Lipid-Protein Interactions: Methods and Protocols PDF
Preview Lipid-Protein Interactions: Methods and Protocols
Methods in Molecular Biology 2003 Jörg H. Kleinschmidt Editor Lipid-Protein Interactions Methods and Protocols Second Edition M M B ETHODS IN OLECULAR IO LO GY SeriesEditor JohnM.Walker School of Lifeand MedicalSciences University ofHertfordshire Hatfield, Hertfordshire, UK Forfurther volumes: http://www.springer.com/series/7651 For over 35 years, biological scientists have come to rely on the research protocols and methodologiesinthecriticallyacclaimedMethodsinMolecularBiologyseries.Theserieswas thefirsttointroducethestep-by-stepprotocolsapproachthathasbecomethestandardinall biomedicalprotocolpublishing.Eachprotocolisprovidedinreadily-reproduciblestep-by- step fashion, opening with an introductory overview, a list of the materials and reagents neededtocompletetheexperiment,andfollowedbyadetailedprocedurethatissupported with a helpful notes section offering tips and tricks of the trade as well as troubleshooting advice. These hallmark features were introduced by series editor Dr. John Walker and constitutethekeyingredientineachandeveryvolumeoftheMethodsinMolecularBiology series. Tested and trusted, comprehensive and reliable, all protocols from the series are indexedinPubMed. Lipid-Protein Interactions Methods and Protocols Second Edition Edited by Jörg H. Kleinschmidt Department of Biophysics, Institute of Biology, FB10 and Center for Interdisciplinary Nanostructure Science and Technology (CINSaT), University of Kassel, Kassel, Germany Editor Jo¨rgH.Kleinschmidt DepartmentofBiophysics,InstituteofBiology FB10andCenterforInterdisciplinaryNanostructure ScienceandTechnology(CINSaT),UniversityofKassel Kassel,Germany ISSN1064-3745 ISSN1940-6029 (electronic) MethodsinMolecularBiology ISBN978-1-4939-9511-0 ISBN978-1-4939-9512-7 (eBook) https://doi.org/10.1007/978-1-4939-9512-7 ©SpringerScience+BusinessMedia,LLC,partofSpringerNature2019 Thisworkissubjecttocopyright.AllrightsarereservedbythePublisher,whetherthewholeorpartofthematerialis concerned,specificallytherightsoftranslation,reprinting,reuseofillustrations,recitation,broadcasting,reproduction onmicrofilmsorinanyotherphysicalway,andtransmissionorinformationstorageandretrieval,electronicadaptation, computersoftware,orbysimilarordissimilarmethodologynowknownorhereafterdeveloped. Theuseofgeneraldescriptivenames,registerednames,trademarks,servicemarks,etc.inthispublicationdoesnotimply, evenintheabsenceofaspecificstatement,thatsuchnamesareexemptfromtherelevantprotectivelawsandregulations andthereforefreeforgeneraluse. Thepublisher,theauthors,andtheeditorsaresafetoassumethattheadviceandinformationinthisbookarebelievedto betrueandaccurateatthedateofpublication.Neitherthepublishernortheauthorsortheeditorsgiveawarranty, expressorimplied,withrespecttothematerialcontainedhereinorforanyerrorsoromissionsthatmayhavebeenmade. Thepublisherremainsneutralwithregardtojurisdictionalclaimsinpublishedmapsandinstitutionalaffiliations. ThisHumanaimprintispublishedbytheregisteredcompanySpringerScience+BusinessMedia,LLC,partofSpringer Nature Theregisteredcompanyaddressis:233SpringStreet,NewYork,NY10013,U.S.A. Preface Proteins and lipids are the main components of biological membranes that are essential structuring elements of all living cells. Natural phospholipids spontaneously form lipid bilayers. In biomembranes, the phospholipid bilayer constitutes a hydrophobic barrier that prevents the arbitrary exchange of solutes, while membrane-spanning proteins allow the regulated exchange of solutes or the transduction of signals from one side of the membrane to the other. Many enzymatic reactions take place at the membrane-water interface. Specific lipid-protein interactions are important for the stable integration and activity of integral and peripheral membrane proteins. The unique structure of the lipid bilayer requires specific surface properties of integral and peripheral proteins for their function. Protein surfaces exposed to the fatty core of the membrane are typically hydro- phobic,whileproteinsurfacesexposedtotheaqueousspaceusuallyarecomposedofpolar aminoacidresidues.Thepolar-apolarinterfaceofthelipidbilayerisformedbytheglycerol backboneandbythepolarheadgroupofthevariousphospholipidspeciesandthereforean importantregionforlipid-proteininteractions.Thefattyacylchainsofthelipidscanvarya lot in length and degree of unsaturation and the membranes may contain cholesterol, sphingolipids, etc. This has consequences, e.g., for membrane thickness and fluidity. Fur- thermore, the complex membrane composition often leads to the formation of micro- domains with distinct physicochemical properties. To gain detailed insight into membrane properties, it is therefore of great importance to understand the complex nature of the interactionsofmembraneproteinswithlipids. This volume provides a selection of protocols to examine protein-lipid interactions, membraneandmembraneproteinstructure,howmembraneproteinsaffectlipids,andhow theyareinturnaffectedbythelipidbilayerandlipidproperties.Numerousmethodologies havebeendevelopedinthepast,eachwithitsownadvantagesandlimitations.Themethods describedhereareallactivelyused,complementary,andnecessarytoobtaincomprehensive informationaboutmembranestructureandfunction.Themethodofchoiceisdetermined by the information that is sought, but is dependent on the properties of the sample, the availablequantity,andtherequiredsensitivity.Label-freeapproachesdescribedinthisbook include methodologies like quartz-crystal microbalances with dissipation, surface plasmon resonance,isothermaltitrationcalorimetry,anddifferentialscanningcalorimetry.Theseare usefulmethods,e.g.,tomonitorbindingeventsandtoobtainthefreeenergies,enthalpies, andentropiesofprotein-lipidinteractions.Imagingtechniqueslikeelectronmicroscopyand atomicforcemicroscopyareusedtoexaminethestructureandorganizationofprotein-lipid complexes in membranes. Atomic force spectroscopy allows the probing of mechanical properties of macromolecules, e.g., the force necessary to unfold a single protein in a lipid environment.Neutronscatteringisanemergingtechniquetostudythestructureofprotein- lipid complexes, which in combination with deuteration of either lipids or proteins, allows resolving the inner structure of big and dynamic lipid-protein complexes. The secondary structure of native and nonnative proteins in lipid membranes can conveniently be moni- tored by circular dichroism spectroscopy and synchrotron radiation circular dichroism spectroscopy. The development of the latter greatly extended the recordable wavelength range, strengthening structural investigations. Secondary structure and in addition the orientation and order parameters of membrane proteins in lipid bilayers can be obtained v vi Preface from infrared-spectroscopic methods. In combination with isotope editing methods, these are also used to determine changes in local protein conformation. The specificity and selectivity of protein interactions with lipid species is efficiently investigated by combining the labeling of lipids and proteins with either fluorescence or electron paramagnetic reso- nance spectroscopy, which are both very sensitive techniques to examine the protein-lipid interface. These methods are applied with great success to probe the topology of peptides and proteins in membranes. Fluorescence quenching is a fast and reliable technique to determine the location of fluorescent amino acids especially tryptophan residues in lipid bilayers. Fo¨rster energy transfer is a highly sensitive fluorescence method that is useful to measuredistancesupto10nmandabletodetectdirectbindingaswellasdeviationsfrom homogeneity of the lipid distribution around a protein. Fluorescence methodologies have alsobeensuccessfullyapplied,e.g.,totracksinglemoleculesliketransmembraneproteinsin planar supported membranes. Single particle tracking allows imaging and tracking single fluorescent molecules with good spatial and temporal resolution. Particle association and dissociation events can be monitored. Fluorescence correlation spectroscopy uses the time correlationoftemporalfluctuationsoffluorescence,whicharedetectedinafocalvolume,to explore dynamic events with high temporal resolution and statistical accuracy. Lipid spin labeling and electron paramagnetic resonance (EPR also called electron spin resonance, ESR)spectroscopyhavebeenhighlysuccessfulinthedeterminationoftheprotein-solvating lipid shell, that is, the stoichiometry of the lipid interactions with integral membrane proteins. Since the technique allows the estimation of mobile and protein-immobilized lipidsandtheirexchangerates,ithasalsobeenverysuccessfulinprobingthelipidselectivity of transmembrane proteins. In combination with site-directed mutagenesis, EPR of spin- labeled proteins has become a powerful tool to examine protein structure and dynamics, even in complex systems that are not accessible with other approaches. Nuclear magnetic resonance (NMR) spectroscopy, combined with isotopic labeling, is widely used to probe thestructureanddynamicsofproteinseitherinsolutionorinalipidenvironment.Solution- phase NMR isperformed withdetergent solubilizedmembraneproteins and usuallyyields high-resolution structures. Solid-state NMR is performed either as magic angle spinning (MAS) NMR to obtain highly resolved protein structures with spectra resembling fast isotropically tumbling proteins in solution or with oriented samples. When applied to oriented samples, NMR gives valuable information on the dynamics and orientation of lipids and proteins in membranes and allows determining, e.g., peptide orientation, lipid- order parameters, and lipid phases. Lipid-protein interactions have been investigated in small, large, and giant vesicles, in supported lipid bilayers, in lipid monolayers, with short- chain lipid micelles, or even with single lipids. More recently lipid nanodiscs have been developed,whicharedisc-likefragmentsoflipidbilayersthatarestabilizedbyamphipathic helical proteins. Nanodiscs have been shown to be a robust means for stabilizing and investigating protein-lipid interactions, and nanodisc applications are reviewed here. A range of molecular dynamics simulation approaches are applied to examine lipid-protein interactionsindetail. For the present second edition, all chapters have been updated to include recent developments. Six new chapters were added. The new chapters cover examinations of lipid-protein interactions by mass spectrometry, the use of protein microarrays to identify andexaminelipidinteractionsoflargesetsofdifferentproteins,investigationsonmembrane protein structure and dynamics by UV resonance Raman spectroscopy, examinations of peptide-inducedporeformationinmembranes,andinvestigationsonlipid-proteininterac- tionsinfoldingandinsertionofβ-barrelmembraneproteins.Lipid-proteininteractionsare Preface vii heavilyinvestigatedbymanyteamsworldwideandwhileitisclear thatnotallmethodscan bedescribedinasinglebook,thepresentvolumecoversawiderangeofthemethodsusedin thisareaofresearch. Ithankallcontributingauthorsforprovidinginterestingandhighlyvaluablemethods, insights,andreviewsfor thisvolumeofMethodsinMolecularBiology. Kassel,Germany J¨orgH.Kleinschmidt Contents Preface ..................................................................... v Contributors................................................................. xi 1 MultiscaleModelingandSimulationApproachestoLipid–Protein Interactions ............................................................ 1 RolandG.Huber,TimothyS.Carpenter,NamitaDube, DanielA.Holdbrook,HelgiI.Ing(cid:1)olfsson,WilliamA.Irvine, JanK.Marzinek,FirdausSamsudin,JaneR.Allison, SymaKhalid,andPeterJ.Bond 2 QuartzCrystalMicrobalancesasToolsforProbingProtein–Membrane Interactions ............................................................ 31 SørenB.NielsenandDanielE.Otzen 3 SurfacePlasmonResonanceforMeasuringInteractionsofProteins withLipidsandLipidMembranes......................................... 53 AleksandraSˇakanovicˇ,VesnaHodnik,andGregorAnderluh 4 ThermodynamicAnalysisofProtein–LipidInteractionsbyIsothermal TitrationCalorimetry.................................................... 71 MustiJ.Swamy,RajeshwerS.Sankhala,andBhanuPratapSingh 5 DifferentialScanningCalorimetryofProtein–LipidInteractions.............. 91 OlgaCan˜adasandCristinaCasals 6 ImagingandForceSpectroscopyofSingleTransmembraneProteins withtheAtomicForceMicroscope........................................ 107 K.TanujSapra 7 KineticsofInsertionandFoldingofOuterMembraneProteins byGelElectrophoresis................................................... 145 AndreSchu¨ßler,SaschaHerwig,andJ¨orgH.Kleinschmidt 8 OptimizedNegative-StainingProtocolforLipid–ProteinInteractions InvestigatedbyElectronMicroscopy ...................................... 163 JianfangLiu,HaoWu,ChangyuHuang,DongshengLei, MengZhang,WeiXie,JinpingLi,andGangRen 9 ProbingHeterogeneousLipidInteractionswithMembrane ProteinsUsingMassSpectrometry........................................ 175 JohnW.PatrickandArthurLaganowsky 10 ProteinMicroarraysandLiposome:AMethodforStudyingLipid–Protein Interactions ............................................................ 191 SamuelHerianto,Chien-ShengChen,andHengZhu 11 StructuralInvestigationsofProtein–LipidComplexesUsing NeutronScattering...................................................... 201 LukeA.Clifton,StephenC.L.Hall,NajetMahmoudi, TimothyJ.Knowles,FrankHeinrich,andJeremyH.Lakey ix x Contents 12 Circular-DichroismandSynchrotron-RadiationCircular-Dichroism SpectroscopyasToolstoMonitorProteinStructureinaLipidEnvironment... 253 KoichiMatsuoandKunihikoGekko 13 FTIRAnalysisofProteinsandProtein–MembraneInteractions............... 281 SurenA.Tatulian 14 UVResonanceRamanSpectroscopyasaTooltoProbeMembrane ProteinStructureandDynamics.......................................... 327 DeeAnnK.AsamotoandJudyE.Kim 15 AnalyzingTransmembraneProteinandHydrophobicHelix TopographybyDualFluorescenceQuenching ............................. 351 GregoryA.CaputoandErwinLondon 16 Fo¨rsterResonanceEnergyTransferasaToolforQuantification ofProtein–LipidSelectivity .............................................. 369 Luı´sM.S.Loura,ManuelPrieto,andFa´bioFernandes 17 AGuidetoTrackingSingleMembraneProteinsandTheirInteractions inSupportedLipidBilayers .............................................. 383 EvanL.Taylor,KumudRajPoudel,andJamesA.Brozik 18 FluorescenceCorrelationSpectroscopytoExamineProtein–Lipid InteractionsinMembranes............................................... 415 ViktoriaBetaneli,JonasMu¨cksch,andPetraSchwille 19 MembranePoreFormationbyPeptidesStudiedbyFluorescence Techniques............................................................. 449 SurenA.TatulianandNabinKandel 20 Foldingofβ-BarrelMembraneProteinsintoLipidMembranes bySite-DirectedFluorescenceSpectroscopy................................ 465 LisaGerlach,OmkolsumGholami,NicoleSchu¨rmann, andJ¨orgH.Kleinschmidt 21 EPRTechniquestoProbeInsertionandConformation ofSpin-LabeledProteinsinLipidBilayers.................................. 493 EnricaBordignon,SvetlanaKucher,andYevhenPolyhach 22 StudyingLipid–ProteinInteractionswithElectronParamagnetic ResonanceSpectroscopyofSpin-LabeledLipids............................ 529 TiborPa´liandZolta´nK(cid:1)ota 23 Solid-StateNMRApproachestoStudyProteinStructure andProtein–LipidInteractions ........................................... 563 ChristopherAisenbrey,EvgeniyS.Salnikov,JesusRaya, MatthiasMichalek,andBurkhardBechinger 24 SolutionNMRSpectroscopyfor theDeterminationofStructures ofMembraneProteinsinaLipidEnvironment ............................. 599 AshishArora 25 NanodiscsasaNewTooltoExamineLipid–ProteinInteractions ............. 645 IliaG.Denisov,MaryA.Schuler,andStephenG.Sligar Index ...................................................................... 673
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