Chemistry of Protein and Nucleic Acid Cross-Linking and Conjugation, Second Edition PDF
Preview Chemistry of Protein and Nucleic Acid Cross-Linking and Conjugation, Second Edition
7491_cover 8/29/11 10:06 AM Page 1 C M Y CM MY CY CMY K BIOCHEMISTRY Wong Chemistr y of • Chemistry of Jameson Protein and Nucleic Acid Protein and Nucleic Acid Cross-Linking and Cross-Linking and Conjugation Conjugation Second Edition P r o t Since the publication of the first edition of Chemistry of Protein Conjugation and Cross- e i Linking in 1991, new cross-linking reagents, notably multifunctional cross-linkers, have been n developed and synthesized. The completion of the human genome project has opened a new a area for studying nucleic acid and protein interactions using nucleic acid cross-linking reagents, n and advances have also been made in the area of biosensors and microarray biochips for the a d detection and analysis of genes, proteins, and carbohydrates. In addition, developments in n N C physical techniques with unprecedented sensitivity and resolution have facilitated the analysis d u h of cross-linked products. C c e l o e m n i Updated to reflect the advances of the 21st century, this book offers: c i j s • An overview of the chemical principles underlying the processes of cross-linking u A t g r and conjugation c y a i d • A thorough list of cross-linking reagents published in the literature since the first edition, t o i covering monofunctional, homobifunctional, heterobifunctional, multifunctional, and zero- o C f n r length cross-linkers o • Reviews of the use of these reagents in studying protein tertiary structures, geometric s s arrangements of subunits within complex proteins and nucleic acids, near-neighbor analysis, - L protein-to-protein or ligand–receptor interactions, and conformational changes of i n biomolecules k • Discusses the application of immunoconjugation for immunoassays, immunotoxins for i n targeted therapy, microarray technology for analysis of various biomolecules, and solid g state chemistry for immobilizations Second Edition 7491 Second Shan S. Wong Edition David M. Jameson 6000 Broken Sound Parkway, NW Suite 300, Boca Raton, FL 33487 711 Third Avenue an informa business New York, NY 10017 www.crcpress.com 2 Park Square, Milton Park w w w. c r c p r e s s . c o m Abingdon, Oxon OX14 4RN, UK Composite Chemistry of Protein and Nucleic Acid Cross-Linking and Conjugation Second Edition Chemistry of Protein and Nucleic Acid Cross-Linking and Conjugation Second Edition Shan S. Wong David M. Jameson Boca Raton London New York CRC Press is an imprint of the Taylor & Francis Group, an informa business CRC Press Taylor & Francis Group 6000 Broken Sound Parkway NW, Suite 300 Boca Raton, FL 33487-2742 © 2012 by Taylor & Francis Group, LLC CRC Press is an imprint of Taylor & Francis Group, an Informa business No claim to original U.S. Government works International Standard Book Number-13: 978-1-4200-0764-0 (eBook - PDF) This book contains information obtained from authentic and highly regarded sources. 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Visit the Taylor & Francis Web site at http://www.taylorandfrancis.com and the CRC Press Web site at http://www.crcpress.com Contents Prefacexv Authorsxvii Chapter 1 OverviewofProteinConjugation1 References6 Chapter 2 ReviewofProteinandNucleicAcidChemistry9 21 Introduction9 22 ProteinComposition10 221 AminoAcids10 222 ProstheticGroups10 23 ProteinFunctionalGroups13 231 ReactiveAminoAcidSideChains13 2311 RelationshipbetweenNucleophilicityandReactivity14 2312 EffectsofpH15 2313 EffectsofMicroenvironment16 232 ChemicallyIntroducedReactiveGroups17 2321 ReductionofDisulfideBonds18 2322 InterconversionofFunctionalGroups19 2323 IntroductionofCarbohydrateProstheticGroups25 2324 ActivationofCarbohydratesbyPeriodate27 24 NucleicAcidChemistry27 241 PhotochemicalReactivitiesofNucleicAcids27 242 ChemicalReactivitiesofNucleicAcids29 References31 Chapter 3 ReagentsTargetedtoSpecificFunctionalGroups35 31 Introduction35 32 SulfhydrylReagents35 321 α-HaloacetylCompounds35 322 N-MaleimideDerivatives37 323 MercurialCompounds38 324 DisulfideReagents38 33 AminoGroup–SpecificReagents38 331 AlkylatingAgents39 3311 α-HaloacetylCompounds39 3312 N-MaleimideDerivatives39 3313 ArylHalides40 3314 AldehydesandKetones41 332 AcylatingAgents42 v vi Contents 34 ReagentsDirectedtowardCarboxylGroups43 341 DiazoacetateEstersandDiazoacetamides43 342 Carbodiimides44 35 TyrosineSelectiveReagents44 351 AcylatingAgents44 352 ElectrophilicReagents45 36 Arginine-SpecificReagents45 37 Histidine-SelectiveReagents46 38 Methionine-AlkylatingReagents47 39 Tryptophan-SpecificReagents47 310 Serine-ModifyingReagents48 References48 Chapter 4 HowtoDesignandChooseCross-LinkingReagents53 41 Introduction53 42 UseofNucleophilicReactions55 421 TheBasicReaction55 4211 ElectrophilicityoftheSubstrate55 4212 LeavingGroupReactivity56 422 Alkylation56 423 Acylation58 43 UseofElectrophilicReactions60 44 IncorporatingGroup-DirectedReagents61 441 DisulfideReagents62 442 MercurialReagents62 443 ReductiveAlkylation62 444 VicinalDicarbonylReagents63 45 IncorporatingPhotoactivatableNonspecificGroups63 46 ChangingtheWaterSolubilityofCross-Linkers65 47 IncorporatingSpecialCharacteristicsintheBridgeSpacer66 471 IncorporationofCleavableBonds66 4711 DisulfideBond66 4712 MercurialGroup66 4713 VicinalGlycolBond66 4714 AzoLinkage66 4715 SulfoneLinkage69 4716 SelenoethyleneGroup69 4717 EsterBond69 4718 ThioesterBond69 4719 MaleylamideLinkage69 47110 Acetals,Ketals,andOrthoEsters69 472 IncorporatingMolecularDistanceRulers70 473 IncorporatingReporterGroups72 4731 UV–VISAbsorptionChromophores72 4732 Infrared-AbsorbingChromophores73 4733 FluorescentProbes73 4734 SpinLabels74 4735 RadioactiveandNonradioactiveIsotopes75 References76 Contents vii Chapter 5 HomobifunctionalCross-LinkingReagents81 51 Introduction81 52 AminoGroup–DirectedCross-Linkers82 521 Bisimidoesters(Bisimidates)82 522 Bis-SuccinimidylDerivatives(N-Hydroxysuccinimidyl Esters, NHSEsters)85 523 BifunctionalArylHalides86 524 DiIsocyanatesandDiIsothiocyanates87 525 BifunctionalSulfonylHalides87 526 Bis-NitrophenylEsters88 527 BifunctionalAcylazides88 528 DicarbonylCompounds88 529 OtherAminoGroup–ReactingCross-LinkingReagents91 53 SulfhydrylGroup–DirectedCross-Linkers93 531 MercurialReagents95 532 Disulfide-FormingReagents95 533 Bismaleimides97 534 Bis-HaloacetylDerivatives98 535 Di-AlkylHalides98 536 Chloro-s-Triazines99 537 Aziridines(Ethyleneimines)99 538 Bis-Epoxides(Bisoxiranes)99 539 SulfoneDerivatives100 54 CarboxylGroup–DirectedCross-LinkingAgents101 55 PhenolateandImidazolylGroup–DirectedCross-LinkingReagents102 56 ArginineResidue–DirectedCross-Linkers102 57 MethionineResidueCross-LinkingAgent103 58 CarbohydrateMoiety–SpecificReagents103 59 NondiscriminatoryPhotoactivatableCross-Linkers104 510 NoncovalentHomobifunctionalCross-LinkingReagents104 511 NucleicAcidCross-LinkingReagents105 5111 MetalCompounds105 5112 AzinomycinBis-Epoxides140 5113 Bis-Pyrrolobenzodiazepines141 5114 Bis-Cyclopropylpyrroloindole(CPI)-BasedReagents143 5115 Bis-Cyclopropanebenz[e]indoline(CBI)-BasedReagents145 5116 DiaziridinylBenzoquinones146 5117 MitomycinCDimers147 5118 Bis-ChloroethylamineDerivatives147 5119 Bis-CarbamateDerivatives158 51110PyrrolizidineAlkaloids(PAs)160 51111Bis-CatecholDerivatives161 51112QuinoneMethides162 51113NitrosoureaDerivatives164 References165 Chapter 6 HeterobifunctionalCross-Linkers191 61 Introduction191 62 Group-SelectiveHeterobifunctional Reagents for Protein Cross- Linking191 viii Contents 621 Amino-andSulfhydryl-Group–DirectedCross-Linkers191 622 Cross-LinkersDirectedtowardCarboxyland Either Sulfhydryl orAminoGroups199 623 Carbonyl-andAmino-orSulfhydryl-Group–Directed Cross-Linkers200 624 MiscellaneousHeterobifunctionalCross-Linkers with UndefinedSpecificity200 63 Protein-PhotosensitiveHeterobifunctionalCross-LinkingReagents202 631 AminoGroup–AnchoredPhotosensitiveReagents203 632 SulfhydrylGroup–AnchoredPhotoactivatableReagents204 633 GuanidinylGroup–AnchoredPhotoactivatableReagents205 634 Carboxyl-,Carboxamide-,andCarbonyl- Group–Anchored PhotoactivatableReagents205 635 Photoaffinity-LabelingReagents205 64 NoncovalentImmunoglobulinCross-LinkingSystem206 65 HeterobifunctionalNucleicAcidCross-LinkingReagents208 References225 Chapter 7 MultifunctionalCross-LinkingReagents239 71 Introduction239 72 TrifunctionalCross-Linkers239 73 TetrafunctionalCross-Linkers256 74 MultifunctionalCross-Linkers257 75 NoncovalentCross-Linkers258 751 AvidinandStreptavidin258 752 Lectins259 753 MultifunctionalAntibodies260 References261 Chapter 8 Monofunctional andZero -LengthCross -LinkingReagents265 81 Introduction265 82 MonofunctionalCross-LinkingReagents266 821 Imidoesters266 822 Formaldehyde266 823 Chloroformates268 824 MercuricIon269 825 FunctionalGroup–ModifyingReagents269 83 Zero-LengthCross-LinkingReagents270 831 CarboxylGroup–ActivatingReagents270 8311 Carbodiimides270 8312 IsoxazoliumCompounds276 8313 Ethylchloroformate276 8314 Carbodiimidazole277 8315 N-Alkoxycarbonyl-2-Alkoxy-1,2-Dihydroquinolines278 8316 Diethylpyrocarbonate279 832 ReagentsforDisulfideFormation279 833 OxidationCross-LinkingReagents280 834 CarbohydrateActivationReagents281 835 EnzymesasZero-LengthCross-Linkers282 Contents ix 8351 Transglutaminase282 8352 Tyrosinase282 8353 Peroxidases283 8354 XanthineOxidaseandOthers283 836 RadiationasZero-LengthCross-Linker284 837 MiscellaneousReagents285 8371 Tetranitromethane285 8372 PotassiumNitrosylDisulfonate286 8373 Bisulfite286 References286 Chapter 9 GeneralApproachesfor ChemicalCross-Linking297 91 Introduction297 92 ClassificationofCross-LinkingProcedures297 921 One-StepCross-LinkingReactions297 922 Two-StepCross-LinkingReactions298 923 Three-StepCross-LinkingReactions300 924 MultistepCross-LinkingReactions300 93 GeneralConditionsforCross-Linking303 931 ChoiceofReactionMedium303 932 ChoiceofReactionTemperatureandTime303 933 ChoiceofReactantConcentrations304 94 Cross-LinkingProtocolsforCommonlyUsedReagents304 941 ExamplesforZero-LengthCross-Linker304 9411 Cross-LinkingaPeptideandaProteinUsingEDC304 9412 Cross-LinkingofPorcineLuteinizingHormone with EDC to StudyaandbSubunitInteractions305 942 ExamplesforHomobifunctionalReagents305 9421 Bis-Imidoesters305 9422 Bis-N-Hydroxysuccinimide(NHS)Esters305 9423 Bis-MaleimidoReagents306 9424 Bis-α-HaloacetylReagents307 943 ExamplesforHeterobifunctionalReagents307 9431 ConjugationofHumanSerumAlbumin(HSA) and MonoclonalAntibody(mAb)withSPDP308 9432 Cross-LinkingofDemineralizedBoneMatrix(DBM) andMonoclonalAntibodywithSulfo-SMCC308 944 ExamplesforHeterobifunctionalPhotosensitiveReagents309 9441 Cross-LinkingofProteinswiththePhotoreagent N-(4-Azido-2,3,5,6-Tetrafluorobenzyl)-3- Maleimidylpropionamide(TFPAM-3)309 9442 Cross-LinkingUvsYHexamerProteinComplex with thePhoto-ReagentRuthenium(II) Tris-Bipyridyl Dichloride(Ru(II)bpyCl )310 3 2 95 Cross-LinkingProtocolsBasedonBiologicalSystems310 951 SolubleMacromolecules310 9511 Cross-LinkingNonassociatedProteins310 9512 Cross-LinkingMultisubunitComplexes311 952 Membrane-BoundProteins311 953 NucleicAcidsandNucleicAcid–ProteinComplexes312
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