Chemical and Synthetic Approaches in Membrane Biology PDF
Preview Chemical and Synthetic Approaches in Membrane Biology
Arun K. Shukla Editor Chemical and Synthetic Approaches in Membrane Biology Springer Protocols Handbooks More information about this series at http://www.springer.com/series/8623 Arun K. Shukla Editor Chemical and Synthetic Approaches in Membrane Biology Editor ArunK.Shukla IndianInstituteofTechnology Kanpur,India ISSN1949-2448 ISSN1949-2456 (electronic) SpringerProtocolsHandbooks ISBN978-1-4939-6835-0 ISBN978-1-4939-6836-7 (eBook) DOI10.1007/978-1-4939-6836-7 LibraryofCongressControlNumber:2017942745 #SpringerScience+BusinessMediaLLC2017 Thisworkis subjectto copyright.Allrightsarereservedbythe Publisher,whetherthe wholeorpartofthe materialis concerned,specificallytherightsoftranslation,reprinting,reuseofillustrations,recitation,broadcasting,reproductionon microfilms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computersoftware,orbysimilarordissimilarmethodologynowknownorhereafterdeveloped. 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Preface Cellsinourbodyaresurroundedbylipidmembranesthatactasselectivitybarriersfortheflow of signals and messages from outside to cell interior and vice-versa. Biological membranes have been a focal point of intense research over the years in terms of understanding their composition and contribution to specific cellular functions. Over the last decade or so, many noveltoolsandtechniqueshavebeendevelopedtodirectlyprobethephysico-chemicalproper- ties, overall architecture, and network of interactions that determine the basic features of biological membranes. Especially, the interaction of proteins embedded in the membranes with their surrounding lipid environment and how these interactions shape the membrane structure and function is at the center stage of membrane biology research. Development and optimization of streamlined protocols to assemble and reconstitute synthetic membrane-like platforms in vitro for direct investigation of lipid-protein interactions in a defined setting has provided many meaningful insights in the area of membrane research. Moreover, directly probing the structure, function, and dynamics of proteins embedded in the biological mem- branes such as receptor, ion channels, and transporters has emerged as one of the most productive research areas in modern biology. Considering that integral membrane proteins representthelargestclassofdrugtargets,researchinthisareahasdirectimplicationsfornovel therapeutics for many different human diseases. In this volume of Springer Protocols entitled ChemicalandSyntheticApproachesinMembraneBiology,webringtogetherabroadrangeof topics related to membrane biology research with particular emphasis on novel approaches, technologyplatforms,andemergingtoolsinthisarea. Thefirstthreechaptersinthisbookpertaintoartificialordesignermembranemimeticsthat canbeutilizedforinvitrostudiesofmembrane-lipidinteractions.Reedandcoworkersdescribe aprotocolforpreparingandcharacterizinglipid-coatedgoldnanoparticlesandhowtheycanbe used to generate hybrid lipid membranes for investigating protein-membrane interactions. Roemer and coauthors elegantly present the assembly protocol of giant unilamellar vesicles as an approach to study novel paradigms of endocytosis in a minimal biomimetic membrane environment. Surface patterning with supported lipid bilayers has been gaining momentum lately wherephotolithographic and soft lithographicmethodshave madeit possible topattern different types of biomolecules for wide ranging applications. Carrer and Sanchez present a streamlined protocol for generating lipid bilayer-based micropattern using one-photon lithographyandmicrocontactprinting. The next nine chapters in the book cover the approaches and methodologies to directly investigate membrane protein structure, localization, and dynamics. Mahalakshmi and collea- gues provide a comprehensive discussion of the commonly utilized approaches to extract and v vi Preface purifytransmembraneb-barrelproteinsandalsotouchuponthemethodsforefficientrefolding and biophysical studies of these proteins. Carla and coauthors describe a method using total internal reflection fluorescence microscopy to investigate the trafficking of a glutamate trans- porter,anapproachthatcanbepotentiallyextendedtootherintegralmembraneproteins.Janesh Kumar and colleagues present an overview of a fluorescence-based technique that is being widely utilized these days for rapid, efficient, and relatively inexpensive screening of mem- braneproteinsintermsofconstructengineeringandmembraneextraction. High-resolution imaging of membrane proteins in their native environment is a very important aspect in membrane protein research. Francisco Barrantes provides a detailed protocol for imaging synaptic proteins using single-molecule super-resolution microscopy. The steps described here for fixing, handling, and imaging primary culture of hippocampal neuronal cells as a case example should be transferrable to other neuronal cultures.Quantum dots haveemerged as a wonderful toolnotonly forprobing moleculardynamics and imaging but also for profiling at single-molecule level and in the context of large cellular population. Rosenthal and coworkers present a layout for using the quantum dot tool box to investigate localization and trafficking patterns of neurotransmitter transporters and discuss specific advantagesassociatedwiththeuseofquantumdotsoverothermethods. Post-translational modifications and ligand-induced trafficking of membrane proteins are critical regulatory steps in their functional targeting and downregulation, respectively. Hang and Yuan introduce various types of protein fatty-acylation, their roles in membrane interac- tion,activity,andtraffickingfollowedbyastep-by-stepprotocolformonitoringproteinfatty- acylationviametaboliclabelingprotocolusingchemicalreporters.IkedaandKumagaipresent aHalo Tag-based pulse-chase labelingplatform forsimpleand versatile assessmentof GPCR endocytosis. They also discuss the potential advantages of this approach over conventional methodstomonitoragonist-inducedGPCRinternalization. High-qualityantibodiesareoneofthemostcovetedtoolsintheareaofmembraneprotein research, and phage display-based methodologies are emerging as a robust platform for antibodygeneration.UysalandKossiakoffdescribeastrategythathasbeensuccessfullyused forgeneratingsyntheticantibodyfragmentsagainstmembraneproteintargets.Thistechnology shows great promise in yielding synthetic antibodies that are wonderful tools not only for structuralpurposesbutalsoformolecular,cellbiological,andtherapeuticapplications.Despite recentadvancesintheareaofmembraneproteinproductionandisolation,NMR-basedstudies onmembraneproteintargetsstillremainatechnicallychallengingtask.Inthefinalchapterof thisbook,Brownandcoauthorsdescribeastrategythattheyhavedevelopedandsuccessfully implementedtopreparesensoryrhodopsininnativemembraneenvironmentandsubsequently useitforsolid-stateNMRanalysis. ItakethisopportunitytosincerelythankSpringer’sproductionteamwhodidawonderful jobofgettingthechaptersreadyforpublication.Ihopethatyouenjoythetopicscoveredinthis volume and find it useful in your own research endeavors. Please feel free to share your feedbackwithme. DepartmentofBiologicalSciencesandBioengineering ArunK.Shukla IndianInstituteofTechnology,Kanpur208016India Contents Lipid-CoatedGoldNanoparticlesasProbesforMembraneBinding. . . . . . . . . . . . . . . 1 DesmondJ.Hamilton,YuhengCai,RupinderKaur,GrantW.Marquart, MarilynR.Mackiewicz,andScottM.Reed DelvingintoLipid-DrivenEndocyticMechanismsUsingBiomimeticMembranes. . . . . 17 JosefMadl,SarahVillringer,andWinfriedRo¨mer LipidBilayerPatternsFabricationbyOne-PhotonLithography. . . . . . . . . . . . . . . . . . 37 M.FlorenciaSa´nchezandDoloresC.Carrer ApproachesforPreparationandBiophysicalCharacterization ofTransmembraneb-Barrels. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49 BharatRamasubramanianIyer,AnkitGupta,andRadhakrishnanMahalakshmi ProbingtheDynamicsofPlasmaMembraneGlutamateTransporters inRealTimebyTotalInternalFluorescenceReflectionMicroscopy. . . . . . . . . . . . . . . 117 ElianaS.DiCairano,PaolaMarciani,StefaniaMoretti,andCarlaPerego Fluorescence-BasedScreeningofMembraneProteinsforStructuralStudies. . . . . . . . 141 JyotiKumari,SurbhiDhingra,andJaneshKumar Single-MoleculeLocalizationSuper-ResolutionMicroscopyofSynapticProteins. . . . . 157 FranciscoJ.Barrantes ChemicalMethodsforMonitoringProteinFattyAcylation. . . . . . . . . . . . . . . . . . . . . . 199 XiaoqiuYuanandHowardC.Hang QuantumDotToolboxinMembraneNeurotransmitterTransporterResearch. . . . . . . 219 LucasB.Thal,DanielleM.Bailey,OlegKovtun,andSandraJ.Rosenthal GenerationofSyntheticAntibodyFragmentstoDetergentSolubilized MembraneProteins. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 231 SerdarUysalandAnthonyKossiakoff Pulse-ChaseCovalentLabelingTechniqueforMonitoringGPCREndocytosis. . . . . . . 245 HidetoshiKumagaiandYuichiIkeda SamplePreparationofRhodopsinsintheE.coliMembraneforInSituMagic AngleSpinningSolid-StateNuclearMagneticResonanceStudies. . . . . . . . . . . . . . . . . 253 MeaghanE.Ward,VladimirLadizhansky,andLeonidS.Brown Index. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 269 vii Contributors DanielleM.BaileyDepartmentofChemistry,VanderbiltUniversity,Nashville,TN,USA DepartmentofPharmacology,VanderbiltUniversity,Nashville,TN,USA DepartmentofInterdisciplinaryMaterialsScience,VanderbiltUniversity,Nashville,TN,USA FranciscoJ.BarrantesLaboratoryofMolecularNeurobiology,InstituteofBiomedicalResearch (BIOMED),UCA-CONICET,BuenosAires,Argentina Leonid S. Brown Department of Physics and Biophysics Interdepartmental Group, University of Guelph,Guelph,ON,Canada YuhengCaiDepartmentofChemistry,UniversityofColoradoDenver,Denver,CO,USA Dolores C. Carrer Instituto de Investigacio´n Me´dica Mercedes y Mart´ın Ferreyra (INIMEC), CONICET-UniversidadNacionaldeCo´rdoba,Co´rdoba,Argentina ElianaS.DiCairanoLaboratoryofMolecularandCellularPhysiology,DepartmentofPharmaco- logicalandBiomolecularSciences,Universita` degliStudidiMilano,Milan,Italy SurbhiDhingraNationalCentreforCellScience,Pune,Maharashtra,India M. FlorenciaSa´nchez Instituto deInvestigacio´n Me´dica Mercedes yMart´ın Ferreyra (INIMEC), CONICET-UniversidadNacionaldeCo´rdoba,Co´rdoba,Argentina Desmond J. Hamilton Department of Chemistry, University of Colorado Denver, Denver, CO, USA Howard C. Hang Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University,NewYork,NY,USA YuichiIkedaDepartmentofCardiovascularMedicine,GraduateSchoolofMedicine,TheUniver- sityofTokyo,Tokyo,Japan RupinderKaurDepartmentofChemistry,UniversityofColoradoDenver,Denver,CO,USA ix x Contributors AnthonyKossiakoffFacultyofMedicine,BezmialemVakifUniversity,Istanbul,Turkey OlegKovtunDepartmentofChemistry,VanderbiltUniversity,Nashville,TN,USA Hidetoshi Kumagai Department of Cardiovascular Medicine, Graduate School of Medicine, The UniversityofTokyo,Tokyo,Japan Department of Advanced Clinical Science and Therapeutics, The University of Tokyo, Tokyo, Japan JaneshKumarWellcomeTrust/DBTIndiaAlliance,Hyderabad,India NationalCentreforCellScience,Pune,Maharashtra,India JyotiKumariNationalCentreforCellScience,Pune,Maharashtra,India Vladimir Ladizhansky Department of Physics and Biophysics Interdepartmental Group, Univer- sityofGuelph,Guelph,ON,Canada MarilynR.MackiewiczDepartmentofChemistry,PortlandStateUniversity,Portland,OR,USA JosefMadlFacultyofBiology,Albert-Ludwigs-UniversityFreiburg,Freiburg,Germany Centre for Biological Signalling Studies (BIOSS), Albert-Ludwigs-University Freiburg, Freiburg, Germany Freiburg Center for Interactive Materials and Bioinspired Technology (FIT), Albert-Ludwigs- UniversityFreiburg,Freiburg,Germany R.MahalakshmiWellcomeTrust/DBTIndiaAlliance,Hyderabad,India Molecular Biophysics Laboratory, Department of Biological Sciences, Indian Institute of Science EducationandResearch,Govindpura,Bhopal,India PaolaMarcianiLaboratoryofMolecularandCellularPhysiology,DepartmentofPharmacological andBiomolecularSciences,Universita` degliStudidiMilano,Milan,Italy GrantW.MarquartDepartmentofChemistry,PortlandStateUniversity,Portland,OR,USA StefaniaMorettiLaboratoryofMolecularandCellularPhysiology,DepartmentofPharmacologi- calandBiomolecularSciences,Universita` degliStudidiMilano,Milan,Italy Carla Perego Laboratory of Molecular and Cellular Physiology, Department of Pharmacological andBiomolecularSciences,Universita` degliStudidiMilano,Milan,Italy ScottM.ReedDepartmentofChemistry,UniversityofColoradoDenver,Denver,CO,USA WinfriedRo¨merFacultyofBiology,Albert-Ludwigs-UniversityFreiburg,Freiburg,Germany Centre for Biological Signalling Studies (BIOSS), Albert-Ludwigs-University Freiburg, Freiburg, Germany Freiburg Center for Interactive Materials and Bioinspired Technology (FIT), Albert-Ludwigs- UniversityFreiburg,Freiburg,Germany Contributors xi SandraJ.RosenthalDepartmentofChemistry,VanderbiltUniversity,Nashville,TN,USA DepartmentofPharmacology,VanderbiltUniversity,Nashville,TN,USA DepartmentofInterdisciplinaryMaterialsScience,VanderbiltUniversity,Nashville,TN,USA Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA DepartmentofPhysicsandAstronomy,VanderbiltUniversity,Nashville,TN,USA VanderbiltInstituteof Nanoscale Science and Engineering,VanderbiltUniversity,Nashville,TN, USA MaterialsScienceandTechnologyDivision,OakRidgeNationalLaboratory,OakRidge,TN,USA LucasB.ThalDepartmentofChemistry,VanderbiltUniversity,Nashville,TN,USA SerdarUysalFacultyofMedicine,BezmialemVakifUniversity,Istanbul,Turkey SarahVillringerFacultyofBiology,Albert-Ludwigs-UniversityFreiburg,Freiburg,Germany Centre for Biological Signalling Studies (BIOSS), Albert-Ludwigs-University Freiburg, Freiburg, Germany MeaghanE.WardDepartmentofPhysicsandBiophysicsInterdepartmentalGroup,Universityof Guelph,Guelph,ON,Canada Xiaoqiu Yuan Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University,NewYork,NY,USA
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