Chemistry of Protein and Nucleic Acid Cross-Linking and Conjugation, Second Edition

608 Pages·2011·18.32 MB·English

by  Shan S. Wong

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
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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
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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