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Amino Acids, Peptides and Proteins in Organic Chemistry. V.5. Analysis and Function of Amino Acids and Peptides PDF

510 Pages·2016·9.29 MB·English
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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 TheEditor AllbookspublishedbyWiley-VCHarecarefully produced.Nevertheless,authors,editors,and AndrewB.Hughes publisherdonotwarranttheinformationcontained LaTrobeUniversity inthesebooks,includingthisbook,tobefreeof DepartmentofChemistry errors.Readersareadvisedtokeepinmindthat Victoria3086 statements,data,illustrations,proceduraldetailsor Australia otheritemsmayinadvertentlybeinaccurate. LibraryofCongressCardNo.: appliedfor BritishLibraryCataloguing-in-PublicationData Acataloguerecordforthisbookisavailablefromthe BritishLibrary. Bibliographicinformationpublishedby theDeutscheNationalbibliothek TheDeutscheNationalbibliothekliststhis publicationintheDeutscheNationalbibliografie; detailedbibliographicdataareavailableonthe Internetathttp://dnb.d-nb.de. #2012Wiley-VCHVerlag&Co.KGaA, Boschstr.12,69469Weinheim,Germany Allrightsreserved(includingthoseoftranslationinto otherlanguages).Nopartofthisbookmaybe reproducedinanyform–byphotoprinting, microfilm,oranyothermeans–nortransmittedor translatedintoamachinelanguagewithoutwritten permissionfromthepublishers.Registerednames, trademarks,etc.usedinthisbook,evenwhennot specificallymarkedassuch,arenottobeconsidered unprotectedbylaw. Composition ThomsonDigital,Noida,India PrintingandBinding betz-druckGmbH,Darmstadt CoverDesign SchulzGrafikDesign,Fußgönheim PrintedintheFederalRepublicofGermany Printedonacid-freepaper PrintISBN:978-3-527-32104-9 ePDFISBN:978-3-527-63185-8 oBookISBN:978-3-527-63184-1 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

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