Amino Acids, Peptides and Proteins in Organic Chemistry: Analysis and Function of Amino Acids and Peptides, Volume 5

501 Pages·2011·5.22 MB·English

Edited by
Andrew B. Hughes
Amino Acids, Peptides
and Proteins in
Organic Chemistry
Further Reading
Pignataro, B.(ed.) Fessner,W.-D.,Anthonsen, T.
Ideas in Chemistry and Modern Biocatalysis
Molecular Sciences StereoselectiveandEnvironmentally
FriendlyReactions
AdvancesinSyntheticChemistry
2009
2010
ISBN:978-3-527-32071-4
ISBN:978-3-527-32539-9
Lutz, S., Bornscheuer,U. T. (eds.)
Tulla-Puche, Judit /Albericio,
Protein Engineering Handbook
Fernando (eds.)
ThePowerofFunctionalResins 2VolumeSet
2009
in Organic Synthesis
ISBN:978-3-527-31850-6
2008
ISBN:978-3-527-31936-7 Castanho, Miguel/Santos, Nuno(eds.)
Peptide Drug Discovery and
Eicher, T., Hauptmann,S., Speicher, A.
Development
The Chemistry of Heterocycles
TranslationalResearchinAcademia
Structure,Reactions,Synthesis,and andIndustry
Applications
2011
2011 ISBN:978-3-527-32891-8
ISBN:978-3-527-32868-0(Hardcover)
ISBN:978-3-527-32747-8(Softcover) Sewald, N., Jakubke,H.-D.
Royer,J. (ed.) Peptides: Chemistry and
Biology
Asymmetric Synthesis of
Nitrogen Heterocycles 2009
ISBN:978-3-527-31867-4
2009
ISBN:978-3-527-32036-3
JNicolaou,K. C.,Chen,J. S.
Drauz, K.,Gröger,H., May,O. (eds.) Classics in Total Synthesis III
Enzyme Catalysis in Organic NewTargets,Strategies,Methods
Synthesis 2011
ISBN:978-3-527-32958-8(Hardcover)
Third,CompletelyRevisedand
ISBN:978-3-527-32957-1(Softcover)
EnlargedEdition
3Volumes
2011
ISBN:978-3-527-32547-4
Edited by
Andrew B. Hughes
Amino Acids, Peptides and Proteins
in Organic Chemistry
Volume 5 - Analysis and Function of
Amino Acids and Peptides
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V
Contents
List of Contributors XV
1 MassSpectrometryofAminoAcidsandProteins 1
SiminD.MalekniaandRichardJohnson
1.1 Introduction 1
1.1.1 MassTerminology 1
1.1.2 ComponentsofaMassSpectrometer 4
1.1.3 ResolutionandMassAccuracy 6
1.1.4 AccurateAnalysisofESIMultiplyChargedIons 10
1.1.5 FragmentIons 11
1.2 BasicProteinChemistryandHowitRelatestoMS 21
1.2.1 MassPropertiesofthePolypeptideChain 21
1.2.2 InVivoProteinModifications 21
1.2.3 ExVivoProteinModifications 26
1.3 SamplePreparationandDataAcquisition 28
1.3.1 Top-DownVersusBottom-UpProteomics 28
1.3.2 ShotgunVersusTargetedProteomics 28
1.3.3 EnzymaticDigestionforBottom-UpProteomics 29
1.3.4 LiquidChromatographyandCapillaryElectrophoresisfor
MixturesinBottom-Up 30
1.4 DataAnalysisofLC-MS/MS(orCE-MS/MS)ofMixtures 32
1.4.1 IdentificationofProteinsfromMS/MSSpectraofPeptides 32
1.4.2 DeNovoSequencing 35
1.5 MSofProteinStructure,Folding,andInteractions 36
1.5.1 MethodstoMass-TagStructuralFeatures 37
1.6 ConclusionsandPerspectives 40
References 40
2 X-RayStructureDeterminationofProteinsandPeptides 51
AndrewJ.Fisher
2.1 Introduction 51
2.1.1 LightMicroscopy 51
2.1.2 X-RaysandCrystallographyattheStart 52
VI Contents
2.1.3 X-RayCrystallographyToday 53
2.1.4 LimitationsofX-RayCrystallography 54
2.2 GrowingCrystals 55
2.2.1 WhyCrystals? 55
2.2.2 BasicMethodsofGrowingProteinCrystals 55
2.2.3 ProteinSample 59
2.2.4 PreliminaryCrystalAnalysis 59
2.2.5 MountingCrystalsforX-RayAnalysis 61
2.3 SymmetryandSpaceGroups 62
2.3.1 CrystalsandtheUnitCell 62
2.3.2 PointGroups 65
2.3.3 SpaceGroups 66
2.3.4 AsymmetricUnit 67
2.4 X-RayScatteringandDiffraction 67
2.4.1 X-RaysandMathematicalRepresentationofWaves 67
2.4.2 InteractionofX-RayswithMatter 70
2.4.3 CrystalLattice,MillerIndices,andtheReciprocalSpace 73
2.4.4 X-RayDiffractionfromaCrystal:Bragg’sLaw 75
2.4.5 Bragg’sLawinReciprocalSpace 77
2.4.6 FourierTransformEquationfromaLattice 79
2.4.7 Friedel’sLawandtheElectronDensityEquation 80
2.5 CollectingandProcessingDiffractionData 82
2.5.1 DataCollectionStrategy 82
2.5.2 SymmetryandScalingData 83
2.6 SolvingtheStructure(DeterminingPhases) 83
2.6.1 MolecularReplacement 83
2.6.2 IsomorphousReplacement 85
2.6.3 MAD 88
2.7 AnalyzingandRefiningtheStructure 90
2.7.1 ElectronDensityInterpretationandModelBuilding 90
2.7.2 ProteinStructureRefinement 91
2.7.3 ProteinStructureValidation 93
References 94
3 NuclearMagneticResonanceofAminoAcids,Peptides,
andProteins 97
AndreaBerniniandPierandreaTemussi
3.1 Introduction 97
3.1.1 ActiveNucleiinNMR 98
3.1.2 EnergyLevelsandSpinStates 98
3.1.3 MainNMRParameters(Glossary) 99
3.1.3.1 ChemicalShift 99
3.1.3.2 ScalarCouplingConstants 100
3.1.3.3 NOE 100
3.1.3.4 RDC 101
Contents VII
3.2 AminoAcids 101
3.2.1 HistoricalSignificance 101
3.2.2 AminoAcidsStructure 101
3.2.3 RandomCoilChemicalShift 102
3.2.4 SpinSystems 105
3.2.5 LabileProtons 110
3.2.6 ContemporaryRelevance:Metabolomics 112
3.3 Peptides 113
3.3.1 HistoricalSignificance 113
3.3.2 OligopeptidesasModelsforConformationalTransitions
inProteins 114
3.3.3 BioactivePeptides 116
3.3.4 ChoiceoftheSolvent 117
3.3.4.1 TransportFluids 118
3.3.4.2 Membranes 120
3.3.4.3 ReceptorCavities 122
3.3.5 EnsembleCalculations 125
3.3.6 SelectedExamplesfromtheMajorFieldsofBioactivePeptides 125
3.3.6.1 Aspartame 125
3.3.6.2 Opioids 126
3.3.6.3 TransmembraneHelices 127
3.3.6.4 Cyclopeptides 128
3.4 Proteins 129
3.4.1 AnAlternativetooraValidationofDiffractometric
Methods? 129
3.4.2 ProteinSpectra 129
3.4.3 Wüthrich’sProtocol 130
3.4.3.1 SamplePreparation 131
3.4.3.2 RecordingNMRSpectra 131
3.4.3.3 SequentialAssignment 131
3.4.3.4 ConformationalConstraints 132
3.4.3.5 ModelBuilding 134
3.4.4 RecentDevelopments 134
3.4.5 SelectedStructures 136
3.4.5.1 SuperoxideDismutases 137
3.4.5.2 MalateSynthaseG 137
3.4.5.3 Interactions 138
3.5 Conclusions 145
References 146
4 StructureandActivityofN-MethylatedPeptides 155
RaymondS.Norton
4.1 Introduction 155
4.2 ConformationalEffectsofN-Methylation 157
4.3 EffectsofN-MethylationonBioactivePeptides 159
VIII Contents
4.3.1 Thyrotropin-ReleasingHormone 159
4.3.2 CyclicPeptides 159
4.3.3 SomatostatinAnalogs 160
4.3.4 AntimalarialPeptide 161
4.4 ConcludingRemarks 162
References 163
5 High-PerformanceLiquidChromatographyofPeptides
andProteins 167
ReinhardI.BoysenandMiltonT.W.Hearn
5.1 Introduction 167
5.2 BasicTermsandConceptsinChromatography 169
5.3 ChemicalStructureofPeptidesandProteins 173
5.3.1 BiophysicalPropertiesofPeptidesandProteins 173
5.3.2 ConformationalPropertiesofPeptidesandProteins 176
5.3.3 OpticalPropertiesofPeptidesandProteins 176
5.4 HPLCSeparationModesinPeptideandProtein
Analysis 177
5.4.1 SEC 178
5.4.2 RPC 179
5.4.3 NPC 181
5.4.4 HILIC 181
5.4.5 ANPC 183
5.4.6 HIC 184
5.4.7 IEX 187
5.4.8 AC 188
5.5 MethodDevelopmentfromAnalyticaltoPreparativeScale
IllustratedforHP-RPC 189
5.5.1 DevelopmentofanAnalyticalMethod 190
5.5.2 ScalingUptoPreparativeChromatography 196
5.5.3 Fractionation 198
5.5.4 AnalysisoftheQualityoftheFractionation 198
5.6 MultidimensionalHPLC 198
5.6.1 PurificationofPeptidesandProteinsbyMD-HPLC
Methods 200
5.6.2 FractionationofComplexPeptideandProteinMixtures
byMD-HPLC 202
5.6.3 OperationalStrategiesforMD-HPLCMethods 202
5.6.3.1 Off-lineCouplingModeforMD-HPLCMethods 202
5.6.3.2 On-LineCouplingModeforMD-HPLCMethods 203
5.6.4 DesignofanEffectiveMD-HPLCScheme 203
5.6.4.1 OrthogonalityofChromatographicModes 203
5.6.4.2 CompatibilityMatrixofChromatographicModes 205
5.7 Conclusions 206
References 207
Contents IX
6 LocalSurfacePlasmonResonanceandElectrochemicalBiosensing
SystemsforAnalyzingFunctionalPeptides 211
MasatoSaitoandEiichiTamiya
6.1 LocalizedSurfacePlasmonResonance(LSPR)-BasedMicrofluidics
BiosensorfortheDetectionofInsulinPeptideHormone 211
6.1.1 LSPRandMicroTotalAnalysisSystems 211
6.1.2 MicrofluidicLSPRChipFabricationandLSPRMeasurement 212
6.1.3 DetectionoftheInsulin–Anti-InsulinAntibodyReaction
onaChip 213
6.2 ElectrochemicalLSPR-BasedLabel-FreeDetectionofMelittin 215
6.2.1 MelittinandE-LSPR 215
6.2.2 FabricationofE-LSPRSubstrateandFormationoftheHybrid
BilayerMembrane 215
6.2.3 MeasurementsofMembrane-BasedSensorsforPeptideToxin 217
6.3 Label-FreeElectrochemicalMonitoringofb-Amyloid(Ab)
PeptideAggregation 218
6.3.1 Alzheimer’sAbAggregationandElectrochemical
DetectionMethod 218
6.3.2 Label-FreeElectrochemicalDetectionofAbAggregation 219
References 221
7 SurfacePlasmonResonanceSpectroscopyintheBiosciences 225
JingYuan,YinqiuWu,andMarie-IsabelAguilar
7.1 Introduction 225
7.2 SPR-BasedOpticalBiosensors 225
7.3 PrincipleofOperationofSPRBiosensors 226
7.4 DescriptionofaSPRInstrument 228
7.4.1 SensorSurface 228
7.4.2 FlowSystem 229
7.4.3 DetectionSystem 230
7.5 ApplicationofSPRinImmunosensorDesign 230
7.5.1 AssayDevelopment 232
7.5.1.1 ImmobilizationoftheAnalytetoaSpecificChipSurface 232
7.5.1.2 AssayDesign 233
7.6 ApplicationofSPRinMembraneInteractions 234
7.6.1 GeneralProtocolsforMembraneInteraction
StudiesbySPR 236
7.6.1.1 LiposomePreparation 236
7.6.1.2 FormationofBilayerSystems 236
7.6.1.3 AnalyteBindingtotheMembraneSystem 237
7.6.1.4 MembraneBindingofAntimicrobialPeptidesbySPR 238
7.7 DataAnalysis 240
7.7.1 LinearizationAnalysis 240
7.7.2 NumericalIntegrationAnalysis 241
7.7.3 Steady-StateApproximations 242
X Contents
7.8 Conclusions 243
References 244
8 AtomicForceMicroscopyofProteins 249
AdamMechler
8.1 Foreword 249
8.1.1 ImportanceofAskingtheRightQuestion 250
8.2 AFM 250
8.2.1 PrincipleandBasicModesofOperation 250
8.2.2 HowDoesaTipTap? 251
8.3 BioimagingHighlights 253
8.3.1 ProteinOligomerization,Aggregation,andFibers 253
8.3.2 MembraneBindingandLysis 255
8.3.3 IonChannelActivity 257
8.3.4 Protein–DNA-SpecificBinding 261
8.4 Issues 261
8.4.1 Resolution 262
8.4.2 ImagingForce 263
8.4.3 RepetitiveStress 264
8.4.4 ArtifactsRelatedtotooLowFreeAmplitude 265
8.4.5 TransientForceandBandwidth 266
8.4.6 AccuracyofSurfaceTracking 266
8.4.7 StepArtifacts 268
8.5 ForceMeasurements 269
8.6 LiquidImaging 269
8.7 SamplePreparationforBioimaging 272
8.7.1 Adhesion 272
8.7.2 PhysicalEntrapment 273
8.7.3 ChemicalBinding 274
8.8 Outlook 274
References 275
9 SolventInteractionswithProteinsandOtherMacromolecules 277
SatoshiOhtake,YoshikoKita,KouheiTsumoto,andTsutomuArakawa
9.1 Introduction 277
9.2 SolventApplications 280
9.2.1 Research 280
9.2.2 Precipitation 287
9.2.3 Chromatography 288
9.2.4 ProteinRefolding 296
9.2.5 Formulation 297
9.3 SolventApplicationforViruses 300
9.3.1 IsolationandPurificationofViruses 301
9.3.2 StabilizationandFormulationofViruses 302
9.3.3 InactivationofViruses 309