NMR of Biomolecules: Towards Mechanistic Systems Biology

630 Pages·2012·19.155 MB·English

Editedby
IvanoBertini,
KathleenS.McGreevy,
andGiacomoParigi
NMRofBiomolecules
Related Titles
Keeler,J.
Understanding NMR Spectroscopy
2010
ISBN:978-0-470-74608-0
de Graaf, R.
In Vivo NMR Spectroscopy
PrinciplesandTechniques
2007
ISBN:978-0-470-02670-0
Edited by
Ivano Bertini,
Kathleen S. McGreevy,
and Giacomo Parigi
NMR of Biomolecules
Towards Mechanistic Systems Biology
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Theartworkonthecoverattemptstoconveytheidea 69469Weinheim,Germany
ofthesystemsofinteractingbiomoleculesthatareat
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j
V
Contents
Preface XXI
ListofContributors XXIII
ListofAbbreviations XXIX
PartOne Introduction 1
1 NMRanditsPlaceinMechanisticSystemsBiology 3
IvanoBertini,KathleenS.McGreevy,andGiacomoParigi
2 StructureofBiomolecules:Fundamentals 7
2.1 StructuralFeaturesofProteins 7
LuciaBanciandFrancescaCantini
2.1.1 Introduction:FromPrimarytoQuaternaryStructure 7
2.1.2 GeometricalandConformationalProperties 8
2.1.2.1 BackboneDihedralAngles 8
2.1.2.2 Side-ChainDihedralAngles 9
2.1.3 SecondaryStructureElementsinProteins 9
2.1.4 PredictionofSecondaryStructure 13
2.1.5 StructuralMotifsandStructuralDomains–CombinationofSecondaryStructuralElementsandStructuralMotifs 13
2.1.6 TypesofFoldsandtheirClassification 15
2.1.6.1 FoldsoftheaClass 15
2.1.6.2 FoldsinthebClass 16
2.1.6.3 Foldsinthea/bClass 17
2.1.6.4 Foldsinthea þ bClass 17
2.1.7 TertiaryStructure 18
2.1.8 QuaternaryStructure 19
2.2 NucleicAcids 21
MirkoCevec,HendrikR.A.Jonker,SenadaNozinovic,ChristianRichter,andHaraldSchwalbe
2.2.1 Introduction 21
2.2.1.1 Conformations 22
2.2.2 DNAStructure 24
2.2.2.1 B-DNAandDerivatives 24
2.2.2.2 A-DNA 25
2.2.2.3 Z-DNA 25
2.2.2.4 NonstandardDNAStructures 25
2.2.2.4.1 CircularDNA 25
2.2.2.4.2 HelicalJunction 26
2.2.2.4.3 TripleHelix 26
2.2.2.4.4 i-Motif 26
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VI Contents
2.2.2.4.5 QuadruplexDNA 26
2.2.3 RNAStructure 27
2.2.3.1 RegularRNAStructure–A-FormHelices 28
2.2.3.2 Mismatches,Bulges,andUnusualBasePairing 29
2.2.3.3 ReversalandAlterationofStrandDirection:Commonly
ObservedLoopandTurnMotifs 29
2.2.3.3.1 U-Turn 29
2.2.3.3.2 K-Turn 29
2.2.3.3.3 C-Loop 29
2.2.3.3.4 E-Loop 30
2.2.3.4 TetraloopsandTetraloop–ReceptorContact 30
2.2.3.5 Higher-OrderRNATertiaryStructureElements:
CoaxialStackingMotifs 31
2.2.3.6 DNA–RNAHybrids 31
3 WhatCanbeLearnedAbouttheStructureandDynamics
ofBiomoleculesfromNMR 33
3.1 ProteinsStudiedbyNMR 33
LucioFerella,AntonioRosato,andPaolaTurano
3.1.1 WhyNMRStructures? 33
3.1.2 NMRBundle 37
3.1.3 ProteinDynamics 41
3.1.4 IntermolecularInteractionsInvolvingProteins 44
3.2 NucleicAcidsStudiedbyNMR 47
JanezPlavec
3.2.1 Structure,Mobility,andFunction 47
PartTwo RoleofNMRintheStudyoftheStructureandDynamics
ofBiomolecules 51
4 DeterminationofProteinStructureandDynamics 53
LucioFerella,AntonioRosato,andPaolaTurano
4.1 DeterminationofProteinStructures 53
4.1.1 ResonanceAssignment 53
4.2 NMRRestraints 58
4.2.1 DistanceRestraints 58
4.2.2 DihedralAngles 59
4.2.3 ResidualDipolarCouplings 61
4.3 StructureCalculations 65
4.3.1 Traditional 65
4.3.2 AutomatedNOESYAssignment 69
4.3.3 EnergyRefinementofProteinStructures 70
4.3.4 ChemicalShift-BasedApproachesforProteinStructureDetermination 71
4.4 ValidationofProteinStructures 72
4.4.1 ExperimentalData 72
4.4.2 GeometricQuality 74
4.5 ProteinDynamicsandNMRObservables 76
4.5.1 NMRObservablesAffectedbyDynamics 76
4.5.2 NMRExperimentstoMeasureDynamicsandtheirInterpretation 78
4.6 Protocols 83
4.6.1 SampleLabeling 83
4.6.2 NMRAssignment 83
4.6.3 ManualCollectionofRestraints 86
4.6.4 StructureCalculations 87
4.6.5 StructureRefinement 89
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Contents VII
4.6.6 ChemicalShift-BasedStructureCalculations 90
4.6.7 StructureValidation 90
4.6.8 ProteinDynamics 91
4.7 Troubleshooting 92
4.7.1 DataCollection 92
4.7.2 StructureCalculations 93
FurtherReading 94
5 DNA 97
JanezPlavec
5.1 NMRSpectroscopyofDNA 97
5.2 AssessmentoftheFoldingTopology 99
5.3 ResonanceAssignmentthroughSequentialandInterstrand
Interactions 100
5.4 PseudorotationofDeoxyribofuranoseRings 104
5.5 BackboneConformation 105
5.6 NaturalAbundanceNucleobaseSubstitutions 106
5.7 NaturalAbundanceHeteronuclearExperiments 106
5.8 Site-SpecificLowIsotopicEnrichment 107
5.9 TranslationalDiffusionCoefficients 107
5.10 DeterminationofThree-DimensionalStructure 107
5.11 SearchforTransientStructures 109
5.12 Protocols 110
5.12.1 SamplePreparationandInitialNMRExperiments 110
5.12.2 StoichiometricAnalysisthroughTranslationalDiffusion 111
5.12.3 SequentialAssignment 111
5.12.4 AssessmentofthePreferredSugarPucker 112
5.12.5 ConformationsalongtheBackbone 112
5.12.6 NucleobaseSubstitutionsandSite-SpecificLow13C/15N
IsotopicEnrichment 112
5.12.7 TopologyandAtomic-DetailThree-DimensionalStructure
Determination 113
5.13 ExampleExperimentsandTroubleshooting 114
FurtherReading 115
6 RNA 119
RichardS(cid:2)teflandVladim(cid:3)ırSklen(cid:3)a(cid:2)r
6.1 NMRSpectroscopyofRNA 119
6.2 PreparationofRNASamplesforNMR 120
6.2.1 InVitroTranscriptionUsingT7RNAPolymerase 120
6.2.2 InVivoRecombinantRNASynthesis 120
6.2.3 ChemicalSynthesis 120
6.2.4 SegmentalLabeling 121
6.3 ProbingoftheRNAFold 121
6.4 AssessmentoftheSpectralResolution 122
6.5 StrategyfortheResonanceAssignment 123
6.5.1 HydrogenBondFormationandBasePairIdentification 123
6.5.2 Through-Bond-TypeExperiments–BaseSpinSystemIdentification 124
6.5.3 Through-Bond-TypeExperiments–SugarSpinSystemIdentification 124
6.5.4 SequentialConnectivities 125
6.6 CollectionofStructuralInformation 126
6.6.1 CollectionofDistance-DependentStructuralRestraints 126
6.6.2 CollectionofTorsion-Angle-DependentStructuralRestraints 127
6.6.3 CollectionofLong-RangeStructuralRestraints 127
6.7 StructuralCalculationofRNA 128
6.8 AssessmentofQualityofNMRStructures 129
6.9 Protocols 129
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VIII Contents
6.9.1 Flowcharts 130
6.9.1.1 SamplePreparation 130
6.9.1.2 CollectionoftheExperimentalData 130
6.9.1.3 StructureCalculation 131
6.9.2 ProtocolforInVitroTranscriptionUsingBacteriophageT7RNA
Polymerase 132
6.9.2.1 TemplateDesign 132
6.9.2.2 TranscriptionProtocol 133
6.9.2.3 PurificationofRNA 134
6.9.2.4 SimpleProtocolforBacteriophageT7RNAPolymerasePreparation 134
6.10 Troubleshooting 135
FurtherReading 135
7 IntrinsicallyDisorderedProteins 137
IsabellaC.Felli,RobertaPierattelli,andPeterTompa
7.1 IntrinsicallyDisorderedProteins 137
7.1.1 WhentheConceptwasFirstIntroduced 137
7.1.2 FunctionsandFunctionalAdvantagesAssociatedwithDisorder 138
7.2 ImportanceofNMRtoStudyIDPs 140
7.3 StructuralandDynamicInformationonIDPs–NMRObservables 141
7.3.1 ReducedChemicalShiftDispersionandSequence-
SpecificAssignment 141
7.3.2 ChemicalShiftsandSecondaryStructuralPropensities 142
7.3.3 AdditionalObservablesandConformationalAveraging 143
7.3.4 ScalarCouplings 143
7.3.5 ResidualDipolarCouplings 143
7.3.6 SolventExposure 144
7.3.7 15NRelaxationandHeteronuclearNOEs 144
7.3.8 ParamagneticRelaxationRateEnhancements 145
7.3.9 Proton–ProtonNOEs 145
7.3.10 RelevanceofStructuralDisorderinInVivoandIn-CellStudiesofIDPs 146
7.4 Protocols 146
7.4.1 UseofBioinformaticToolsandDatabases 146
7.4.2 UseofNMRintheCharacterizationofIDPs 148
7.5 Troubleshooting 150
7.5.1 BioinformaticsCanHelp! 150
7.5.2 UnderstandingtheFunctionofUnfoldedProteinRegions 151
7.5.3 DoesInVitroReflectInVivoBehavior? 152
FurtherReading 152
8 ParamagneticMolecules 155
IvanoBertini,ClaudioLuchinat,andGiacomoParigi
8.1 Paramagnetism-AssistedNMR 155
8.2 ScalarandDipolarElectronSpin–NuclearSpinInteractions:
HyperfineShift 157
8.2.1 ContactContributionstotheHyperfineShift 157
8.2.2 PseudocontactContributionstotheHyperfineShift 158
8.3 ScalarandDipolarElectronSpin–NuclearSpinInteractions:PRE 159
8.4 IndirectElectronSpin–NuclearSpinEffects:
Paramagnetism-InducedRDCs 161
8.5 Cross-CorrelationBetweenCurieandDipolarRelaxation 162
8.6 “Good”MetalIonsand“Bad”MetalIons 163
8.7 Paramagnetism-BasedDrugDiscovery 164
8.8 Protocols 165
8.8.1 CollectingtheParamagnetism-BasedRestraints 165
8.8.2 ProtocolstoExtractStructuralInformationfromthePCS,
PRDC,PREandPCCR 166
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Contents IX
8.8.3 ProtocolsforProtein–ProteinInteractions 167
8.8.4 ProtocolsfortheAnalysisofConformationalFreedom
inTwo-DomainProteins 168
8.8.5 ExampleExperiment 169
8.9 Troubleshooting 169
8.9.1 TipsandTrickstoOptimizeSignalDetectioninParamagneticSystems 169
8.9.2 SelectionoftheParamagneticIon 170
8.9.3 SwitchingBetweenDiamagneticandParamagneticSystems 170
FurtherReading 170
PartThree RoleofNMRintheStudyoftheStructureandDynamics
ofBiomolecularInteractions 173
9 NMRMethodologiesfortheAnalysisofProtein–ProteinInteractions 175
TobiasMadlandMichaelSattler
9.1 Introduction 175
9.2 DynamicsandLigandBinding 176
9.3 GeneralStrategy 177
9.4 OverviewofMethods 178
9.4.1 SamplePreparation 178
9.4.2 StructuresofDomains/Subunits 179
9.4.3 Interfaces 180
9.4.3.1 ChemicalShiftPerturbations(CSPs) 180
9.4.3.2 NOEs 180
9.4.3.3 Cross-Saturation 181
9.4.3.4 DifferentialLine-Broadening 181
9.4.3.5 HydrogenExchange 182
9.4.3.6 SolventPREs 182
9.4.4 Domain/SubunitOrientation 183
9.4.4.1 NMRRelaxationData 183
9.4.4.2 ResidualDipolarCouplings(RDCs) 184
9.4.4.3 ParamagneticRestraints 184
9.4.5 StructureCalculations 185
9.5 Outlook 186
9.6 ProtocolsfortheAnalysisofProteinComplexes 186
9.6.1 SpinLabelingandParamagneticTagging 186
9.6.2 StructuresoftheIndividualDomains/Subunits 188
9.6.3 OptimizingConditionsforStructuralStudiesoftheProteinComplex 189
9.6.4 DetectionofDynamics 189
9.6.5 DeterminingInteractionInterfacesUsingSolventPREs 189
9.6.6 StructureCalculationApproach 191
9.6.7 ExampleExperiment 193
9.7 Troubleshooting 194
FurtherReading 194
10 Metal-MediatedInteractions 197
SimoneCiofi-Baffoni
10.1 TheoreticalBackground 197
10.2 ProtocolfortheStructuralDeterminationofa
Metal-MediatedComplex 200
10.2.1 OptimizationofExperimentalConditionstoObtainthe
Protein–ProteinComplex 200
10.2.2 TitrationstoMapProtein–ProteinInterfacesandObtain
BindingCharacteristics 201
10.2.3 Modeling 201
10.2.4 DefinitionofMetalCoordination 201
10.2.5 DeterminationofThree-DimensionalStructure 202
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X Contents
10.3 ExampleExperiment 202
10.4 Troubleshooting 202
FurtherReading 203
11 Protein–ParamagneticProteinInteractions 205
PeterH.J.Keizers,YoshitakaHiruma,andMarcellusUbbink
11.1 ParamagneticSourcesinProteinComplexes 205
11.2 TypesofNMRRestraintsObtainedfromParamagneticCenters 206
11.3 ProteinComplexes 207
11.3.1 StructuresofProteinComplexes 207
11.3.2 DynamicsinProteinComplexes 208
11.3.2.1 PlastocyaninandCytochromef 209
11.3.2.2 CytochromecandCytochromecPeroxidase 209
11.3.2.3 HistidinePhosphocarrierProteinandEnzymeI 209
11.3.2.4 AdrenodoxinandCytochromec 210
11.3.2.5 CalmodulinDomainDynamics 211
11.4 Protocols 211
11.4.1 ProteinTitrationstoObtaintheK andaBindingMap 211
d
11.4.2 ParamagneticTaggingandUseofParamagnetsinNMR 212
11.4.3 EnsembleModeling 214
11.5 ExampleExperiment 215
11.6 Troubleshooting 215
FurtherReading 217
12 Protein–RNAInteractions 219
VijayalaxmiManoharan,JoseManuelP(cid:3)erez-Can~adillas,andAndresRamos
12.1 Introduction 219
12.1.1 Post-TranscriptionalRegulationandRNARecognition
Domains 219
12.1.2 Protein–RNAInterfaces 219
12.2 NMRMethodology 221
12.2.1 UsingNMRtoInvestigateProtein–RNAInteractions 221
12.2.2 MappingInteractionSites 222
12.2.2.1 ChemicalShiftPerturbation 222
12.2.2.2 Cross-Saturation 223
12.2.2.3 ParamagneticRelaxationEnhancement 224
12.2.3 AffinityandSpecificity 226
12.2.3.1 DeterminingDissociationConstants 226
12.2.3.2 DeterminingStoichiometry 226
12.2.3.3 Scaffold-IndependentAnalysis 227
12.2.4 High-ResolutionStructureDeterminationandDynamics 227
12.3 ProtocolsandTroubleshooting 228
12.3.1 PreparationofProtein–RNAComplexes 228
12.3.1.1 MaterialsandSamplePreparation 229
12.3.1.2 Troubleshooting 229
12.3.2 ProtocolandExampleExperiment1:CalculatingtheAffinityofa
Protein–RNAInteraction 230
12.3.2.1 MaterialsandSamplePreparation 230
12.3.2.2 Troubleshooting 231
12.3.3 ProtocolandExampleExperiment2:ParamagneticLabeling 232
12.3.3.1 MaterialsandSamplePreparation 233
12.3.3.2 Troubleshooting 233
12.3.4 ProtocolandExampleExperiment3:SIA 234
12.3.4.1 MaterialsandSamplePreparation 234
12.3.4.2 Troubleshooting 235
FurtherReading 235