Protein-ligand interactions : methods and applications

484 Pages·2021·12.606 MB·English

by  Tina Daviter (editor), Christopher M. Johnson (editor), Dr. Mark A. Williams (editor), Stephen H. McLaughlin (editor)

Methods in
Molecular Biology 2263
Tina Daviter
Christopher M. Johnson
Stephen H. McLaughlin
Mark A. Williams Editors
Protein-Ligand
Interactions
Methods and Applications
Third Edition
M M B
ETHODS IN OLECULAR IO LO GY
SeriesEditor
JohnM.Walker
School of Lifeand MedicalSciences
University ofHertfordshire
Hatfield, Hertfordshire, UK
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Protein-Ligand Interactions
Methods and Applications
Third Edition
Edited by
Tina Daviter
The Institute of Cancer Research, London, UK
Christopher M. Johnson
MRC Laboratory of Molecular Biology, Cambridge, UK
Stephen H. McLaughlin
MRC Laboratory of Molecular Biology, Cambridge, UK
Mark A. Williams
ISMB BiophysX Centre, Birkbeck, University of London, London, UK
Editors
TinaDaviter ChristopherM.Johnson
TheInstituteofCancerResearch MRCLaboratoryofMolecularBiology
London,UK Cambridge,UK
StephenH.McLaughlin MarkA.Williams
MRCLaboratoryofMolecularBiology ISMBBiophysXCentre,Birkbeck
Cambridge,UK UniversityofLondon
London,UK
ISSN1064-3745 ISSN1940-6029 (electronic)
MethodsinMolecularBiology
ISBN978-1-0716-1196-8 ISBN978-1-0716-1197-5 (eBook)
https://doi.org/10.1007/978-1-0716-1197-5
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Frontcover:Interactionof initiator tRNA(teal)andinitiationfactorsIF1(purple)andIF3(orange)withthesmall
ribosomal subunit (30S) from structural work on the pre-initiation complexes determined in the lab of Venki
Ramakrishnan.CopyrightVisualAids,MRCLaboratoryofMolecularBiology,Cambridge.
ThisHumanaimprintispublishedbytheregisteredcompanySpringerScience+BusinessMedia,LLC,partofSpringer
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Preface
Proteins are central in life at the molecular level. They are catalysts, transporters, and
messengers. They provide or create much of the cellular architecture and go beyond the
cell to seek nutrients and neutralize antigens. They each function in large interaction net-
workswithotherproteins,smallmolecules,andthegenome:dynamicallybinding,unbind-
ing,competingforandchangingpartners,orformingfunctionalmultimolecularassemblies.
All these interactions are intricately regulated, and their dysregulation often results in
disease. One way of understanding the detail of the function and regulation of proteins is
todissectandmeasuretheirinteractions.
As in previous editions, this volume aims to provide an overview of common methods
for characterizing the interactions of proteins. This edition does not replace previous
editions, but seeks to supplement them with new methods and perspectives. Unlike the
previouseditions,whichwerestructuredbytypesofmethod,thiseditionisorganizedbythe
typesofligandwithwhichproteinsinteract.Wehopethatthiswillmakethebookevenmore
useful to researchers new to these techniques of biophysical investigation by suggesting
approachessuitedtoparticularbiologicalproblemsfromthegreat,andperhapsconfusing,
rangeofpossibilities.
Many ofour authors lead researchfacilities in academic or pharmaceutical settings and
haveconsiderableexperienceofmakingtheirinstrumentationandexpertiseavailabletothe
wider research community. Chapters provide clear instructions for the nonspecialist, for
graduatestudents,orresearchersnewtoagivenapproachandcoverallstagesoftheresearch
process, from the screening and discovery of interactions to the detailed quantitative
understandingofthemechanismsinvolved.
London,UK TinaDaviter
Cambridge,UK ChristopherM.Johnson
Cambridge,UK StephenH.McLaughlin
London,UK MarkA.Williams
v
Contents
Preface ..................................................................... v
Contributors................................................................. ix
PART I OVERVIEW
1 AssessingandImprovingProteinSampleQuality ........................... 3
BertrandRaynal,Se´bastienBruˆle´,StephanUebel,andStefanH.Knauer
2 AFamiliarProtein–LigandInteractionRevisitedwithMultipleMethods....... 47
XiaochunLi-Blatter,LudovitZweifel,andTimothySharpe
PART II UNIVERSAL METHODS FOR PROTEIN INTERACTIONS
3 InteractionsofaSignalTransductionProteinInvestigatedby
FluorescenceStopped-FlowKinetics ...................................... 83
StephenR.MartinandMariaJ.Schilstra
4 KineticMethodsofDeducingBindingMechanismsInvolving
IntrinsicallyDisorderedProteins.......................................... 105
ElinKarlssonandPerJemth
5 IsothermalTitrationCalorimetry ......................................... 135
ChristopherM.Johnson
6 MeasuringtheK ofProtein–LigandInteractionsUsing
D
MicroscaleThermophoresis .............................................. 161
Shih-ChiaTsoandChadA.Brautigam
7 QuartzCrystalMicrobalancewithDissipationMonitoring
(QCM-D):PreparingFunctionalizedLipidLayersfor theStudy
ofComplexProtein–LigandInteractions................................... 183
HollyL.BirchenoughandThomasA.Jowitt
PART III SCREENING FOR LIGAND BINDING
8 IndirectDetectionofLigandBindingbyThermalMeltAnalysis.............. 201
JosephShawandChristopherStubbs
9 TheUseofAcousticMistIonizationMassSpectrometryfor
High-ThroughputScreening............................................. 217
HelenPlant,DavidMurray,HannahSemple,GarethDavies,
IanSinclair,andGeoffreyA.Holdgate
10 LigandDiscovery:High-ThroughputBinding:Fluorescence
Polarization(Anisotropy)................................................ 231
Geoffrey A.HoldgateandPaulE.Hemsley
11 FragmentScreeningbyNMR ............................................ 247
BenJ.Davis
vii
viii Contents
PART IV NUCLEOTIDE BINDING AND HYDROLYSIS
12 AQuickPrimerinFluorescence-BasedEquilibriumandPre-steady
StateMethodsforDeterminingProtein–NucleotideAffinities................ 273
HarlandE.BrandonandHans-JoachimWieden
13 MeasurementofNucleotideHydrolysisUsingFluorescent
BiosensorsforPhosphate ................................................ 289
SimoneKunzelmann
PART V BINDING NUCLEIC ACIDS
14 Gel-BasedAnalysisofProtein–NucleicAcidInteractions..................... 321
JamesA.W.Stowell,TerenceT.L.Tang,MaximilianSeidel,
andLoriA.Passmore
15 BiophysicalStudiesoftheBindingofViralRNAwiththe80S
RibosomeUsingswitchSENSE........................................... 341
EmmaSchenckbecher,GuillaumeBec,TaiichiSakamoto,
BenoitMeyer,andEricEnnifar
16 BiolayerInterferometry:Protein–RNAInteractions......................... 351
StephenR.Martin,AndresRamos,andLauraMasino
17 AnalysisofProtein–DNAInteractionsUsingSurfacePlasmon
ResonanceandaReDCaTChip .......................................... 369
ClareE.M.StevensonandDavidM.Lawson
18 CharacterizationofProtein–NucleicAcidComplexesbySize-Exclusion
ChromatographyCoupledwithLightScattering,Absorbance,
andRefractiveIndexDetectors........................................... 381
EwaFolta-Stogniew
19 AnalyticalUltracentrifugationforAnalysisofProtein–Nucleic
AcidInteractions ....................................................... 397
AndreaBogutzkiandUteCurth
20 StudyingRNA–ProteinComplexesUsingX-RayCrystallography............. 423
AndrewP.TurnbullandXiaoqiuWu
PART VI MEMBRANE BINDING
21 FlowLinearDichroismofProtein–MembraneSystems...................... 449
MatthewR.Hicks,SarahR.Dennison,AdewaleOlamoyesan,
andAlisonRodger
22 ProbingProtein–MembraneInteractionsandDynamicsUsing
Hydrogen–DeuteriumExchangeMassSpectrometry(HDX-MS)............. 465
JordanT.B.Stariha,ReeceM.Hoffmann,DavidJ.Hamelin,
andJohnE.Burke
Index ...................................................................... 487
Contributors
GUILLAUMEBEC • InstitutdeBiologieMole´culaireetCellulaire,CNRS,Universite´de
Strasbourg,Strasbourg,France
HOLLY L.BIRCHENOUGH • FacultyofBiology,MedicineandHealth,Universityof
Manchester,Manchester,UK;WellcomeTrustCentreforCellMatrixResearch,University
ofManchester,Manchester,UK
ANDREA BOGUTZKI • HannoverMedicalSchool,InstituteforBiophysicalChemistry,
Hannover,Germany
HARLANDE.BRANDON • DepartmentofChemistryandBiochemistry,AlbertaRNA
ResearchandTrainingInstitute(ARRTI),UniversityofLethbridge,Lethbridge,
AB,Canada
CHAD A.BRAUTIGAM • DepartmentsofBiophysicsandMicrobiology,UTSouthwestern
MedicalCenter,Dallas,TX,USA
SE´BASTIENBRUˆLE´ • Plate-formedeBiophysiqueMole´culaire,InstitutPasteur,UMR3528
CNRS,Paris,France
JOHNE.BURKE • DepartmentofBiochemistryandMicrobiology,UniversityofVictoria,
Victoria,BC,Canada;DepartmentofBiochemistryandMolecularBiology,TheUniversity
ofBritishColumbia,Vancouver,BC,Canada
UTECURTH • HannoverMedicalSchool,InstituteforBiophysicalChemistry,
Hannover,Germany
GARETHDAVIES • HitDiscovery,DiscoverySciences,R&DBioPharmaceuticals,
AstraZeneca,AlderleyPark,UK
BENJ.DAVIS • VernalisResearch,Cambridge,UK
SARAH R.DENNISON • SchoolofPharmacyandBiomedicalSciences,UniversityofCentral
Lancashire,Preston,UK
ERICENNIFAR • InstitutdeBiologieMole´culaireetCellulaire,CNRS,Universite´de
Strasbourg,Strasbourg,France
EWAFOLTA-STOGNIEW • W.M.KeckBiotechnologyResourceLaboratory,Departmentof
MolecularBiophysicsandBiochemistry,YaleUniversitySchoolofMedicine,NewHaven,
CT,USA
DAVIDJ.HAMELIN • DepartmentofBiochemistryandMicrobiology,UniversityofVictoria,
Victoria,BC,Canada
PAULE.HEMSLEY • AstraZenecaR&DDiscoverySciences,Cambridge,UK
MATTHEWR.HICKS • LinearDiagnosticsLimited,TheBioHub,Birmingham,UK
REECEM.HOFFMANN • DepartmentofBiochemistryandMicrobiology,Universityof
Victoria,Victoria,BC,Canada
GEOFFREYA.HOLDGATE • HitDiscovery,DiscoverySciences,R&DBioPharmaceuticals,
AstraZeneca,AlderleyPark,UK
PERJEMTH • DepartmentofMedicalBiochemistryandMicrobiology,BMC,Uppsala
University,Uppsala,Sweden
CHRISTOPHERM.JOHNSON • MRCLaboratoryofMolecularBiology,Cambridge,UK
THOMASA.JOWITT • FacultyofBiology,MedicineandHealth,UniversityofManchester,
Manchester,UK;WellcomeTrustCentreforCellMatrixResearch,Universityof
Manchester,Manchester,UK
ix
x Contributors
ELINKARLSSON • DepartmentofMedicalBiochemistryandMicrobiology,BMC,Uppsala
University,Uppsala,Sweden
STEFANH.KNAUER • Biopolymers,UniversityofBayreuth,Bayreuth,Germany
SIMONEKUNZELMANN • StructuralBiologyScienceTechnologyPlatform,TheFrancisCrick
Institute,London,UK
DAVIDM.LAWSON • DepartmentofBiologicalChemistry,JohnInnesCentre,Norwich
SciencePark,Norwich,UK
XIAOCHUNLI-BLATTER • BiophysicsFacility,Biozentrum,UniversityofBasel,
Basel,Switzerland
STEPHENR.MARTIN • StructuralBiologyScienceTechnologyPlatform,TheFrancisCrick
Institute,London,UK
LAURA MASINO • StructuralBiologyScienceTechnologyPlatform,TheFrancisCrick
Institute,London,UK
BENOITMEYER • InstitutdeBiologieMole´culaireetCellulaire,CNRS,Universite´de
Strasbourg,Strasbourg,France
DAVIDMURRAY • HitDiscovery,DiscoverySciences,R&DBioPharmaceuticals,AstraZeneca,
AlderleyPark,UK
ADEWALEOLAMOYESAN • DepartmentofMolecularSciences,MacquarieUniversity,Sydney,
NSW,Australia
LORI A.PASSMORE • MRCLaboratoryofMolecularBiology,Cambridge,UK
HELENPLANT • HitDiscovery,DiscoverySciences,R&DBioPharmaceuticals, AstraZeneca,
AlderleyPark,UK
ANDRESRAMOS • DepartmentofStructural&MolecularBiology,UniversityCollegeLondon,
London,UK
BERTRAND RAYNAL • Plate-formedeBiophysiqueMole´culaire,InstitutPasteur,UMR3528
CNRS,Paris,France
ALISONRODGER • DepartmentofMolecularSciences,MacquarieUniversity,Sydney,
NSW,Australia
TAIICHISAKAMOTO • InstitutdeBiologieMole´culaireetCellulaire,CNRS,Universite´de
Strasbourg,Strasbourg,France;DepartmentofLifeScience,FacultyofAdvanced
Engineering,ChibaInstituteofTechnology,Chiba,Japan
EMMASCHENCKBECHER • InstitutdeBiologieMole´culaireetCellulaire,CNRS,Universite´de
Strasbourg,Strasbourg,France
MARIAJ.SCHILSTRA • StructuralBiologyTechnologyPlatform,TheFrancisCrickInstitute,
London,UK
MAXIMILIANSEIDEL • MRCLaboratoryofMolecularBiology,Cambridge,UK
HANNAHSEMPLE • HitDiscovery,DiscoverySciences,R&DBioPharmaceuticals,
AstraZeneca,AlderleyPark,UK
TIMOTHYSHARPE • BiophysicsFacility,Biozentrum,UniversityofBasel,Basel,Switzerland
JOSEPH SHAW • DiscoveryBiology,DiscoverySciences,IMEDBiotechUnit,AstraZeneca,
Cambridge,UK
IANSINCLAIR • HitDiscovery,DiscoverySciences,R&DBioPharmaceuticals,AstraZeneca,
AlderleyPark,UK
JORDANT.B.STARIHA • DepartmentofBiochemistryandMicrobiology,Universityof
Victoria,Victoria,BC,Canada
CLAREE.M.STEVENSON • DepartmentofBiologicalChemistry,JohnInnesCentre,Norwich
ResearchPark,Norwich,UK
JAMESA.W.STOWELL • MRCLaboratoryofMolecularBiology,Cambridge,UK