Protein Structure, Stability, and Interactions PDF
Preview Protein Structure, Stability, and Interactions
Protein Structure, Stability, and Interactions M E T H O D S I N M O L E C U L A R B I O L O G Y TM John M. Walker, SERIES EDITOR 502. Bacteriophages:MethodsandProtocols,Volume2:Mole- 468. Wnt Signaling, Volume 1: Pathway Methods and cularandAppliedAspects,editedbyMarthaR.J.Clokie MammalianModels,editedbyElizabethVincan,2008 andAndrewM.Kropinski2009 467. Angiogenesis Protocols: Second Edition, edited by 501. Bacteriophages:MethodsandProtocols,Volume1:Isola- StewartMartinandCliffMurray,2008 tion,Characterization,andInteractions,editedby 466. Kidney Research: Experimental Protocols, edited by MarthaR.J.ClokieandAndrewM.Kropinski2009 TimD.HewitsonandGavinJ.Becker,2008 496. DNAandRNAProfilinginHumanBlood:Methods 465. Mycobacteria,SecondEdition,editedbyTanyaPar- andProtocols,editedbyPeterBugert,2009 ishandAmandaClaireBrown,2008 493. AuditoryandVestibularResearch:MethodsandProto- 464. 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Alcohol: Methods and Protocols, edited by Laura E. byPatrickParfreyandBrendonBarrett,2008 Nagy,2008 446. Post-translationalModificationsofProteins:Toolsfor 472. CancerEpidemiology,Volume2:ModifiableFactors, FunctionalProteomics,SecondEdition,editedby editedbyMukeshVerma,2008 ChristophKannicht,2008 471. CancerEpidemiology,Volume1:HostSusceptibility 445. Autophagosome and Phagosome, edited by Vojo Factors,editedbyMukeshVerma,2008 Deretic,2008 470. Host-Pathogen Interactions: Methods and Protocols, 444. PrenatalDiagnosis,editedbySinhueHahnandLaird editedbySteffenRuppandKaiSohn,2008 G.Jackson,2008 469. WntSignaling,Volume2:PathwayModels,editedby 443. MolecularModelingofProteins,editedbyAndreas ElizabethVincan,2008 Kukol,2008 M M B TM E T H O D S I N O L E C U L A R I O L O G Y Protein Structure, Stability, and Interactions Edited by John W. Shriver Departments of Chemistry University of Alabama in Huntsville, Huntsville, AL 35899 USA Editor JohnW.Shriver DepartmentsofChemistry UniversityofAlabamainHuntsville Huntsville,AL35899 USA [email protected] SeriesEditor JohnM.Walker SchoolofLifeSciences UniversityofHertfordshire Hatfield,Hertfordshire,AL109AB,UK ISBN:978-1-58829-954-3 e-ISBN:978-1-59745-367-7 ISSN:1064-3745 e-ISSN:1940-6029 DOI:10.1007/978-1-59745-367-7 LibraryofCongressControlNumber:2008938551 #HumanaPress,apartofSpringerScienceþBusinessMedia,LLC2009 Allrightsreserved.Thisworkmaynotbetranslatedorcopiedinwholeorinpartwithoutthewrittenpermissionofthe publisher(HumanaPress,c/oSpringerScience+BusinessMedia,LLC,233SpringStreet,NewYork,NY10013,USA), except for brief excerpts in connection with reviews or scholarly analysis. Use in connection with any form of informationstorageandretrieval,electronicadaptation,computersoftware,orbysimilarordissimilarmethodology nowknownorhereafterdevelopedisforbidden. Theuseinthispublicationoftradenames,trademarks,servicemarks,andsimilarterms,eveniftheyarenotidentified assuch,isnottobetakenasanexpressionofopinionastowhetherornottheyaresubjecttoproprietaryrights. Printedonacid-freepaper springer.com Preface Characterizations of protein folding (stability) and molecular interactions (binding) areessentialinmanyareasofbiochemistryandcellbiology.Neithercanbeviewedasan all-or-none phenomenon, and a healthy cell requires exquisite adjustment of both. Although initial descriptions of stability and interactions tend to be qualitative, an understanding of their importance requires a quantitative approach with a level of precisionthatmatchestheirfine-tuninginalivingcell. TwovolumesintheMethodsinMolecularBiologySeriespublishedbyHumanahave beendevotedtoproteinstabilityandfolding.Thefirst,ProteinStabilityandFolding: Theory and Practice (edited by Bret A. Shirley), appeared in 1995 and was primarily devoted to the basic methods utilized for studies of the thermodynamics of protein folding. The second was entitled Protein Structure, Stability, and Folding (edited by Kenneth ‘‘Kip’’ Murphy) and appeared in 2001. The goal of the second volume as stated by Kip was to serve as a companion to the first with more of an emphasis on theory, with some chapters focusing on some exciting new methods. This volume follows that path with a slight change in title to reflect the shift in emphasis: Protein Structure,Stability,andInteractions. We present here an overview of some of the methods currently used to study proteinstabilityandproteininteractions,includingscanningandtitrationcalorimetry, high-fieldNMR and other spectroscopic methods,and analytical ultracentrifugation. Recentadvancesintheareaofproteininteractionswithwater,salts,andothersolutes, aswellastheeffectsofcrowdinghavebeenimpressiveandaredescribedinacoupleof chapters.Methodsforstudyingflexibilityandintramolecularinteractionsinproteins, along with characterization of the unfolded state, are also included. Exciting new techniquesincludesingle-moleculemethodsaswellasanewapplicationofdenaturants toaddressproteinstabilityinvivo. Iwouldliketothankalloftheauthors,theSeriesEditorJohnM.Walker,andthe publisher for their hard work and patience in putting together this volume. We hope that it proves useful to many students and workers, not only in the field of protein structuralbiology,butalsoinrelatedfieldssuchascellbiologywheretheapplicationof physicalmethodswillbecomeincreasinglynecessaryaswemovetowardaquantitative description of the chemistry and physics of life. Finally, I would like to thank my colleagues,andespeciallymyfamily,fortheirunderstandingandsupport. JohnW.Shriver v Contents Preface..............................................................v Contributors......................................................... ix 1 MicrocalorimetryofProteinsandTheirComplexes........................1 PeterL.Privalov 2 DeterminingtheConformationalStabilityofaProteinUsing UreaDenaturationCurves..........................................41 KevinL.Shaw,J.MartinScholtz,C.NickPace,andGeraldR.Grimsley 3 DefiningtheStabilityofMultimericProteins ...........................57 JohnW.Shriver,andStephenP.Edmondson 4 Protein–ProteinandLigand–ProteinInteractionsStudiedbyAnalytical Ultracentrifugation ...............................................83 WalterF.Stafford,III 5 MonitoringMolecularInteractionsbyNMR...........................115 JamesM.Lipchock,andJ.PatrickLoria 6 Ligand-BindingInteractionsandStability .............................135 JohnW.Shriver,andStephenP.Edmondson 7 AMethodforDirectMeasurementofProteinStabilityInVivo ............165 ZoyaIgnatova,andLilaM.Gierasch 8 QuantifyingtheRolesofWaterandSolutes(Denaturants,Osmolytes, andHofmeisterSalts)inProteinandModelProcessesUsingtheSolute PartitioningMode ...............................................179 LaurelM.Pegram,andM.ThomasRecord,Jr. 9 MolecularCrowdingandSolvation:DirectandIndirectImpactonProtein Reactions ......................................................195 Jo¨rgR¨osgen 10 DefiningtheRoleofSaltBridgesinProteinStability ....................227 IlianJelesarov,andAndreyKarshikoff 11 ProteinStabilizationbytheRationalDesignofSurfaceCharge–Charge Interactions ....................................................261 KatrinaL.Schweiker,andGeorgeI.Makhatadze 12 NMRAnalysisofNative-StateProteinConformationalFlexibility byHydrogenExchange...........................................285 GriseldaHerna´ndez,andDavidM.LeMaster 13 Single-MoleculeFluorescenceStudiesofProteinFolding.................311 G.UlrichNienhaus 14 ExperimentalCharacterizationoftheDenaturedStateEnsemble ofProteins.....................................................339 Jae-HyunCho,andDanielP.Raleigh Index .............................................................353 vii Contributors JAE-HYUNCHO (cid:2) DepartmentofBiochemistryandMolecularBiophysics,Columbia University,NewYork,NY,USA STEPHENP.EDMONDSON (cid:2) DepartmentofChemistry,UniversityofAlabamain Huntsville,Huntsville,AL,USA LILAGIERASCH (cid:2) DepartmentsofBiochemistryandMolecularBiologyandChemistry, UniversityofMassachusetts-Amherst,Amherst,MA,USA G.R.GRIMSLEY (cid:2) DepartmentofMolecularandCellularMedicine,TexasA&M HealthScienceCenter,CollegeStation,TX,USA GRISELDAHERNANDEZ (cid:2) WadsworthCenter,NewYorkStateDepartmentofHealth, andDepartmentofBiomedicalSciences,UniversityatAlbany–SUNY,Albany, NY,USA ZOYAIGNATOVA (cid:2) CellularBiochemistry,InstituteofBiologyandBiochemistry, UniversityofPotsdam,Karl-Liebknecht-Str.24–25,Haus25,14476Potsdam-Golm, Germany ILIANJELESAROV (cid:2) BiochemischesInstitutderUniversita¨tZu¨rich,Zu¨rich,Switzerland ANDREYKARSHIKOFF (cid:2) KarolinskaInstitute,DepartmentofBiosciencesandNutrition, Stockholm,Sweden DAVIDM.LEMASTER (cid:2) WadsworthCenter,NewYorkStateDepartmentofHealth,and DepartmentofBiomedicalSciences,UniversityatAlbany–SUNY,Albany,NY,USA JAMESM.LIPCHOCK (cid:2) DepartmentofChemistry,YaleUniversity,NewHaven,CT, USA J.PATRICKLORIA (cid:2) DepartmentofChemistry,YaleUniversity,NewHaven,CT,USA GEORGEI.MAKHATADZE (cid:2) CenterforBiotechnologyandInterdisciplinaryStudies, RensselaerPolytechnicInstitute,Troy,NY,USA G.ULRICHNIENHAUS (cid:2) InstituteofBiophysics,UniversityofUlm,Ulm,Germany C.NICKPACE (cid:2) DepartmentofMolecularandCellularMedicine,TexasA&MHealth ScienceCenter,andDepartmentofBiochemistryandBiophysics,TexasA&M University,CollegeStation,TX,USA LAURELM.PEGRAM (cid:2) DepartmentofChemistry,UniversityofWisconsin-Madison, Madison,WI,USA PETERL.PRIVALOV (cid:2) DepartmentofBiology,JohnsHopkinsUniversity,Baltimore, MD,USA DANIELP.RALEIGH (cid:2) DepartmentofChemistry,StonyBrookUniversity,StonyBrook, NY,USA M.THOMASRECORD (cid:2) DepartmentsofChemistryandBiochemistry,Universityof Wisconsin-Madison,Madison,WI,USA Jo¨ RGRo¨ SGEN (cid:2) DepartmentofBiochemistryandMolecularBiology,UniversityofTexas MedicalBranch,Galveston,TX,USA ix x Contributors J.MARTINSCHOLTZ (cid:2) DepartmentofMolecularandCellularMedicine,TexasA&M HealthScienceCenter,andDepartmentofBiochemistryandBiophysics,TexasA&M University,CollegeStation,TX,USA KATARINAL.SCHWEIKER (cid:2) CenterforBiotechnologyandInterdisciplinaryStudies, RensselaerPolytechnicInstitute,Troy,NY,USA KEVINL.SHAW (cid:2) DepartmentofBiology,GroveCityCollege,GroveCity,PA,USA JOHNW.SHRIVER (cid:2) DepartmentsofChemistryandBiologicalSciences,Universityof AlabamainHuntsville,Huntsville,AL,USA WALTERF.STAFFORD (cid:2) BostonBiomedicalResearchInstitute,Watertown,MA,USA Chapter 1 Microcalorimetry of Proteins and Their Complexes Peter L. Privalov Abstract Ultrasensitive microcalorimetric techniques for measuring the heat capacities of proteins in dilute solutionsoverabroadtemperaturerange(DSC)andtheheatsofproteinreactionsatfixedtemperatures (ITC) are described and the methods of working with these instruments are considered. Particular attentionispaidtoanalyzingthethermalpropertiesofindividualproteins,theirstability,theenergetics of their folding, and their association with specific macromolecular partners. Use of these calorimetric methods is illustrated with examples of small compact globular proteins, small proteins having loose noncompactstructure,multidomainproteins,andproteincomplexes,particularlywithDNA. Keywords:microcalorimetry,proteins,complexes,folding,stability,energetics. 1. Introduction Eversinceitwasrealizedthattheformationoftheuniquespatial structures of proteins and their complexes is in principle a rever- sible, thermodynamically driven process, investigation of their energeticshasgainedhighpriority.Thishasrequireddirectmea- surements of the heat effects of intra- and intermacromolecular reactions of proteins in highly dilute solutions preventing their nonspecificinteractions.Thatneededdevelopmentofsupersensi- tive calorimetrictechniques, differential scanning and isothermal reaction microcalorimetry, for measuring the heats associated with change in temperature at fixed solvent conditions or with change in solvent conditions at fixed temperature, respectively (1, 2). The differential scanning microcalorimeter (DSC) gained particular importance in studying the thermal properties of pro- teins, providing information on the stability of protein structure and its domain organization. Measurements of the heats of JohnW.Shriver(ed.),ProteinStructure,Stability,andInteractions,vol.490 (cid:2)2009HumanaPress,apartofSpringerScienceþBusinessMedia DOI:10.1007/978-1-59745-367-7_1Springerprotocols.com 1
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