Microcalorimetry of Biological Molecules: Methods and Protocols

264 Pages·2019·6.42 MB·English

by  Eric Ennifar

Methods in
Molecular Biology 1964
Eric Ennifar Editor
Microcalorimetry
of Biological
Molecules
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
Microcalorimetry of Biological
Molecules
Methods and Protocols
Edited by
Eric Ennifar
Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, CNRS, Strasbourg, France
Editor
EricEnnifar
InstitutdeBiologieMole´culaireetCellulaire
Universite´deStrasbourg,CNRS
Strasbourg,France
ISSN1064-3745 ISSN1940-6029 (electronic)
MethodsinMolecularBiology
ISBN978-1-4939-9178-5 ISBN978-1-4939-9179-2 (eBook)
https://doi.org/10.1007/978-1-4939-9179-2
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Preface
Although structural biology is key to elucidate molecular architecture of biological mole-
cules, thermodynamic and kinetic data are yet an essential and necessary complement to
structuralstudies foracomprehensiveunderstandingofbindingmechanisms andmechan-
ismsofaction.Structuraldataalone,evenwhenassociatedwithsophisticatedcomputational
methods, cannot fully define the driving forces for binding interactions or even accurately
predict their binding affinities or kinetics. Thermodynamics and kinetics provide quantita-
tivedatarequiredtounderstandthesedrivingforces,thetimeinwhichdruganditstarget
associateanddissociate,andforevaluatingandunderstandingatadeeperleveltheeffectsof
substituentchangesonbindingaffinity.Microcalorimetryistheonlydirectmethodyielding
thermodynamic parameters without the use of any label. Among the key advantages, it is
relatively artifacts-free, not limited by the ligand or protein sizes, and offers a precise
determinationofaffinitiesamongotherkeydata.
Thefirstpartofthisvolumeisdedicatedtodifferentialscanningcalorimetry(DSC),the
techniqueofchoiceforevaluationofproteinstability,butwhichcanalsobevaluableforthe
studyofbiofluidsas shownhere. DSCisaquitewell-established techniqueinthepharma-
ceuticalindustrybutwouldalsobenefittoacademicresearchwhereitisnotwidelyavailable.
The second part is devoted to isothermal titration calorimetry (ITC). The use of ITC in
biology has considerably grown in the past 10 years, mostly as a consequence of the
availabilityofhigh-sensitivitymicrocalorimetersrequiringlowsamplevolume.Theinevita-
ble side effect of this rapid dissemination is a frequent misuse of this technique, being
recurrentlyusedtodecoratepublicationsinstructuralbiologybyprovidingKd(dissociation
constant)tables.However,alternativetechniquescanprovidesimilardataaboutaffinitywith
muchlowersamplerequirements.ITC,however,candomuchmoreandcangowellbeyond
Kds.ITCusersandthescientificcommunitywouldclearlybenefitfromtakingfulladvantage
of the technique as illustrated in these chapters. The third and last part includes advanced
dataprocessingandisintendedtoamoreexperiencedaudience.Itwillbeusefulforreaders
dealing with complex molecular systems (most interactions are much more complex than
initiallythought!)or for thosewhoareinterestedintoretrievingkineticdatainadditionto
thermodynamicdata.ITCindeedrecentlyappearsasaninterestingandreliabletechniqueto
gain insights into kinetic data, similarly to surface plasmon resonance. It is a safe bet that
thesekineticaspectsofITCarelikelytogrowinthefuture.
Finally, I would like to thank the authors who participated in the production of this
book, for their contribution and for their patience. I hope this volume will provide new
stimulatingideasfor readersinusingmicrocalorimetryfor theirexperiments.
Strasbourg,France EricEnnifar
v
Contents
Preface ..................................................................... v
Contributors................................................................. ix
PART I DIFFERENTIAL SCANNING CALORIMETRY
1 TheContributionofDifferentialScanningCalorimetryfor theStudy
ofPeptide/LipidInteractions ............................................ 3
Marie-LiseJobinandIsabelD.Alves
2 ProtocolsofIATC,DSC,andPPC:TheMultistateStructural
TransitionofCytochromec .............................................. 17
ShigeyoshiNakamuraandShun-ichiKidokoro
3 ValueofDSCinCharacterizationandOptimizationofProteinStability....... 33
KatherineBowersandNataliaMarkova
4 PlasmaticSignatureofDiseasebyDifferentialScanningCalorimetry(DSC).... 45
PhilippO.TsvetkovandFranc¸oisDevred
PART II ISOTHERMAL TITRATION CALORIMETRY
5 IntrinsicThermodynamicsofProtein-LigandBindingbyIsothermal
TitrationCalorimetryasAidtoDrugDesign............................... 61
VaidaPaketuryte˙,AstaZubriene˙,JohnE.Ladbury,
andDaumantasMatulis
6 IsothermalTitrationCalorimetryMeasurementsofRiboswitch-Ligand
Interactions ............................................................ 75
ChristopherP.Jones,GrzegorzPiszczek,andAdrianR.Ferre´-D’Amare´
7 ITCStudiesofRibosome/AntibioticsInteractions.......................... 89
EmmaSchenckbecher,BenoıˆtMeyer,andEricEnnifar
8 High-QualityDataofProtein/PeptideInteractionbyIsothermal
TitrationCalorimetry.................................................... 99
JuanRamirezandYvesNomine´
9 ITCMeasurementforHigh-AffinityAptamersBindingtoTheirTarget
Proteins................................................................ 119
RyoAmano,TomohisaFurukawa,andTaiichiSakamoto
10 ThermodynamicsofMolecularMachinesUsingIncrementalITC ............ 129
BenoıˆtMeyer,CyrielledaVeiga,PhilippeDumas,andEricEnnifar
11 MeasuringtheMetabolicActivityofMatureMycobacterialBiofilms
UsingIsothermalMicrocalorimetry....................................... 141
AnnaSolokhina,GernotBonkat,andOlivierBraissant
vii
viii Contents
12 CharacterizationofMicrotubule-AssociatedProteins(MAPs)
andTubulinInteractionsbyIsothermalTitrationCalorimetry(ITC).......... 151
PhilippO.Tsvetkov,RomainLaRocca,SoazigMalesinski,
andFranc¸oisDevred
PART III ADVANCED DATA PROCESSING AND KINETICS
13 AnalysisofIsothermalTitrationCalorimetryDataforComplex
InteractionsUsingI2CITC .............................................. 169
IbrahimQ.SaeedandNiklaasJ.Buurma
14 TinkeringwithBindingPolynomialsinIsothermalTitrationCalorimetry...... 185
RafaelClaveria-Gimeno,SoniaVega,OlgaAbian,
andAdrianVelazquez-Campoy
15 TheUseofITCandtheSoftwareAFFINImeter for theQuantification
oftheAnticoagulantPentasaccharideinLowMolecularWeightHeparin ...... 215
EvaMun˜ozandJuanSabı´n
16 ThermodynamicandKineticAnalysisofIsothermalTitration
CalorimetryExperimentsbyUsingKinITCinAFFINImeter................. 225
EvaMun˜oz,JuanSabı´n,JavierRial,DanielPe´rez,EricEnnifar,
PhilippeDumas,andA´ngelPin˜eiro
17 EnzymeKineticsDeterminedbySingle-InjectionIsothermalTitration
Calorimetry............................................................ 241
ColetteF.QuinnandLeeD.Hansen
18 CharacterizationofEnzymaticReactionsUsingITC........................ 251
BarbaraZambelli
Index ...................................................................... 267
Contributors
OLGAABIAN (cid:1) InstituteofBiocomputationandPhysicsofComplexSystems(BIFI),Joint
UnitsIQFR-CSIC-BIFI,andGBsC-CSIC-BIFI,UniversidaddeZaragoza,Zaragoza,
Spain;InstitutoAragone´sdeCienciasdelaSalud(IACS),Zaragoza,Spain;Aragon
InstituteforHealthResearch(IISAragon),Zaragoza,Spain;DepartmentofBiochemistry
andMolecularandCellBiology,UniversidaddeZaragoza,Zaragoza,Spain;Centrode
Investigaci(cid:1)onBiome´dicaenRedenelA´reaTema´ticadeEnfermedadesHepa´ticasy
Digestivas(CIBERehd),Barcelona,Spain
ISABEL D.ALVES (cid:1) ChimieetBiologiedesMembranesetNanoobjets,CBMNCNRSUMR
5248,Universite´Bordeaux1,Pessac,France
RYOAMANO (cid:1) FacultyofAdvancedEngineering,DepartmentofLifeScience,ChibaInstitute
ofTechnology,Narashino-shi,Chiba,Japan
GERNOT BONKAT (cid:1) altauroAG,Basel,Switzerland
KATHERINEBOWERS (cid:1) PrincipalScientist/GroupLeaderAnalyticalandFormulation
Development,FUJIFILMDiosynthBiotechnologiesU.S.A.,Inc.,Morrisville,NC,USA
OLIVIER BRAISSANT (cid:1) CenterofBiomechanicsandBiocalorimetry,UniversityBasel,c/o
DepartmentofBiomedicalEngineering(DBE),Allschwil,Switzerland
NIKLAASJ.BUURMA (cid:1) PhysicalOrganicChemistryCentre,SchoolofChemistry,Cardiff
University,Cardiff,UK
RAFAELCLAVERIA-GIMENO (cid:1) InstituteofBiocomputationandPhysicsofComplexSystems
(BIFI),JointUnitsIQFR-CSIC-BIFI,andGBsC-CSIC-BIFI,UniversidaddeZaragoza,
Zaragoza,Spain;InstitutoAragone´sdeCienciasdelaSalud(IACS),Zaragoza,Spain;
AragonInstituteforHealthResearch(IISAragon),Zaragoza,Spain
CYRIELLEDAVEIGA (cid:1) InstitutdeBiologieMole´culaireetCellulaire,Universite´deStrasbourg,
CNRS,Strasbourg,France
FRANC¸OIS DEVRED (cid:1) Aix-MarseilleUniv,CNRS,INP,InstNeurophysiopathol,FacPharm,
Marseille,France
PHILIPPEDUMAS (cid:1) InstitutdeBiologieMole´culaireetCellulaire,Universite´deStrasbourg,
CNRS,Strasbourg,France
ERICENNIFAR (cid:1) InstitutdeBiologieMole´culaireetCellulaire,Universite´deStrasbourg,
CNRS,Strasbourg,France
ADRIAN R.FERRE´-D’AMARE´ (cid:1) BiochemistryandBiophysicsCenter,NationalHeart,Lung
andBloodInstitute,NationalInstitutesofHealth,Bethesda,MD,USA
TOMOHISAFURUKAWA (cid:1) FacultyofAdvancedEngineering,DepartmentofLifeScience,Chiba
InstituteofTechnology,Narashino-shi,Chiba,Japan
LEED.HANSEN (cid:1) DepartmentofChemistryandBiochemistry,BrighamYoungUniversity,
Provo,UT,USA
MARIE-LISEJOBIN (cid:1) InstituteforPharmacologyandToxicology,RudolfVirchowCenter—Bio-
ImagingCenter,UniversityofWu¨rzburg,Wu¨rzburg,Germany
CHRISTOPHERP.JONES (cid:1) BiochemistryandBiophysicsCenter,NationalHeart,Lungand
BloodInstitute,NationalInstitutesofHealth,Bethesda,MD,USA
SHUN-ICHIKIDOKORO (cid:1) DepartmentofBioengineering,NagaokaUniversityofTechnology,
Nagaoka,Japan
ix
x Contributors
JOHNE.LADBURY (cid:1) DepartmentofMolecularandCellBiologyandAstburyCentrefor
StructuralBiology,UniversityofLeeds,Leeds,UK
ROMAINLAROCCA (cid:1) Aix-MarseilleUniv,CNRS,INP,InstNeurophysiopathol,FacPharm,
Marseille,France
SOAZIGMALESINSKI (cid:1) Aix-MarseilleUniv,CNRS,INP,InstNeurophysiopathol,FacPharm,
Marseille,France
NATALIA MARKOVA (cid:1) MicroCal,MalvernPanalytical,Uppsala,Sweden
DAUMANTASMATULIS (cid:1) DepartmentofBiothermodynamicsandDrugDesign,Instituteof
Biotechnology,VilniusUniversity,Vilnius,Lithuania
BENOIˆTMEYER (cid:1) InstitutdeBiologieMole´culaireetCellulaire,Universite´deStrasbourg,
CNRS,Strasbourg,France
EVAMUN˜OZ (cid:1) AFFINImeterScientific&DevelopmentTeam,Software4Science
Developments,S.L.Ed.Emprendia,SantiagodeCompostela,ACorun˜a,Spain
SHIGEYOSHINAKAMURA (cid:1) DepartmentofGeneralEducation,NationalInstituteof
Technology,UbeCollege,Ube,Japan
YVESNOMINE´ (cid:1) EquipeLabelise´eLigue2015,DepartmentofIntegrativeStructuralBiology,
InstitutdeGe´ne´tiqueetdeBiologieMole´culaireetCellulaire(IGBMC),INSERMU964
UMR7104CNRS,Universite´deStrasbourg,Illkirch,France
VAIDAPAKETURYTE˙ (cid:1) DepartmentofBiothermodynamicsandDrugDesign,Instituteof
Biotechnology,VilniusUniversity,Vilnius,Lithuania
DANIELPE´REZ (cid:1) AFFINImeterScientific&DevelopmentTeam,Software4Science
Developments,S.L.Ed.Emprendia,SantiagodeCompostela,ACorun˜a,Spain
´
ANGELPIN˜EIRO (cid:1) AFFINImeterScientific&DevelopmentTeam,Software4Science
Developments,S.L.Ed.Emprendia,SantiagodeCompostela,ACorun˜a,Spain;Soft
Matter&MolecularBiophysicsGroup,DepartamentodeFı´sicaAplicada,Facultadde
Fı´sica,UniversidadedeSantiagodeCompostela,SantiagodeCompostela,Spain
GRZEGORZ PISZCZEK (cid:1) BiophysicsCoreFacility,NationalHeart,LungandBloodInstitute,
NationalInstitutesofHealth,Bethesda,MD,USA
COLETTEF.QUINN (cid:1) ApplicationsLab,TAInstruments,Lindon,UT,USA
JUANRAMIREZ (cid:1) InstituteofNanotechnology(INT),KarlsruheInstituteofTechnology(KIT),
Eggenstein-Leopoldshafen,Germany
JAVIERRIAL (cid:1) AFFINImeterScientific&DevelopmentTeam,Software4Science
Developments,S.L.Ed.Emprendia,SantiagodeCompostela,ACorun˜a,Spain
JUANSABI´N (cid:1) AFFINImeterScientific&DevelopmentTeam,Software4Science
Developments,S.L.Ed.Emprendia,SantiagodeCompostela,ACorun˜a,Spain
IBRAHIMQ.SAEED (cid:1) DepartmentofChemistry,CollegeofScience,SalahaddinUniversity,
Erbil,KurdistanRegion,Iraq
TAIICHISAKAMOTO (cid:1) FacultyofAdvancedEngineering,DepartmentofLifeScience,Chiba
InstituteofTechnology,Narashino-shi,Chiba,Japan
EMMA SCHENCKBECHER (cid:1) InstitutdeBiologieMole´culaireetCellulaire,Universite´de
Strasbourg,CNRS,Strasbourg,France
ANNASOLOKHINA (cid:1) CenterofBiomechanicsandBiocalorimetry,UniversityBasel,c/o
DepartmentofBiomedicalEngineering(DBE),Allschwil,Switzerland
PHILIPPO.TSVETKOV (cid:1) Aix-MarseilleUniv,CNRS,INP,InstNeurophysiopathol,
FacPharm,Marseille,France
SONIAVEGA (cid:1) InstituteofBiocomputationandPhysicsofComplexSystems(BIFI),JointUnits
IQFR-CSIC-BIFI,andGBsC-CSIC-BIFI,UniversidaddeZaragoza,Zaragoza,Spain
Contributors xi
ADRIAN VELAZQUEZ-CAMPOY (cid:1) InstituteofBiocomputationandPhysicsofComplexSystems
(BIFI),JointUnitsIQFR-CSIC-BIFI,andGBsC-CSIC-BIFI,UniversidaddeZaragoza,
Zaragoza,Spain;AragonInstituteforHealthResearch(IISAragon),Zaragoza,Spain;
DepartmentofBiochemistryandMolecularandCellBiology,UniversidaddeZaragoza,
Zaragoza,Spain;CentrodeInvestigaci(cid:1)onBiome´dicaenRedenelA´reaTema´ticade
EnfermedadesHepa´ticasyDigestivas(CIBERehd),Barcelona,Spain;FundacionARAID,
GovernmentofAragon,Zaragoza,Spain
BARBARAZAMBELLI (cid:1) LaboratoryofBioinorganicChemistry,DepartmentofPharmacyand
Biotechnology,UniversityofBologna,Bologna,Italy
ASTAZUBRIENE˙ (cid:1) DepartmentofBiothermodynamicsandDrugDesign,Instituteof
Biotechnology,VilniusUniversity,Vilnius,Lithuania