Analysis of Membrane Lipids PDF
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Rajendra Prasad Ashutosh Singh Editors Analysis of Membrane Lipids S P H PRINGER ROTOCOLS ANDBOOKS Forfurther volumes: http://www.springer.com/series/8623 SpringerProtocols Handbooks collects adiverse range ofstep-by-steplaboratorymethods andprotocolsfromacrossthelifeandbiomedicalsciences.Eachprotocolisprovidedinthe Springer Protocol format: readily-reproducible in a step-by-step fashion. Each protocol openswithanintroductoryoverview,alistofthematerialsandreagentsneededtocomplete theexperiment,andisfollowedbyadetailedproceduresupportedbyahelpfulnotessection offeringtipsandtricksofthetradeaswellastroubleshootingadvice.Withafocusonlarge comprehensive protocol collections and an international authorship, Springer Protocols Handbooksareavaluableadditiontothelaboratory. Analysis of Membrane Lipids Edited by Rajendra Prasad Amity Institute of Biotechnology and Amity Institute of Integrative Sciences and Health, Amity University Haryana, Gurgaon, Haryana, India Ashutosh Singh Department of Biochemistry, University of Lucknow, Lucknow, Uttar Pradesh, India Editors RajendraPrasad AshutoshSingh AmityInstituteofBiotechnologyand DepartmentofBiochemistry AmityInstituteofIntegrativeSciences UniversityofLucknow andHealth Lucknow,UttarPradesh,India AmityUniversityHaryana Gurgaon,Haryana,India ISSN1949-2448 ISSN1949-2456 (electronic) SpringerProtocolsHandbooks ISBN978-1-0716-0630-8 ISBN978-1-0716-0631-5 (eBook) https://doi.org/10.1007/978-1-0716-0631-5 ©SpringerScience+BusinessMedia,LLC,partofSpringerNature2020 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, expressedorimplied,withrespecttothematerialcontainedhereinorforanyerrorsoromissionsthatmayhavebeen made.Thepublisherremainsneutralwithregardtojurisdictionalclaimsinpublishedmapsandinstitutionalaffiliations. Cover illustration: The crystal structure of green fluorescent protein (GFP) displaying a β-barrel structure with the chromophore(highlightedinorange)locatedinthecoreoftheprotein. GFPhasbeenmostwidelyusedinthecontextof studyinglateraldiffusionofmembraneproteins. ThisSpringerimprintispublishedbytheregisteredcompanySpringerScience+BusinessMedia,LLC,partofSpringer Nature. Theregisteredcompanyaddressis:1NewYorkPlaza,NewYork,NY10004,U.S.A. Preface The first edition of Manual on Membrane Lipids was published back in 1996. Various techniques and protocols described in the first edition remain relevant to membrane lipid analysis to date. However in recent years, several major cutting-edge technological break- throughs have changed the manner in which we can analyze lipids and membrane proper- ties. For example, improved lipid extraction and purification protocols now allow higher extractionefficiencyforbothpolarandnon-polarlipids;thelastdecadehasseentheeraof “lipidomics,” which is mass spectrometry-based characterization of lipids, allowing robust andaccuratequantificationmethodsusingadvancedtechniqueslikeelectrosprayionization tandem mass spectrometry (ESI-MS/MS), gas chromatography mass spectrometry (GCMS), and nuclear magnetic resonance spectroscopy (NMR), among others; develop- ment of fluorescence-based techniques like fluorescence recovery after photobleaching (FRAP), time-resolved fluorescence spectroscopy (TRFS), and various imaging techniques now allows better visualization and understanding of membrane components and their properties. This second edition serves as a reference lipid recipe book which provides a timely overview of the groundbreaking advances made in analytical tools in the last two decades and presents methodological approaches to study high-throughput lipidomics, lipid–protein interactions, signaling pathways, regulation of lipid metabolism, functions in modulatingimmunesystems,anddiseases,amongothers.Theluciddescriptionprecededby updated background will make it very user friendly which every researcher and teacher wouldliketouseitasabench-topbook.Leadingexpertsinthefieldhavecontributedtothis user-friendly bench-top manualwhich offers anideal reference guide for membrane biolo- gists, researchers, graduate and undergraduate students, clinicians, and mycologists. This bookwasayearlongproject.Therefore,wemustthankalltheauthorsandSpringerteamfor their patience and support toward successful completion of this project. In the end, we wouldliketosaythatapartfrombeingareferencebookforthoserelatedinlipidresearch,it is extremely useful and most suited for biochemistry, microbiology, and biotechnology teaching. Gurgaon,Haryana,India RajendraPrasad Lucknow,UttarPradesh,India AshutoshSingh v Contents Preface .......................................................................... v Contributors..................................................................... ix 1 BackgroundofMembraneLipids ......................................... 1 AshokKumar,AtanuBanerjee,AshutoshSingh,andRajendraPrasad 2 LipidRegulationinPathogenicFungi..................................... 13 TejasBouklas,MansaMunshi,MaurizioDelPoeta,andBettinaC.Fries 3 Sphingolipids:FunctionalandBiologicalAspectsinMammals, Plants,andFungi ....................................................... 21 RodrigoRollin-Pinheiro,MarianaCollodettiBernardino,and ElianaBarreto-Bergter 4 InsightsintoYeastPhospholipidTra(ffi)cking .............................. 41 MalathiSrinivasanandRamRajasekharan 5 WhatCanMS,NMR,andTLCTellUsAbouttheComposition ofLipidMembranes?.................................................... 59 KathrinM.Engel,YuliaPopkova,JennyLeopold,andJu¨rgenSchiller 6 AnalysisofSterolsbyGasChromatography–MassSpectrometry.............. 83 AshutoshSingh,SanaAkhtarUsmani,KhushbooArya,andNitinBhardwaj 7 QuantitationofSphingolipidsinMammalianCellLinesbyLiquid Chromatography–MassSpectrometry ..................................... 103 NihalMedatwalandUjjainiDasgupta 8 ExploringMembraneLipidandProteinDiffusionbyFRAP.................. 119 ParijatSarkarandAmitabhaChattopadhyay 9 CyclodextrinsforProbingPlasmaMembraneLipids ........................ 143 AmidVahediandAmirM.Farnoud 10 NewFamilyofFluorescentProbesforCharacterizingDepth-Dependent StaticandDynamicPropertiesofLipid/WaterInterfaces.................... 161 MoirangthemKiranSingh,HimShweta,andSobhanSen 11 Two-DimensionalInfraredSpectroscopyofNitrileLabelsasaTooltoProbe DynamicsandInteractionsinLipidMembranes ............................ 189 IlyaVinogradovandSachinDevVerma 12 EstimationandImagingTechniquestoStudyLipidsinMammalianSamples... 213 SudhanshuShuklaandSanghamitraMishra vii Contributors KHUSHBOO ARYA • DepartmentofBiochemistry,UniversityofLucknow,Lucknow,Uttar Pradesh,India ATANUBANERJEE • AmityInstituteofIntegrativeScienceandHealthandAmityInstituteof Biotechnology,AmityUniversityHaryana,Gurgaon,Haryana,India ELIANABARRETOBERGTER • DepartmentofGeneralMicrobiology,InstituteofMicrobiology PaulodeGo´es,FederalUniversityofRiodeJaneiro(UFRJ),RiodeJaneiro,Brazil MARIANA COLLODETTIBERNARDINO • DepartmentofGeneralMicrobiology,Instituteof MicrobiologyPaulodeGo´es,FederalUniversityofRiodeJaneiro(UFRJ),RiodeJaneiro, Brazil NITINBHARDWAJ • DepartmentofZoologyandEnvironmentalScience,GurukulKangri University,Haridwar,India TEJASBOUKLAS • DepartmentofBiologicalSciences,StateUniversityofNewYorkCollegeat OldWestbury,OldWestbury,NY,USA AMITABHA CHATTOPADHYAY • CSIR-CentreforCellularandMolecularBiology,Hyderabad, India UJJAINIDASGUPTA • LaboratoryofSphingolipidBiology,AmityInstituteofIntegrative SciencesandHealth,AmityUniversityHaryana,Gurgaon,Haryana,India MAURIZIODELPOETA • DepartmentofMolecularGeneticsandMicrobiology,StonyBrook University,StonyBrook,NY,USA;VeteransAdministrationMedicalCenter,Northport, NY,USA;DepartmentofMedicine,DivisionofInfectiousDiseases,StonyBrookUniversity, StonyBrook,NY,USA KATHRINM.ENGEL • FacultyofMedicine,InstituteforMedicalPhysicsandBiophysics, LeipzigUniversity,Leipzig,Germany AMIRM.FARNOUD • DepartmentofChemicalandBiomolecularEngineering,Ohio University,Athens,OH,USA BETTINAC.FRIES • DepartmentofMolecularGeneticsandMicrobiology,StonyBrook University,StonyBrook,NY,USA;VeteransAdministrationMedicalCenter,Northport, NY,USA;DepartmentofMedicine,DivisionofInfectiousDiseases,StonyBrookUniversity, StonyBrook,NY,USA ASHOKKUMAR • AmityInstituteofIntegrativeScienceandHealthandAmityInstituteof Biotechnology,AmityUniversityHaryana,Gurgaon,Haryana,India JENNY LEOPOLD • FacultyofMedicine,InstituteforMedicalPhysicsandBiophysics,Leipzig University,Leipzig,Germany NIHALMEDATWAL • RegionalCentreforBiotechnology,NCRBiotechScienceCluster, Faridabad,Haryana,India;ManipalAcademyofHigherEducation,Manipal, Karnataka,India SANGHAMITRAMISHRA • MedGenomeLabsLtd.,Bangalore,Karnataka,India MANSAMUNSHI • DepartmentofMolecularGeneticsandMicrobiology,StonyBrook University,StonyBrook,NY,USA RODRIGOROLLINPINHEIRO • DepartmentofGeneralMicrobiology,InstituteofMicrobiology PaulodeGo´es,FederalUniversityofRiodeJaneiro(UFRJ),RiodeJaneiro,Brazil YULIAPOPKOVA • FacultyofMedicine,InstituteforMedicalPhysicsandBiophysics,Leipzig University,Leipzig,Germany ix x Contributors RAJENDRAPRASAD • AmityInstituteofIntegrativeScienceandHealthandAmityInstituteof Biotechnology,AmityUniversityHaryana,Gurgaon,Haryana,India RAMRAJASEKHARAN • CSIR-CentralFoodTechnologicalResearchInstitute,Mysore,India PARIJATSARKAR • CSIR-CentreforCellularandMolecularBiology,Hyderabad,India JU¨RGENSCHILLER • FacultyofMedicine,InstituteforMedicalPhysicsandBiophysics,Leipzig University,Leipzig,Germany SOBHANSEN • SpectroscopyLaboratory,SchoolofPhysicalSciences,JawaharlalNehru University,NewDelhi,India SUDHANSHUSHUKLA • SchoolofMedicine,CaseWesternReserveUniversity,Cleveland,OH, USA HIMSHWETA • SpectroscopyLaboratory,SchoolofPhysicalSciences,JawaharlalNehru University,NewDelhi,India ASHUTOSHSINGH • DepartmentofBiochemistry,UniversityofLucknow,Lucknow,Uttar Pradesh,India MOIRANGTHEM KIRANSINGH • SpectroscopyLaboratory,SchoolofPhysicalSciences, JawaharlalNehruUniversity,NewDelhi,India MALATHISRINIVASAN • CSIR-CentralFoodTechnologicalResearchInstitute,Mysore,India SANAAKHTARUSMANI • DepartmentofBiochemistry,UniversityofLucknow,Lucknow,Uttar Pradesh,India AMIDVAHEDI • DepartmentofChemicalandBiomolecularEngineering,OhioUniversity, Athens,OH,USA SACHINDEVVERMA • DepartmentofChemistry,IndianInstituteofScienceEducationand ResearchBhopal,Bhopal,MadhyaPradesh,India ILYAVINOGRADOV • DepartmentofChemistry,UniversityofCalifornia,Irvine,Irvine,CA, USA Chapter 1 Background of Membrane Lipids Ashok Kumar, Atanu Banerjee, Ashutosh Singh, and Rajendra Prasad Abstract Lipidsareauniquegroupofmoleculesthatuniversallyexistinbothprokaryotesandeukaryotes;however, theywereleastinvestigatedbiomoleculesowingtotheirwater-insolublenature.However,thisscenariohas beenchanginginthelastfewdecadesofintensiveresearchwhichunraveleddiverserolesplayedbythemina widevarietyofbiologicalprocessesinallspectrumoflife.Notwithstandingacommonfootprintoflipids that exists in most organisms, there are specific lipid molecules, which are characteristic of a system. Coincidingwiththedevelopmentofseparationandhigh-throughputanalyticaltools,weareabletodetect minorlipidswhichotherwiseremainedundetected.Wenowknowthateachtypeofphosphoglyceridesor sphingolipidsisenrichedwithahostofmolecularspeciesimpartingadditionaldynamismtolipidcomposi- tion.Theselipidchangesregulatemembranehomeostasis,whichinturnaffectsthephysiologicalfunctions. Thischapterprovidesabackgroundoflipidsthatarepresentinbiologicalsystems.Sincethereexistsavast amountofliteratureonlipidmetabolismofvariousorganisms,wewillonlylimitourdiscussiontoyeast systems. Keywords Lipids,Membrane,Functions 1 Introduction Lipids are well known as a source of biofuel and as membrane structural components; however, these sparingly water-soluble molecules have recently come to prominence due to the discovery oftheirmultidimensionalrolesextendingfromhumandiseasesand infections caused by microbial and fungal organisms [1]. This has fueled greater momentum in lipid research, well supported by the advancement of analytical tools including high-throughput mass spectrometry-based advanced techniques presenting high resolu- tion and detection of lipids which otherwise remained undetected due to their lower content [2]. Among eukaryotic models for unveiling multiple roles of lipids, budding yeast Saccharomyces cereviseae has been a preferred model. The genetic flexibility provided by this haploid yeast has enabled us to unknot various facetsoflipids.Asaresult,afairlygoodknowledgeconcerningthe spectrum of lipid composition, and regulatory circuitry governing RajendraPrasadandAshutoshSingh(eds.),AnalysisofMembraneLipids,SpringerProtocolsHandbooks, https://doi.org/10.1007/978-1-0716-0631-5_1,©SpringerScience+BusinessMedia,LLC,partofSpringerNature2020 1
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