Cell-Wide Identification of Metabolite-Protein Interactions (Methods in Molecular Biology, 2554)

261 Pages·2022·5.539 MB·English

by  Aleksandra Skirycz (editor), Marcin Luzarowski (editor), Jennifer C. Ewald (editor)

Methods in
Molecular Biology 2554
Aleksandra Skirycz
Marcin Luzarowski
Jennifer C. Ewald Editors
Cell-Wide
Identifi cation of
Metabolite-Protein
Interactions
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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Cell-Wide Identification
of Metabolite-Protein Interactions
Edited by
Aleksandra Skirycz
Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam, Germany
Marcin Luzarowski
€
Zentrum für Molekulare Biologie der Universitat Heidelberg, Heidelberg, Germany
Jennifer C. Ewald
Interfaculty Institute of Cell Biology, University of Tübingen, Tübingen, Germany
Editors
AleksandraSkirycz MarcinLuzarowski
Max-Planck-Institutfu¨rMolekulare Zentrumfu¨rMolekulareBiologiederUniversit€atHeidelberg
Pflanzenphysiologie Heidelberg,Germany
Potsdam,Germany
JenniferC.Ewald
InterfacultyInstituteofCellBiology
UniversityofTu¨bingen
Tu¨bingen,Germany
ISSN1064-3745 ISSN1940-6029 (electronic)
MethodsinMolecularBiology
ISBN978-1-0716-2623-8 ISBN978-1-0716-2624-5 (eBook)
https://doi.org/10.1007/978-1-0716-2624-5
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Preface
Interactionsbetweenbiologicalmoleculesenablelife.Thesignificanceofacell-wideunder-
standingofmolecularcomplexesisthusobvious.Recentstudiesattesttotheexistenceofa
stilllargelyhiddenworldofprotein-metaboliteinteractionsimportantfor theregulationof
all cellular processes. To shed light on these important regulatory interactions, we provide
here protocols of proteome- and metabolome-wide strategies for the identification of
protein–small molecule complexes in different organisms. We further discuss experimental
andcomputationalstrategiestocharacterizeprotein-metaboliteinteractions,andhighlight
recentadvancesinenablingtechnologies.
Potsdam,Germany AleksandraSkirycz
Heidelberg,Germany MarcinLuzarowski
Tu¨bingen,Germany JenniferC.Ewald
v
Contents
Preface ..................................................................... v
Contributors................................................................. ix
1 Protein–MetaboliteInteractionsShapeCellularMetabolism
andPhysiology ......................................................... 1
PrathibhaMuralidharaandJenniferC.Ewald
2 AffinityPurificationProtocolStartingwithaSmallMoleculeasBait .......... 11
Nicola´sE.Figueroa,ItzellE.Hernandez-Sanchez,
IsraelMaruri-Lopez,andMonikaChodasiewicz
3 CellularThermalShiftAssayfor theDetectionofSmallMolecule–Target
InteractionsinArabidopsisCells .......................................... 21
QingLuandEugeniaRussinova
4 Solvent-InducedProteinPrecipitationforDrugTargetDiscovery ............ 35
XiaoleiZhang,LianghaiHu,andMingliangYe
5 IdentificationofPlantProtein–MetaboliteInteractionsbyLimited
Proteolysis-CoupledMassSpectrometry(LiP-MS).......................... 47
JhonVenegas-Molina,PetraVanDamme,andAlainGoossens
6 LimitedProteolysis–MassSpectrometrytoIdentifyMetabolite–Protein
Interactions ............................................................ 69
AleˇsHolfeld,Jan-PhilippQuast,RolandBruderer,
LukasReiter,NataliedeSouza,andPaolaPicotti
7 ProteomeIntegralSolubilityAlteration(PISA)forHigh-Throughput
LigandTargetDeconvolutionwithIncreasedStatisticalSignificance
andReducedSampleAmount ............................................ 91
MassimilianoGaetaniandRomanA.Zubarev
8 ParallelAnalysisofProtein–ProteinandProtein–MetaboliteComplexes
UsingaSingle-StepAffinityPurification ................................... 107
MarcinLuzarowskiandAleksandraSkirycz
9 DetectingandCharacterizingInteractionsofMetaboliteswithProteins
bySaturationTransferDifferenceNuclearMagneticResonance
(STDNMR)Spectroscopy............................................... 123
RuslanNedielkovandHeikoM.M¨oller
10 PROMIS:Co-fractionationMassSpectrometryforAnalysis
ofProtein–MetaboliteInteractions........................................ 141
MarcinLuzarowski,EwelinaM.Sokolowska,DennisSchlossarek,
andAleksandraSkirycz
11 Metabolomics:GoingDeeper,GoingBroader,GoingFurther ............... 155
SofiaMocoandJoergM.Buescher
vii
viii Contents
12 SpecificsofMetabolite-ProteinInteractionsandTheirComputational
AnalysisandPrediction.................................................. 179
DirkWalther
13 BiophysicalApproachesfor theCharacterizationofProtein-Metabolite
Interactions ............................................................ 199
AnjaThalhammerandNinaK.Br¨oker
14 DatabasesandToolstoInvestigateProtein-MetaboliteInteractions........... 231
LeonardoPerezdeSouzaandAlisdairR.Fernie
Afterword .................................................................. 251
Index ...................................................................... 259
Contributors
NINAK.BRO¨KER • PhysicalBiochemistry,UniversityofPotsdam,Potsdam,Germany;Health
andMedicalUniversityPotsdam,Potsdam,Germany
ROLAND BRUDERER • BiognosysAG,Schlieren,Switzerland
JOERGM.BUESCHER • MetabolomicsCoreFacility,MaxPlanckInstituteofImmunobiology
andEpigenetics,FreiburgimBreisgau,Germany
MONIKACHODASIEWICZ • Center forDesertAgriculture,BiologicalandEnvironmental
ScienceandEngineeringDivision,KingAbdullahUniversityofScienceandTechnology,
Thuwal,SaudiArabia
LEONARDOPEREZDESOUZA • Max-Planck-InstituteofMolecularPlantPhysiology,Potsdam-
Golm,Germany
NATALIEDESOUZA • InstituteofMolecularSystemsBiology,DepartmentofBiology,ETH
Zurich,Zurich,Switzerland;DepartmentofQuantitativeBiomedicine,Universityof
Zurich,Zurich,Switzerland
JENNIFERC.EWALD • InterfacultyInstituteofCellBiology,UniversityofTu¨bingen,
Tu¨bingen,Germany
ALISDAIR R.FERNIE • Max-Planck-InstituteofMolecularPlantPhysiology,Potsdam-Golm,
Germany
NICOLA´SE.FIGUEROA • Center forDesertAgriculture,BiologicalandEnvironmental
ScienceandEngineeringDivision,KingAbdullahUniversityofScienceandTechnology,
Thuwal,SaudiArabia
MASSIMILIANO GAETANI • DivisionofPhysiologicalChemistryI,DepartmentofMedical
BiochemistryandBiophysics,KarolinskaInstitute,Stockholm,Sweden;ChemicalProteomics
CoreFacility,DepartmentofMedicalBiochemistryandBiophysics,KarolinskaInstitute,
Stockholm,Sweden;ChemicalProteomics,ScienceforLifeLaboratory(SciLifeLab),
Stockholm,Sweden
ALAINGOOSSENS • DepartmentofPlantBiotechnologyandBioinformatics, Ghent
University,Ghent,Belgium;VIBCenter forPlantSystemsBiology,Ghent,Belgium
ITZELLE.HERNANDEZ-SANCHEZ • Center forDesertAgriculture,Biologicaland
EnvironmentalScienceandEngineeringDivision,KingAbdullahUniversityofScience
andTechnology,Thuwal,SaudiArabia
ALESˇ HOLFELD • InstituteofMolecularSystemsBiology,DepartmentofBiology,ETHZurich,
Zurich,Switzerland
LIANGHAIHU • Center forSupramolecularChemicalBiology,StateKeyLaboratoryof
SupramolecularStructureandMaterials,SchoolofLifeSciences,JilinUniversity,
Changchun,China
QINGLU • DepartmentofPlantBiotechnologyandBioinformatics,GhentUniversity,Ghent,
Belgium;Center forPlantSystemsBiology,VIB,Ghent,Belgium
MARCINLUZAROWSKI • Zentrumfu¨rMolekulareBiologiederUniversita€tHeidelberg,
Heidelberg,Germany
ISRAELMARURI-LOPEZ • Center forDesertAgriculture,BiologicalandEnvironmental
ScienceandEngineeringDivision,KingAbdullahUniversityofScienceandTechnology,
Thuwal,SaudiArabia
ix
x Contributors
SOFIAMOCO • MolecularandComputationalToxicology,DepartmentofChemistryand
PharmaceuticalSciences,VrijeUniversiteitAmsterdam,Amsterdam,Netherlands
HEIKOM.MO¨LLER • UniversityofPotsdam,InstituteforChemistry,Potsdam,Germany
PRATHIBHAMURALIDHARA • InterfacultyInstituteofCellBiology,UniversityofTuebingen,
Tuebingen,Germany
RUSLAN NEDIELKOV • UniversityofPotsdam,InstituteforChemistry,Potsdam,Germany
PAOLAPICOTTI • InstituteofMolecularSystemsBiology,DepartmentofBiology,ETHZurich,
Zurich,Switzerland
JAN-PHILIPPQUAST • InstituteofMolecularSystemsBiology,DepartmentofBiology,ETH
Zurich,Zurich,Switzerland
LUKAS REITER • BiognosysAG,Schlieren,Switzerland
EUGENIARUSSINOVA • DepartmentofPlantBiotechnologyandBioinformatics, Ghent
University,Ghent,Belgium;Center forPlantSystemsBiology,VIB,Ghent,Belgium
DENNISSCHLOSSAREK • MaxPlanckInstituteofMolecularPlantPhysiology,Potsdam,
Germany
ALEKSANDRASKIRYCZ • MaxPlanckInstituteofMolecularPlantPhysiology,Potsdam,
Germany
EWELINAM.SOKOLOWSKA • MaxPlanckInstituteofMolecularPlantPhysiology,Potsdam,
Germany
ANJATHALHAMMER • PhysicalBiochemistry,UniversityofPotsdam,Potsdam,Germany
PETRAVANDAMME • DepartmentofBiochemistryandMicrobiology,GhentUniversity,
Ghent,Belgium
JHONVENEGAS-MOLINA • DepartmentofPlantBiotechnologyandBioinformatics,Ghent
University,Ghent,Belgium;VIBCenter forPlantSystemsBiology,Ghent,Belgium
DIRKWALTHER • MaxPlanckInstituteofMolecularPlantPhysiology,Potsdam,Germany
MINGLIANGYE • CASKeyLaboratoryofSeparationSciencesforAnalyticalChemistry,
NationalChromatographicR&ACenter,DalianInstituteofChemicalPhysics,Chinese
AcademyofSciences,Dalian,China
XIAOLEIZHANG • Center forSupramolecularChemicalBiology,StateKeyLaboratoryof
SupramolecularStructureandMaterials,SchoolofLifeSciences,JilinUniversity,
Changchun,China;CASKeyLaboratoryofSeparationSciencesforAnalyticalChemistry,
NationalChromatographicR&ACenter,DalianInstituteofChemicalPhysics,Chinese
AcademyofSciences,Dalian,China
ROMANA.ZUBAREV • DivisionofPhysiologicalChemistryI,DepartmentofMedical
BiochemistryandBiophysics,KarolinskaInstitute,Stockholm,Sweden;Departmentof
Pharmacological&TechnologicalChemistry,I.M.SechenovFirstMoscowStateMedical
University,Moscow,Russia