Table Of ContentMethods in
Molecular Biology 1779
Einar M. Sigurdsson
Miguel Calero
María Gasset Editors
Amyloid
Proteins
Methods and Protocols
Third Edition
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
Amyloid Proteins
Methods and Protocols
Third Edition
Edited by
Einar M. Sigurdsson
Department of Neuroscience and Physiology, New York University School of Medicine, New York
University Langone Health, New York, NY, USA; Department of Psychiatry, New York University
School of Medicine, New York University Langone Health, New York, NY, USA
Miguel Calero
Chronic Disease Programme-CROSADIS, CIBERNED, Queen Sofia Foundation Alzheimer Center, CIEN
Foundation, Instituto de Salud Carlos III, Madrid, Spain
María Gasset
Institute of Physical Chemistry “Rocasolano”, Spanish National Research Council (CSIC), Madrid, Spain
Editors
EinarM.Sigurdsson MiguelCalero
DepartmentofNeuroscience ChronicDiseaseProgramme-CROSADIS
andPhysiology CIBERNED,QueenSofiaFoundation
NewYorkUniversitySchool AlzheimerCenter
ofMedicine CIENFoundation,Institutode
NewYorkUniversityLangone SaludCarlosIII
Health Madrid,Spain
NewYork,NY,USA
DepartmentofPsychiatry
NewYorkUniversitySchool
ofMedicine
NewYorkUniversityLangone
Health
NewYork,NY,USA
Mar´ıaGasset
InstituteofPhysicalChemistry“Rocasolano”
SpanishNationalResearchCouncil(CSIC)
Madrid,Spain
ISSN1064-3745 ISSN1940-6029 (electronic)
MethodsinMolecularBiology
ISBN978-1-4939-7815-1 ISBN978-1-4939-7816-8 (eBook)
https://doi.org/10.1007/978-1-4939-7816-8
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Preface
Amyloiddiseasesarecharacterizedbythedepositionofinsolublefibrousamyloidproteins.
Theword“amyloid”indicatesastarch-likecompoundand,thoughamisnomer,continues
tobetheacceptedtermfor thisgroupofproteinconformationaldisorders.Approximately
30differentproteinscanformamyloidandalthoughthereisusually nohomologyintheir
amino acid sequence, all share a β-pleated sheet as the polymer scaffold. Historically, these
β-pleated deposits were detected by histological dyes, and the characteristic fibril structure
confirmedwithelectronmicroscopy.Astheseamyloidswerepurifiedandsequenced,various
in vitro techniques were developed, often using synthetic peptides or highly purified
amyloids derived from diseased tissue. Development of animal models occurred concur-
rently and some of these diseases can now be passed on to animals by injecting them with
amyloid-rich tissue fractions, or shown to spread between cells in vivo or in culture,
suggesting a transmissible nature of these protein polymers. However, for most amyloi-
doses,transgenictechnologyhasbeennecessaryforrecapitulatingthediseasebutitsseverity
canbeenhancedbyamyloidseeding.Together,theseinvitroandinvivomodelshavebeen
usedtounderstandtheetiologyandpathogenesisofamyloiddiseasesaswellastoscreenfor
drugstopreventtheformationofand/orclear theseaggregates.
Several of these methods and protocols are detailed in this third edition of Amyloid
Proteins:MethodsandProtocols,usingexamplesfromvariousamyloids.Substantialchanges
havebeenmadefromthesecondeditionofthisvolume.Severalclassicmethods/protocols
that did not warrant updates are not included in the third edition. Importantly, numerous
new chapters have been added that cover new techniques and topics not addressed in the
second edition. The volume is divided into three parts. Part I contains in vitro assays that
focus on preparation of various amyloids and their precursors or detail specific analytical
methodsforstudyingthesepeptidesandproteins.PartIIdescribescellculturemodelsand
assays for production of amyloid proteins, and Part III consists of protocols for amyloid
extractionfromtissue,itsdetectionandcharacterizationinvitroandinvivo,andassaysthat
are modulated by amyloids. Most of the chapters follow a similar format and are detailed
protocols for performing a particular procedure. However, certain chapters focus more on
generalprinciplesandtheoreticalissuesofaparticular method.
Itisourhopethatthesearticleswillbeusefulbothforstudentsandscientistsnewtothe
amyloid field,as wellas forseasoned investigators learningnewtechniques to further their
research.
Wewouldliketothanktheauthorsfortheircontributionandtheserieseditor,Dr.John
M.Walker,for theopportunitytoeditthisbook.
NewYork,NY,USA EinarM.Sigurdsson
Madrid,Spain MiguelCalero
Madrid,Spain Marı´aGasset
v
Contents
Preface ..................................................................... v
Contributors................................................................. xi
PART I IN VITRO MODELS AND ASSAYS
1 PreparationofPurePopulationsofAmyloidβ-ProteinOligomers
ofDefinedSize ......................................................... 3
EricY.Hayden,JosephL.Conovaloff,AshleyMason,GalBitan,
andDavidB.Teplow
2 PreparationofaWell-DefinedandStableβ-BarrelPore-Forming
Aβ42Oligomer......................................................... 13
MontserratSerra-Batiste,Martı´ Ninot-Pedrosa,EduardPuig,
SoniaCiudad,MargaridaGairı´,andNat`aliaCarulla
3 UnveilingBrainAβHeterogeneityThroughTargeted
ProteomicAnalysis...................................................... 23
AguedaRostagno,ThomasA.Neubert,andJorgeGhiso
4 Preparationofα-SynucleinAmyloidAssembliesforToxicity
Experiments............................................................ 45
SereneW.ChenandNuniloCremades
5 GenerationandCharacterizationofStableα-SynucleinOligomers ............ 61
LeireAlmandoz-Gil,MartinIngelsson,andJoakimBergstr¨om
6 InVitroAnalysisofα-SynucleinAmyloidFormation
andCross-Reactivity..................................................... 73
IstvanHorvath,SandraRocha,andPernillaWittung-Stafshede
7 PreparationofTauOligomersAfter theProteinExtraction
fromBacteriaandBrainCortices.......................................... 85
ElentinaK.Argyrousi,AgnieszkaStaniszewski,RussellE.Nicholls,
andOttavioArancio
8 PurificationandCharacterizationofLow-nTauOligomers .................. 99
SenthilvelrajanKaniyappan,RamReddyChandupatla,
andEckhardMandelkow
9 PreparationandCharacterizationofTauOligomerStrains................... 113
UrmiSengupta,MarianaCarretero-Murillo,andRakezKayed
10 PurificationandFibrillationofRecombinantHumanAmyloid-β,
PrionProtein,andTauUnderNativeConditions........................... 147
AlexanderSandbergandSofieNystr¨om
11 PreparationofAmyloidogenicAggregatesfromEF-Hand
β-ParvalbuminandS100Proteins......................................... 167
JavierMartı´nez,JoanaS.Crist(cid:1)ova˜o,RosaSa´nchez,MariaGasset,
andCla´udioM.Gomes
vii
viii Contents
12 KineticAnalysisofAmyloidFormation.................................... 181
GeorgMeisl,ThomasC.T.Michaels,SaraLinse,andTuomasP.J.Knowles
13 MappingAmyloidRegionsinGadm1withPeptideArrays.................. 197
RosaSa´nchez,JavierMartı´nez,LauraMontoya,MilagrosCastellanos,
andMariaGasset
14 NoninvasiveStructuralAnalysisofIntermediateSpeciesDuring
Fibrillation:AnApplicationofSmall-AngleX-RayScattering................. 209
AnnetteEvaLangkilde,Fa´timaHerranz-Trillo,PauBernad(cid:1)o,
andBenteVestergaard
15 AnalysisofCovalentModificationsofAmyloidogenicProteinsUsing
Two-DimensionalElectrophoresis:PrionProteinandItsSialylation .......... 241
ElizavetaKatorchaandIliaV.Baskakov
16 AmplificationandDetectionofMinusculeAmountsofMisfolded
PrionProteinbyUsingtheReal-TimeQuaking-InducedConversion ......... 257
MatthiasSchmitz,Niccolo` Candelise,FrancLlorens,andIngaZerr
PART II CELL CULTURE MODELS AND ASSAYS
17 BacterialAmyloids ...................................................... 267
MargeryL.Evans,ElizabethGichana,YizhouZhou,
andMatthewR.Chapman
18 AddressingIntracellularAmyloidosisinBacteriawithRepA-WH1,
aPrion-LikeProtein .................................................... 289
LauraMolina-Garcı´a,Fa´timaGasset-Rosa,Marı´aMoreno-delA´lamo,
SusanaMoreno-Dı´azdelaEspina,andRafaelGiraldo
19 StudyofAmyloidsUsingYeast ........................................... 313
ReedB.Wickner,DmitryKryndushkin,FrankShewmaker,
RyanMcGlinchey,andHermanK.Edskes
20 NeurotoxicCa2+SignalingInducedbyAmyloid–βOligomers
inAgedHippocampalNeuronsInVitro................................... 341
Lucı´aNu´n˜ez,Marı´aCalvo-Rodrı´guez,EricaCaballero,
M(cid:1)onicaGarcı´a-Durillo,andCarlosVillalobos
21 PreparationandCulturingofHumanPrimaryVascularCells................. 355
FinnbogiR.Thormodsson,IngvarH.Olafsson,andDadiTh.Vilhjalmsson
22 LiveImagingofPathologicalTauProteinandTauAntibodies
inaNeuron-LikeCellularModel ......................................... 371
DovB.Shamir,YanDeng,andEinarM.Sigurdsson
23 EffectsofAmyloid-βPeptideontheBiologyofHuman
NeuralStemCells....................................................... 381
AdelaBernabeu-Zornoza,RaquelCoronel,Marı´aLachgar,
CharlottePalmer,andIsabelListe
Contents ix
PART III IN VIVO MODELS AND ASSAYS
24 DevelopmentofMouseMonoclonalAntibodiesAgainstHuman
AmyloidFibrilProteinsforDiagnosticandResearchPurposes ............... 401
GunillaT.Westermark,ElisabetIhse,andPerWestermark
25 IdentificationandCharacterizationofAmyloid-βAccumulation
inSynapticMitochondria ................................................ 415
ShiFangYan,FirozAkhter,AlexanderA.Sosunov,andShirleyShiDuYan
26 BiochemicalPropertiesofPathology-RelatedTauSpecies
inTauopathyBrains:AnExtractionProtocolforTauOligomers
andAggregates......................................................... 435
NaruhikoSaharaandTaekoKimura
27 TauAssemblyintoFilaments............................................. 447
MarPe´rez,RaquelCuadros,andMiguelMedina
28 QuantitativeMetabolomicsinAlzheimer’sDisease:Technical
ConsiderationsforImprovedReproducibility .............................. 463
SergioVeiga,JudithWahrheit,Andre´sRodrı´guez-Martı´n,
andDeniseSonntag
29 DetectingCirculatingMicroRNAsasBiomarkersinAlzheimer’sDisease ...... 471
AidanKenny,EvaM.Jimenez-Mateos,MiguelCalero,MiguelMedina,
andTobiasEngel
30 Luminescent-ConjugatedOligothiopheneProbeApplications
forFluorescenceImagingofPureAmyloidFibrilsandProtein
AggregatesinTissues.................................................... 485
K.PeterR.Nilsson,MikaelLindgren,andPerHammarstr¨om
31 CharacterizationofAmyloid-βPlaquesandAutofluorescent
LipofuscinAggregatesinAlzheimer’sDiseaseBrain:AConfocal
MicroscopyApproach ................................................... 497
AlejandraKun,FernandoGonza´lez-Camacho,SilviaHerna´ndez,
AlexandraMoreno-Garcı´a,OlgaCalero,andMiguelCalero
32 InVivoImagingofTauopathyinMice.................................... 513
SenthilkumarKrishnaswamy,QianWu,YanLin,
WajithaJ.Rajamohamedsait,HameethaB.Rajamohamedsait,
andEinarM.Sigurdsson
33 InVivoEvaluationofNeuronalTransportinMurineModels
ofNeurodegenerationUsingManganese-EnhancedMRI.................... 527
AnneBertrand,MariaBaron,DungM.Hoang,LindsayK.Hill,
SebastianL.Mendoza,EinarM.Sigurdsson,andYoussefZ.Wadghiri
Index ...................................................................... 543
Contributors
FIROZAKHTER (cid:1) DepartmentofPharmacologyandToxicology,HiguchiBioscienceCenter,
SchoolofPharmacy,UniversityofKansas,Lawrence,KS,USA
LEIREALMANDOZ-GIL (cid:1) MolecularGeriatrics,DepartmentofPublicHealthandCaring
Sciences,UppsalaUniversity,Uppsala,Sweden
OTTAVIO ARANCIO (cid:1) DepartmentofPathologyandCellBiology,ColumbiaUniversity,
NewYork,NY,USA;TheTaubInstituteforResearchonAlzheimer’sDiseaseandthe
AgingBrain,ColumbiaUniversity,NewYork,NY,USA;DepartmentofMedicine,
ColumbiaUniversity,NewYork,NY,USA
ELENTINAK.ARGYROUSI (cid:1) DepartmentofPathologyandCellBiology,ColumbiaUniversity,
NewYork,NY,USA;TheTaubInstituteforResearchonAlzheimer’sDiseaseandthe
AgingBrain,ColumbiaUniversity,NewYork,NY,USA;DepartmentofPsychiatryand
Neuropsychology,SchoolforMentalHealthandNeuroscience(MHeNS),Maastricht
University,Maastricht,TheNetherlands
MARIABARON (cid:1) DepartmentofRadiology,Center forAdvancedImagingInnovationand
Research(CAI2R),BernardandIreneSchwartzCenter forBiomedicalImaging,
NYUSchoolofMedicineandNYULangoneHealth,NewYork,NY,USA
ILIAV.BASKAKOV (cid:1) DepartmentofAnatomyandNeurobiology,Center forBiomedical
EngineeringandTechnology,UniversityofMarylandSchoolofMedicine,Baltimore,MD,
USA
JOAKIMBERGSTRO¨M (cid:1) MolecularGeriatrics,DepartmentofPublicHealthandCaring
Sciences,UppsalaUniversity,Uppsala,Sweden
ADELABERNABEU-ZORNOZA (cid:1) UnidaddeRegeneraci(cid:1)onNeural,UnidadFuncionalde
Investigaci(cid:1)ondeEnfermedadesCr(cid:1)onicas,InstitutodeSaludCarlosIII(ISCIII),Madrid,
Spain
PAUBERNADO´ (cid:1) CentredeBiochimieStructurale(CBS),INSERM,CNRS,Universitede
Montpellier,Montpellier,France
ANNEBERTRAND (cid:1) DepartmentofRadiology,CenterforAdvancedImagingInnovationand
Research(CAI2R),BernardandIreneSchwartzCenter forBiomedicalImaging,NYU
SchoolofMedicineandNYULangoneHealth,NewYork,NY,USA;InstitutduCerveau
etlaMoelle(ICM),AP-HP—HoˆpitalPitie´-Salpeˆtrie`re,Boulevarddel’hoˆpital,Sorbonne
Universite´s,UPMCUniv.Paris06,INSERM,CNRS,Paris,France;INRIAParis,
AramisProject-Team,Paris,France
GALBITAN (cid:1) DepartmentofNeurology,MolecularBiologyInstitute,BrainResearch
Institute,DavidGeffenSchoolofMedicineatUCLA,UniversityofCalifornia,Los
Angeles,LosAngeles,CA,USA
ERICA CABALLERO (cid:1) InstitutodeBiologı´ayGene´ticaMolecular(IBGM),Universidadde
ValladolidyConsejoSuperiordeInvestigacionesCientı´ficas(CSIC),Valladolid,Spain
MIGUELCALERO (cid:1) ChronicDiseaseProgramme-CROSADIS,CIBERNED,QueenSofia
FoundationAlzheimerCenter,CIENFoundation,InstitutodeSaludCarlosIII,Madrid,
Spain
OLGACALERO (cid:1) ChronicDiseaseProgramme-CROSADIS,CentrodeInvestigaci(cid:1)on
Biome´dicaenRedsobreEnfermedadesNeurodegenerativas(CIBERNED),Institutode
SaludCarlosIII,Madrid,Spain
xi
xii Contributors
MARI´ACALVO-RODRI´GUEZ (cid:1) InstitutodeBiologı´ayGene´ticaMolecular(IBGM),
UniversidaddeValladolidyConsejoSuperiordeInvestigacionesCientı´ficas(CSIC),
Valladolid,Spain;Alzheimer’sDiseaseResearchLaboratory,DepartmentofNeurology,
MassachusettsGeneralInstituteforNeurodegenerativeDisease,MassachusettsGeneral
Hospital,HarvardMedicalSchool,Charlestown,MA,USA
NICCOLO` CANDELISE (cid:1) DepartmentofNeurology,UniversityMedicineGoettingenand
GermanCenter forNeurodegenerativeDiseases(DZNE)–siteGo¨ttingen,Go¨ttingen,
Germany
MARIANA CARRETERO-MURILLO (cid:1) GeorgeP.andCynthiaWoodsMitchellCenter for
NeurodegenerativeDiseases,UniversityofTexasMedicalBranch,Galveston,TX,USA;
DepartmentofNeurology,UniversityofTexasMedicalBranch,Galveston,TX,USA;
DepartmentofNeuroscienceandCellBiology,UniversityofTexasMedicalBranch,
Galveston,TX,USA
NATA`LIACARULLA (cid:1) InstituteforResearchinBiomedicine(IRBBarcelona),TheBarcelona
InstituteScienceandTechnology,Barcelona,Spain;CBMN(UMR5248),Universityof
Bordeaux—CNRS—IPB,InstitutEurope´endeChimieetBiologie,Pessac,France
MILAGROSCASTELLANOS (cid:1) IMDEANacoscience,Madrid,Spain
RAMREDDYCHANDUPATLA (cid:1) GermanCenterforNeurodegenerativeDiseases(DZNE),Bonn,
Germany;Max-Planck-InstituteforMetabolismResearch(Cologne),Hamburg,Germany
MATTHEWR.CHAPMAN (cid:1) DepartmentofMolecular,Cellular,andDevelopmentalBiology,
UniversityofMichigan,AnnArbor,MI,USA
SERENEW.CHEN (cid:1) DepartmentofChemistry,UniversityofCambridge,Cambridge,UK
SONIACIUDAD (cid:1) InstituteforResearchinBiomedicine(IRBBarcelona),TheBarcelona
InstituteScienceandTechnology,Barcelona,Spain;CBMN(UMR5248),Universityof
Bordeaux—CNRS—IPB,InstitutEurope´endeChimieetBiologie,Pessac,France
JOSEPH L.CONOVALOFF (cid:1) DepartmentofNeurology,MolecularBiologyInstitute,Brain
ResearchInstitute,DavidGeffenSchoolofMedicineatUCLA,UniversityofCalifornia,
LosAngeles,LosAngeles,CA,USA
RAQUEL CORONEL (cid:1) UnidaddeRegeneraci(cid:1)onNeural,UnidadFuncionaldeInvestigaci(cid:1)on
deEnfermedadesCr(cid:1)onicas,InstitutodeSaludCarlosIII(ISCIII),Madrid,Spain
NUNILO CREMADES (cid:1) InstituteforBiocomputationandPhysicsofComplexSystems(BIFI)-
JointUnitBIFI-IQFR(CSIC),UniversityofZaragoza,Zaragoza,Spain
JOANA S.CRISTO´VA˜O (cid:1) BiosystemsandIntegrativeSciencesInstitute,FaculdadedeCieˆncias,
UniversidadedeLisboa,Lisboa,Portugal;DepartamentodeQuı´micaeBioquı´mica,
UniversidadedeLisboa,Lisboa,Portugal
RAQUEL CUADROS (cid:1) CentrodeBiologı´aMolecular“SeveroOchoa”CSIC-UAM,Madrid,
Spain
YANDENG (cid:1) MicroscopyCore,NewYorkUniversitySchoolofMedicine,NewYork,NY,USA
HERMANK.EDSKES (cid:1) LaboratoryofBiochemistryandGenetics,NationalInstituteofDiabetes
DigestiveandKidneyDiseases,NationalInstitutesofHealth,Bethesda,MD,USA
TOBIASENGEL (cid:1) DepartmentofPhysiologyandMedicalPhysics,RoyalCollegeofSurgeonsin
Ireland,Dublin2,Ireland
MARGERYL.EVANS (cid:1) DepartmentofMolecular,Cellular,andDevelopmentalBiology,
UniversityofMichigan,AnnArbor,MI,USA
MARGARIDAGAIRI´ (cid:1) NMRFacility,ScientificandTechnologicalCenters,Universityof
Barcelona(CCiTUB),Barcelona,Spain
