (cid:1) LaboratoiredeBioe´lectrochimieetSpectroscopie,UMR7140,
ChimiedelaMatie`reComplexe,Universite´ deStrasbourg,Strasbourg,France;Mauritius
OceanographyInstitute,Albion,Mauritius
LUCNEGRONI (cid:1) CNRS-UMR5248,Universite´ deBordeaux,Bordeaux,France;IGBMC,
CNRS-UMR7104,Illkirch,France
HUGUESNURY (cid:1) Universite´ GrenobleAlpes,CNRS,CEA,CNRS,IBS,Grenoble,France
BENOIˆTODAERT (cid:1) CBMN,CNRS,UMR5248,Pessac,France;Universite´ deBordeaux,
Pessac,France
MARIANO ANIBALOSTUNI (cid:1) UMR-S1134,IntegratedBiologyofRedBloodCells,Inserm,
Universite´ ParisDiderot,SorbonneParisCite´,InstitutNationaldelaTransfusion
Sanguine,Laboratoired’ExcellenceGR-Ex,Paris,France
NOE´MIEOTTELARD (cid:1) BiotechnologyandCellSignalling,IMPReSsProteinFacility,
UMR7242CNRS-UniversityofStrasbourg,Illkirch,France
VASSILIOS PAPADOPOULOS (cid:1) TheResearchInstituteoftheMcGill,UniversityHealthCenter,
Montreal,Quebec,Canada;DepartmentofMedicine,McGillUniversity,Montreal,
Quebec,Canada
LUCIE PECLINOVSKA (cid:1) Universite´ GrenobleAlpes,CNRS,CEA,CNRS,IBS,Grenoble,
France
FRANC¸OIS PENIN (cid:1) InstitutdeBiologieetChimiedesProte´ines,MolecularMicrobiologyand
StructuralBiochemistry,LabexEcofect,UMR5086CNRS,Universite´ deLyon,Lyon,
France
MARTINPICARD (cid:1) LaboratoiredeBiologiePhysico-ChimiquedesProte´inesMembranaires,
UMR7099,InstitutdeBiologiePhysico-Chimique,FRC550,CentreNationaldela
RechercheScientifique,Universite´ Paris7,Paris,France
GINACATALINAREYES-MEJIA (cid:1) Universite´ GrenobleAlpes,InstitutdeBiologieStructurale
(IBS),Grenoble,France;CNRS,IBS,LabExICST,Grenoble,France;CEA,IBS,
Grenoble,France
PHILIPPEROSIER (cid:1) InstitutdeMine´ralogie,PhysiquedesMate´riauxetCosmochimie,UMR
7590CNRS-UPMC-MNHN-IRDCaseCourrier115,Paris,France
DIMITRISALVADOR (cid:1) CBMN,UMRCNRS5248,Universite´ deBordeaux,Pessac,France
CORINNESANCHEZ (cid:1) SysTEMM,IBGC,CNRS,UMR5095,Bordeaux,France;Universite´de
Bordeaux,Bordeaux,France