SNAREs: Methods and Protocols

399 Pages·2019·11.429 MB·English

by  Rutilio Fratti

Methods in
Molecular Biology 1860
Rutilio Fratti Editor
SNAREs
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
SNAREs
Methods and Protocols
Edited by
Rutilio Fratti
Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL, USA
Editor
RutilioFratti
DepartmentofBiochemistry
UniversityofIllinoisUrbana-Champaign
Urbana,IL,USA
ISSN1064-3745 ISSN1940-6029 (electronic)
MethodsinMolecularBiology
ISBN978-1-4939-8759-7 ISBN978-1-4939-8760-3 (eBook)
https://doi.org/10.1007/978-1-4939-8760-3
LibraryofCongressControlNumber:2018956143
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Preface
Eukaryotic cells are compartmentalized into membrane-bound organelles encased by a
plasma membrane. Vesicular content of membrane proteins and luminal constituents are
traffickedthroughcellsusingasetofhighlyregulatedpathwaysthatculminateinfusionwith
atargetmembraneandtransferofproducts.Thefusionofvesiclesiscriticalformaintaining
cellular homeostasis and is essential for the release of neurotransmitters, hormones, anti-
bodies,aswellastheturnoverofreceptors,thedestructionofpathogens,andthegeneration
of antigens. The machinery that controls membrane fusion is conserved from yeast to
mammals,andmechanismsdescribedinonesystemareapplicabletomostfusionmodels.
Althoughmembranetraffickingrequiresnumerousfactorssuchascargoreceptors,coat
proteins, Rab GTPases, and tethering factors, the terminal catalysts of fusion are SNAREs
(soluble N-ethylmaleimide-sensitive factor attachment protein receptors). All SNAREs
contain a canonical heptad repeat, termed a “SNARE motif,” that is flanked by various
N-terminaldomainsandC-terminalmembraneanchors.SNAREsformparallelfourhelical
bundlesthroughtheirSNAREmotifs.Theseregionsareprimarilycomposedofhydropho-
bicresidueswiththeexceptionofacentralpolarglutamine(Q),orarginine(R)thatinteract
in theionic zero layer. Each SNAREbundleiscomposed of3 Q-SNAREs donatedbyone
membraneand1R-SNAREbyitspartner membrane.
ThisbookcoversmanyofthewaysthatSNAREsandtheirfunctionareexaminedinthe
laboratory.Themethodsdescribedineachchapteraredescribedindetailsuchthatnoviceas
wellasexperiencedresearcherscanexplorethemechanismsofSNARE-mediatedmembrane
fusion. Therefore, I expect that this book will serve as a valuable tool for all investigators
interestedinthefield.
ThisvolumeofMethodsinMolecularBiologycontains26chaptersthataregroupedinto
sections, starting with Biophysical and Computational Alaysis of SNAREs. Part II is dedi-
catedBiochemicalmethodologiesforexaminingtheinteractions ofSNAREswith proteins
andlipids.PartIIIincludesFunctionalmethodsformeasuringSNAREcomplexformation,
calciumtransportandandmembranefusion.PartIViscomprisedofadvancedmicroscopy
methodstoobservemembranefusion.
Urbana,IL,USA RutilioFratti
v
Contents
Preface ..................................................................... v
Contributors................................................................. xi
PART I BIOPHYSICS AND COMPUTATIONAL ANALYSIS
1 MolecularDynamicsSimulationsoftheSNAREComplex ................... 3
MariaBykhovskaia
2 MesoscaleComputationalModelingofProtein-Membrane
InteractionsBasedonContinuumMean-FieldTheory ...................... 15
GeorgeKhelashvili
3 EPRLineshapeAnalysistoInvestigatetheSNAREFolding
Intermediates........................................................... 33
RyanKhounlo,BrendenJ.D.Hawk,andYeon-KyunShin
4 DynamicLightScatteringAnalysistoDissectIntermediates
ofSNARE-MediatedMembraneFusion ................................... 53
ByoungjaeKong,YoosooYang,andDae-HyukKweon
5 SNAREpinAssembly:KineticandThermodynamicApproaches .............. 71
FengLiandFredericPincet
6 Single-MoleculeOpticalTweezersStudyofRegulatedSNARE
Assembly............................................................... 95
LuMa,JunyiJiao,andYongliZhang
7 StudyingMunc18:SyntaxinInteractionsUsingSmall-Angle
Scattering.............................................................. 115
AndrewE.Whitten,RussellJ.Jarrott,Shu-HongHu,AnthonyP.Duff,
GordonJ.King,JenniferL.Martin,andMichelleP.Christie
8 UsingForceSpectroscopytoProbeCoiled-CoilAssembly
andMembraneFusion................................................... 145
HannesWittandAndreasJanshoff
PART II BIOCHEMISTRY
9 SNAP-25S-GuanylationandSNAREComplexFormation................... 163
YusukeKishimoto,TakaakiAkaike,andHideshiIhara
10 AnalysisoftheRoleofSec3inSNAREAssembly
andMembraneFusion................................................... 175
KunrongMei,PengYue,andWeiGuo
11 UseofMicroscaleThermophoresis(MST)toMeasureBinding
AffinitiesofComponentsoftheFusionMachinery.......................... 191
RobertP.SparksandRutilioFratti
vii
viii Contents
12 UseofSurfacePlasmonResonance(SPR)toDetermine
BindingAffinitiesandKineticParametersBetweenComponents
ImportantinFusionMachinery .......................................... 199
RobertP.Sparks,JermaineL.Jenkins,andRutilioFratti
13 DeterminationofSec18-LipidInteractionsbyLiposome-Binding
Assay.................................................................. 211
MatthewL.StarrandRutilioFratti
14 UsingNanodiscstoProbeCa2+-DependentMembraneInteraction
ofSynaptotagmin-1..................................................... 221
EkaterinaStroevaandShyamS.Krishnakumar
15 FunctionalReconstitutionofIntracellularVesicleFusion
UsingPurifiedSNAREsandSec1/Munc18(SM)Proteins................... 237
HaijiaYu,LaurenCrisman,MichaelH.B.Stowell,andJingshiShen
PART III FUNCTIONAL ASSAYS
16 AssayofLipidMixingandFusionPoreFormationintheFusion
ofYeastVacuoles........................................................ 253
MassimoD’AgostinoandAndreasMayer
17 ANanodisc-CellFusionAssaywithSingle-PoreSensitivity
andSub-millisecondTimeResolution..................................... 263
NatashaR.Dudzinski,ZhenyongWu,andErdemKaratekin
18 AnInVitroAssayofTrans-SNAREComplexFormationDuringYeast
VacuoleFusionUsingEpitopeTag-FreeSNAREs .......................... 277
YoungsooJun
19 ACell-FreeContentMixingAssayforSNARE-Mediated
MultivesicularBody-VacuoleMembraneFusion ............................ 289
MahmoudAbdulKarim,DieterRonnySamyn,
andChristopherLeonardBrett
20 ReconstitutedProteoliposomeFusionMediatedbyYeast
SNARE-FamilyProteins................................................. 303
JojiMima
21 Real-TimeFluorescenceDetectionofCalciumEfflux
DuringVacuolarMembraneFusion....................................... 323
GregoryE.MinerandRutilioFratti
PART IV MICROSCOPY
22 Single-MoleculeFluorescenceMeasurementofSNARE-Mediated
VesicleFusion .......................................................... 335
YachongHu,ZhiqiTian,andJiajieDiao
23 QuantifyingIntramolecularProteinConformationalDynamics
UnderLipidInteractionUsingsmFRETandFCCS......................... 345
PeiLi,YaweiDai,MarkusSeeger,andYan-WenTan
Contents ix
24 VisualizationofSNARE-MediatedOrganelleMembrane
HemifusionbyElectronMicroscopy ...................................... 361
SevanMattie,TomKazmirchuk,JeannieMui,HojatollahVali,
andChristopherLeonardBrett
25 StudiesoftheSecretoryMachineryDynamicsbyTotalInternal
ReflectionFluorescenceMicroscopyinBovineAdrenalChromaffin
Cells .................................................................. 379
Jose´Villanueva,YolandaGimenez-Molina,andLuisM.Gutie´rrez
26 ImagingSNAP-29inDrosophila ......................................... 391
HaoXuandBryanStewart
Index ...................................................................... 403
Contributors
TAKAAKIAKAIKE (cid:1) DepartmentofEnvironmentalMedicineandMolecularToxicology,Tohoku
UniversityGraduateSchoolofMedicine,Sendai,Japan
CHRISTOPHERLEONARD BRETT (cid:1) DepartmentofBiology,ConcordiaUniversity,Montre´al,
QC,Canada
MARIABYKHOVSKAIA (cid:1) DepartmentofNeurology,WayneStateUniversitySchoolofMedicine,
Detroit,MI,USA;DepartmentofAnatomyandCellBiology,WayneStateUniversity
SchoolofMedicine,Detroit,MI,USA
MICHELLEP.CHRISTIE (cid:1) Bio21MolecularScienceandBiotechnologyInstitute,TheUniversity
ofMelbourne,Parkville,VIC,Australia
LAUREN CRISMAN (cid:1) DepartmentofMolecular,CellularandDevelopmentalBiology,
UniversityofColorado,Boulder,CO,USA
MASSIMOD’AGOSTINO (cid:1) De´partementdeBiochimie,Universite´deLausanne,Epalinges,
Switzerland
YAWEIDAI (cid:1) StateKeyLaboratoryofSurfacePhysicsandDepartmentofPhysics,Fudan
University,Shanghai,China;DepartmentofPhysics,TheUniversityofHongKong,Hong
Kong,China
JIAJIEDIAO (cid:1) DepartmentofCancerBiology,UniversityofCincinnatiCollegeofMedicine,
Cincinnati,OH,USA
NATASHAR.DUDZINSKI (cid:1) InterdepartmentalNeuroscienceProgram,YaleUniversity,New
Haven,CT,USA;NanobiologyInstitute,YaleUniversity,WestHaven,CT,USA
ANTHONYP.DUFF (cid:1) AustralianNuclearScienceandTechnologyOrganisation,Lucas
Heights,NSW,Australia
RUTILIOFRATTI (cid:1) DepartmentofBiochemistry,UniversityofIllinoisatUrbana-Champaign,
Urbana,IL,USA
YOLANDAGIMENEZ-MOLINA (cid:1) InstitutodeNeurociencias,CentroMixtoCSIC-Universidad
MiguelHerna´ndez,SantJoand’Alacant,Alicante,Spain
WEIGUO (cid:1) DepartmentofBiology,UniversityofPennsylvania,Philadelphia,PA,USA
LUIS M.GUTIE´RREZ (cid:1) InstitutodeNeurociencias,CentroMixtoCSIC-UniversidadMiguel
Herna´ndez,SantJoand’Alacant,Alicante,Spain
BRENDENJ.D.HAWK (cid:1) RoyJ.CarverDepartmentofBiochemistry,BiophysicsandMolecular
Biology,IowaStateUniversity,Ames,IA,USA
SHU-HONG HU (cid:1) GriffithInstituteforDrugDiscovery,GriffithUniversity,Nathan,QLD,
Australia
YACHONGHU (cid:1) DepartmentofCancerBiology,UniversityofCincinnatiCollegeofMedicine,
Cincinnati,OH,USA;SchoolofLifeScienceandTechnology,Xi’anJiaotongUniversity,
Xi’an,China
HIDESHIIHARA (cid:1) DepartmentofBiologicalScience,GraduateSchoolofScience,Osaka
PrefectureUniversity,Sakai,Japan
ANDREASJANSHOFF (cid:1) InstituteofPhysicalChemistry,UniversityofGoettingen,Go¨ttingen,
Germany
RUSSELL J.JARROTT (cid:1) GriffithInstituteforDrugDiscovery,GriffithUniversity,Nathan,
QLD,Australia
xi
xii Contributors
JERMAINEL.JENKINS (cid:1) StructuralBiologyandBiophysicsFacility,UniversityofRochester,
Rochester,NY,USA
JUNYIJIAO (cid:1) DepartmentofCellBiology,YaleUniversitySchoolofMedicine,NewHaven,
CT,USA;IntegratedGraduatePrograminPhysicalandEngineeringBiology,New
Haven,CT,USA
YOUNGSOOJUN (cid:1) SchoolofLifeSciences,CellLogisticsResearchCenter,andSilverHealthBio
ResearchCenter,GwangjuInstituteofScienceandTechnology,Gwangju,Republicof
Korea
ERDEM KARATEKIN (cid:1) NanobiologyInstitute,YaleUniversity,WestHaven,CT,USA;
DepartmentofCellularandMolecularPhysiology,YaleUniversitySchoolofMedicine,New
Haven,CT,USA;DepartmentofMolecularBiophysicsandBiochemistry,YaleUniversity,
NewHaven,CT,USA;CentreNationaldelaRechercheScientifique(CNRS),Paris,
France
MAHMOUD ABDUL KARIM (cid:1) DepartmentofBiology,ConcordiaUniversity,Montre´al,QC,
Canada;DepartmentofCellBiology,UniversityofAlberta,Edmonton,AB,Canada
TOMKAZMIRCHUK (cid:1) DepartmentofBiology,ConcordiaUniversity,Montre´al,QC,Canada
GEORGEKHELASHVILI (cid:1) DepartmentofPhysiologyandBiophysics,WeillCornellMedical
CollegeofCornellUniversity,NewYork,NY,USA;InstituteforComputational
Biomedicine,WeillCornellMedicalCollegeofCornellUniversity,NewYork,NY,USA
RYANKHOUNLO (cid:1) RoyJ.CarverDepartmentofBiochemistry,BiophysicsandMolecular
Biology,IowaStateUniversity,Ames,IA,USA
GORDONJ.KING (cid:1) CentreforMicroscopyandMicroanalysis,TheUniversityofQueensland,St
Lucia,QLD,Australia
YUSUKEKISHIMOTO (cid:1) DepartmentofBiologicalScience,GraduateSchoolofScience,Osaka
PrefectureUniversity,Sakai,Japan
BYOUNGJAEKONG (cid:1) DepartmentofIntegrativeBiotechnology,CollegeofBiotechnologyand
Bioengineering,SungkyunkwanUniversity,Suwon,RepublicofKorea
SHYAMS.KRISHNAKUMAR (cid:1) DepartmentofCellBiology,YaleUniversitySchoolofMedicine,
NewHaven,CT,USA;DepartmentofClinicalandExperimentalEpilepsy,Instituteof
Neurology,UniversityCollegeLondon,London,UK
DAE-HYUKKWEON (cid:1) DepartmentofIntegrativeBiotechnology,CollegeofBiotechnologyand
Bioengineering,SungkyunkwanUniversity,Suwon,RepublicofKorea;Biomedical
InstituteforConvergence,SungkyunkwanUniversity,Suwon,RepublicofKorea
FENGLI (cid:1) DepartmentofCellBiologyandNanobiologyInstitute,SchoolofMedicine,Yale
University,NewHaven,CT,USA
PEILI (cid:1) StateKeyLaboratoryofSurfacePhysicsandDepartmentofPhysics,Fudan
University,Shanghai,China
LUMA (cid:1) BeijingNationalLaboratoryforCondensedMatterPhysicsandCASKey
LaboratoryofSoftMatterPhysics,InstituteofPhysics,ChineseAcademyofSciences,Beijing,
China
JENNIFERL.MARTIN (cid:1) GriffithInstituteforDrugDiscovery,GriffithUniversity,Nathan,
QLD,Australia
SEVANMATTIE (cid:1) DepartmentofBiology,ConcordiaUniversity,Montre´al,QC,Canada;
MontrealNeurologicalHospitalandInstitute,McGillUniversity,Montre´al,QC,Canada
ANDREASMAYER (cid:1) De´partementdeBiochimie,Universite´deLausanne,Epalinges,
Switzerland
KUNRONGMEI (cid:1) DepartmentofBiology,UniversityofPennsylvania,Philadelphia,PA,USA
JOJIMIMA (cid:1) InstituteforProteinResearch,OsakaUniversity,Osaka,Japan