NMR of biomolecules towards mechanistic systems biology
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| 245 | 1 | 0 | |a NMR of biomolecules |b towards mechanistic systems biology |c ed. by Ivano Bertini ... |
| 264 | 1 | |a Weinheim |b Wiley-Blackwell |c 2012 | |
| 300 | |a XXXVIII, 612 S. |b Ill., graph. Darst. | ||
| 336 | |b txt |2 rdacontent | ||
| 337 | |b n |2 rdamedia | ||
| 338 | |b nc |2 rdacarrier | ||
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IMAGE 1
CONTENTS
PREFACE X X I
LIST O F CONTRIBUTORS X X I I I
LIST O F ABBREVIATIONS X X I X
PART ONE INTRODUCTION 1
1 NMR AND ITS PLACE IN MECHANISTIC SYSTEMS BIOLOGY 3
IVANO BERTINI, KATHLEEN S. MCCREEVY, AND GIACOMO PARIGI
2 STRUCTURE O F BIOMOLECULES: FUNDAMENTALS 7
2.1 STRUCTURAL FEATURES O F PROTEINS 7
LUCIA BAND AND FRANCESCO CANTINI 2.1.1 INTRODUCTION: FROM PRIMARY TO
QUATERNARY STRUCTURE 7 2.1.2 GEOMETRICAL AND CONFORMATIONAL PROPERTIES 8
2.1.2.1 BACKBONE DIHEDRAL ANGLES 8
2.1.2.2 SIDE-CHAIN DIHEDRAL ANGLES 9 2.1.3 SECONDARY STRUCTURE ELEMENTS
I N PROTEINS 9 2.1.4 PREDICTION O F SECONDARY STRUCTURE 13
2.1.5 STRUCTURAL MOTIFS AND STRUCTURAL DOMAINS - COMBINATION O F
SECONDARY STRUCTURAL ELEMENTS AND STRUCTURAL MOTIFS 2.1.6 TYPES O F
FOLDS AND THEIR CLASSIFICATION 15 2.1.6.1 FOLDS O F THE A CLASS 15
2.1.6.2 FOLDS IN THE |3 CLASS 16
2.1.6.3 FOLDS IN THE A/|3 CLASS 17
2.1.6.4 FOLDS IN THE A + ( 3 CLASS 17
2.1.7 TERTIARY STRUCTURE 18
2.1.8 QUATERNARY STRUCTURE 19
2.2 NUCLEIC ACIDS 21
MIRKO CEVEC, HENDRIK R.A. JONKER, SENADA NOZINOVIC, CHRISTIAN RICHTER,
AND HARALD SCHWALBE 2.2.1 INTRODUCTION 21
2.2.1.1 CONFORMATIONS 22
2.2.2 DNA STRUCTURE 24
2.2.2.1 B-DNA AND DERIVATIVES 24 2.2.2.2 A-DNA 25
2.2.2.3 Z-DNA 25
2.2.2.4 NONSTANDARD DNA STRUCTURES 25 2.2.2.4.1 CIRCULAR DNA 25
2.2.2.4.2 HELICAL JUNCTION 26 2.2.2.4.3 TRIPLE HELIX 26
2.2.2.4.4 I-MOTIF 26
HTTP://D-NB.INFO/1013615476
IMAGE 2
V I CONTENTS
2.2.2.4.5 QUADRUPLEX DNA 26
2.2.3 RNA STRUCTURE 2 7
2.2.3.1 REGULAR RNA STRUCTURE - A-FORM HELICES 28 2.2.3.2 MISMATCHES,
BULGES, AND UNUSUAL BASE PAIRING 29 2.2.3.3 REVERSAL AND ALTERATION O F
STRAND DIRECTION: COMMONLY OBSERVED LOOP AND TURN MOTIFS 29 2.2.3.3.1
U-TURN 29
2.2.3.3.2 K-TURN 29 2.2.3.3.3 C-LOOP 2 9 2.2.3.3.4 E-LOOP 30 2.2.3.4
TETRALOOPS AND TETRALOOP-RECEPTOR CONTACT 30 2.2.3.5 HIGHER-ORDER RNA
TERTIARY STRUCTURE ELEMENTS:
COAXIAL STACKING MOTIFS 31 2.2.3.6 DNA-RNA HYBRIDS 31
3 WHAT CAN BE LEARNED ABOUT THE STRUCTURE AND DYNAMICS
O F BIOMOLECULES FROM NMR 33
3.1 PROTEINS STUDIED BY NMR 33
LUCIO FERELLA, ANTONIO ROSATO, AND PAOLA TURANO 3.1.1 WHY NMR
STRUCTURES? 33
3.1.2 NMR BUNDLE 37
3.1.3 PROTEIN DYNAMICS 41
3.1.4 INTERMOLECULAR INTERACTIONS INVOLVING PROTEINS 44
3.2 NUCLEIC ACIDS STUDIED BY NMR 47
JANEZ PLAVEC
3.2.1 STRUCTURE, MOBILITY, AND FUNCTION 47
PART TWO ROLE O F NMR IN THE STUDY O F THE STRUCTURE AND DYNAMICS O F
BIOMOLECULES 51
4 DETERMINATION O F PROTEIN STRUCTURE AND DYNAMICS 53
LUCIO FERELLA, ANTONIO ROSATO, AND PAOLA TURANO 4.1 DETERMINATION O F
PROTEIN STRUCTURES 53
4.1.1 RESONANCE ASSIGNMENT 53
4.2 NMR RESTRAINTS 58
4.2.1 DISTANCE RESTRAINTS 58
4.2.2 DIHEDRAL ANGLES 59
4.2.3 RESIDUAL DIPOLAR COUPLINGS 61
4.3 STRUCTURE CALCULATIONS 65
4.3.1 TRADITIONAL 65
4.3.2 AUTOMATED NOESY ASSIGNMENT 69 4.3.3 ENERGY REFINEMENT O F PROTEIN
STRUCTURES 70 4.3.4 CHEMICAL SHIFT-BASED APPROACHES FOR PROTEIN
STRUCTURE DETERMINATION 71 4.4 VALIDATION O F PROTEIN STRUCTURES 72
4.4.1 EXPERIMENTAL DATA 72
4.4.2 GEOMETRIC QUALITY 74
4.5 PROTEIN DYNAMICS AND NMR OBSERVABLES 76
4.5.1 NMR OBSERVABLES AFFECTED BY DYNAMICS 76 4.5.2 NMR EXPERIMENTS TO
MEASURE DYNAMICS AND THEIR INTERPRETATION 78 4.6 PROTOCOLS 83
4.6.1 SAMPLE LABELING 83
4.6.2 NMR ASSIGNMENT 83
4.6.3 MANUAL COLLECTION O F RESTRAINTS 86
4.6.4 STRUCTURE CALCULATIONS 87
4.6.5 STRUCTURE REFINEMENT 89
IMAGE 3
CONTENTS | VII
4.6.6 CHEMICAL SHIFT-BASED STRUCTURE CALCULATIONS 90
4.6.7 STRUCTURE VALIDATION 90 4.6.8 PROTEIN DYNAMICS 91
4.7 TROUBLESHOOTING 92
4.7.1 DATA COLLECTION 92
4.7.2 STRUCTURE CALCULATIONS 93 FURTHER READING 94
5 DNA 97
JANEZ PIAVEC
5.1 NMR SPECTROSCOPY O F DNA 97
5.2 ASSESSMENT O F THE FOLDING TOPOLOGY 99 5.3 RESONANCE ASSIGNMENT
THROUGH SEQUENTIAL AND INTERSTRAND INTERACTIONS 100 5.4 PSEUDOROTATION O
F DEOXYRIBOFURANOSE RINGS 104
5.5 BACKBONE CONFORMATION 105
5.6 NATURAL ABUNDANCE NUCLEOBASE SUBSTITUTIONS 106 5.7 NATURAL ABUNDANCE
HETERONUCLEAR EXPERIMENTS 106 5.8 SITE-SPECIFIC LOW ISOTOPIC ENRICHMENT
107 5.9 TRANSLATIONAL DIFFUSION COEFFICIENTS 107
5.10 DETERMINATION O F THREE-DIMENSIONAL STRUCTURE 107 5.11 SEARCH FOR
TRANSIENT STRUCTURES 109 5.12 PROTOCOLS 110
5.12.1 SAMPLE PREPARATION AND INITIAL NMR EXPERIMENTS 110 5.12.2
STOICHIOMETRIC ANALYSIS THROUGH TRANSLATIONAL DIFFUSION 111 5.12.3
SEQUENTIAL ASSIGNMENT 111 5.12.4 ASSESSMENT O F THE PREFERRED SUGAR
PUCKER 112
5.12.5 CONFORMATIONS ALONG THE BACKBONE 112 5.12.6 NUCLEOBASE
SUBSTITUTIONS AND SITE-SPECIFIC LOW 13C/15N ISOTOPIC ENRICHMENT 112
5.12.7 TOPOLOGY AND ATOMIC-DETAIL THREE-DIMENSIONAL STRUCTURE
DETERMINATION 113 5.13 EXAMPLE EXPERIMENTS AND TROUBLESHOOTING 114
FURTHER READING 115
6 RNA 119
RICHARD STEFL AND VLADIMIR SKIENAR 6.1 NMR SPECTROSCOPY O F RNA 119 6.2
PREPARATION O F RNA SAMPLES FOR NMR 120 6.2.1 IN VITRO TRANSCRIPTION
USING T7 RNA POLYMERASE 120
6.2.2 IN VIVO RECOMBINANT RNA SYNTHESIS 120 6.2.3 CHEMICAL SYNTHESIS 120
6.2.4 SEGMENTAL LABELING 121 6.3 PROBING O F THE RNA FOLD 121
6.4 ASSESSMENT O F THE SPECTRAL RESOLUTION 122 6.5 STRATEGY FOR THE
RESONANCE ASSIGNMENT 123 6.5.1 HYDROGEN BOND FORMATION AND BASE PAIR
IDENTIFICATION 123 6.5.2 THROUGH-BOND-TYPE EXPERIMENTS - BASE SPIN
SYSTEM IDENTIFICATION 124
6.5.3 THROUGH-BOND-TYPE EXPERIMENTS - SUGAR SPIN SYSTEM IDENTIFICATION
124 6.5.4 SEQUENTIAL CONNECTIVITIES 125 6.6 COLLECTION OF STRUCTURAL
INFORMATION 126
6.6.1 COLLECTION O F DISTANCE-DEPENDENT STRUCTURAL RESTRAINTS 126 6.6.2
COLLECTION OF TORSION-ANGLE-DEPENDENT STRUCTURAL RESTRAINTS 127 6.6.3
COLLECTION O F LONG-RANGE STRUCTURAL RESTRAINTS 127 6.7 STRUCTURAL
CALCULATION O F RNA 128
6.8 ASSESSMENT O F QUALITY O F NMR STRUCTURES 129 6.9 PROTOCOLS 129
IMAGE 4
VIII CONTENTS
6.9.1 FLOWCHARTS 130
6.9.1.1 SAMPLE PREPARATION 130 6.9.1.2 COLLECTION O F THE EXPERIMENTAL
DATA 130 6.9.1.3 STRUCTURE CALCULATION 131 6.9.2 PROTOCOL FOR IN VITRO
TRANSCRIPTION USING BACTERIOPHAGE T7 RNA
POLYMERASE 132
6.9.2.1 TEMPLATE DESIGN 132 6.9.2.2 TRANSCRIPTION PROTOCOL 133 6.9.2.3
PURIFICATION O F RNA 134 6.9.2.4 SIMPLE PROTOCOL FOR BACTERIOPHAGE T7
RNA POLYMERASE PREPARATION 134 6.10 TROUBLESHOOTING 135
FURTHER READING 135
7 INTRINSICALLY DISORDERED PROTEINS 137
ISABELLA C. FELLI, ROBERTA PIERATTELLI, AND PETER TOMPA 7.1
INTRINSICALLY DISORDERED PROTEINS 137
7.1.1 W H E N THE CONCEPT WAS FIRST INTRODUCED 137 7.1.2 FUNCTIONS AND
FUNCTIONAL ADVANTAGES ASSOCIATED WITH DISORDER 138 7.2 IMPORTANCE O F
NMR TO STUDY IDPS 140
7.3 STRUCTURAL AND DYNAMIC INFORMATION ON IDPS - NMR OBSERVABLES 141
7.3.1 REDUCED CHEMICAL SHIFT DISPERSION AND SEQUENCESPECIFIC ASSIGNMENT
141 7.3.2 CHEMICAL SHIFTS AND SECONDARY STRUCTURAL PROPENSITIES 142
7.3.3 ADDITIONAL OBSERVABLES AND CONFORMATIONAL AVERAGING 143 7.3.4
SCALAR COUPLINGS 143
7.3.5 RESIDUAL DIPOLAR COUPLINGS 143 7.3.6 SOLVENT EXPOSURE 144
7.3.7 1 N RELAXATION AND HETERONUCLEAR NOES 144 7.3.8 PARAMAGNETIC
RELAXATION RATE ENHANCEMENTS 145 7.3.9 PROTON-PROTON NOES 145
7.3.10 RELEVANCE O F STRUCTURAL DISORDER IN IN VIVO AND IN-CELL STUDIES
O F IDPS 146 7.4 PROTOCOLS 146
7.4.1 USE O F BIOINFORMATIC TOOLS AND DATABASES 146 7.4.2 USE O F NMR IN
THE CHARACTERIZATION O F IDPS 148 7.5 TROUBLESHOOTING 150
7.5.1 BIOINFORMATICS CAN HELP! 150 7.5.2 UNDERSTANDING THE FUNCTION O F
UNFOLDED PROTEIN REGIONS 151 7.5.3 DOES IN VITRO REFLECT IN VIVO
BEHAVIOR? 152 FURTHER READING 152
8 PARAMAGNETIC MOLECULES 155
IVANO BERTINI, CLAUDIO LUCHINAT, AND CIACOMO PARIGI 8.1
PARAMAGNETISM-ASSISTED NMR 155 8.2 SCALAR AND DIPOLAR ELECTRON
SPIN-NUCLEAR SPIN INTERACTIONS: HYPERFINE SHIFT 157 8.2.1 CONTACT
CONTRIBUTIONS TO THE HYPERFINE SHIFT 157
8.2.2 PSEUDOCONTACT CONTRIBUTIONS TO THE HYPERFINE SHIFT 158 8.3 SCALAR
AND DIPOLAR ELECTRON SPIN-NUCLEAR SPIN INTERACTIONS: PRE 159 8.4
INDIRECT ELECTRON SPIN-NUCLEAR SPIN EFFECTS: PARAMAGNETISM-INDUCED RDCS
161
8.5 CROSS-CORRELATION BETWEEN CURIE AND DIPOLAR RELAXATION 162 8.6
"GOOD" METAL IONS AND "BAD" METAL IONS 163
8.7 PARAMAGNETISM-BASED DRUG DISCOVERY 164 8.8 PROTOCOLS 165
8.8.1 COLLECTING THE PARAMAGNETISM-BASED RESTRAINTS 165 8.8.2 PROTOCOLS
TO EXTRACT STRUCTURAL INFORMATION FROM THE PCS, PRDC, PRE AND PCCR 166
IMAGE 5
CONTENTS IX
8.8.3 PROTOCOLS FOR PROTEIN-PROTEIN INTERACTIONS 167
8.8.4 PROTOCOLS FOR THE ANALYSIS O F CONFORMATIONAL FREEDOM IN
TWO-DOMAIN PROTEINS 168 8.8.5 EXAMPLE EXPERIMENT 169 8.9 TROUBLESHOOTING
169
8.9.1 TIPS AND TRICKS TO OPTIMIZE SIGNAL DETECTION IN PARAMAGNETIC
SYSTEMS 169 8.9.2 SELECTION O F THE PARAMAGNETIC ION 170 8.9.3 SWITCHING
BETWEEN DIAMAGNETIC AND PARAMAGNETIC SYSTEMS 170 FURTHER READING 170
PART THREE ROLE O F NMR IN THE STUDY O F THE STRUCTURE AND DYNAMICS O F
BIOMOLECULAR INTERACTIONS 173
9 NMR METHODOLOGIES FOR THE ANALYSIS O F PROTEIN-PROTEIN INTERACTIONS
175 TOBIAS MADL AND MICHAEL SATTLER 9.1 INTRODUCTION 175
9.2 DYNAMICS AND LIGAND BINDING 176
9.3 GENERAL STRATEGY 177
9.4 OVERVIEW O F METHODS 178
9.4.1 SAMPLE PREPARATION 178 9.4.2 STRUCTURES O F DOMAINS/SUBUNITS 179
9.4.3 INTERFACES 180
9.4.3.1 CHEMICAL SHIFT PERTURBATIONS (CSPS) 180 9.4.3.2 NOES 180 9.4.3.3
CROSS-SATURATION 181 9.4.3.4 DIFFERENTIAL LINE-BROADENING 181
9.4.3.5 HYDROGEN EXCHANGE 182 9.4.3.6 SOLVENT PRES 182 9.4.4
DOMAIN/SUBUNIT ORIENTATION 183 9.4.4.1 NMR RELAXATION DATA 183
9.4.4.2 RESIDUAL DIPOLAR COUPLINGS (RDCS) 184 9.4.4.3 PARAMAGNETIC
RESTRAINTS 184 9.4.5 STRUCTURE CALCULATIONS 185 9.5 OUTLOOK 186
9.6 PROTOCOLS FOR THE ANALYSIS O F PROTEIN COMPLEXES 186 9.6.1 SPIN
LABELING AND PARAMAGNETIC TAGGING 186 9.6.2 STRUCTURES O F THE
INDIVIDUAL DOMAINS/SUBUNITS 188 9.6.3 OPTIMIZING CONDITIONS FOR
STRUCTURAL STUDIES O F THE PROTEIN COMPLEX 189
9.6.4 DETECTION O F DYNAMICS 189 9.6.5 DETERMINING INTERACTION
INTERFACES USING SOLVENT PRES 189 9.6.6 STRUCTURE CALCULATION APPROACH
191 9.6.7 EXAMPLE EXPERIMENT 193
9.7 TROUBLESHOOTING 194
FURTHER READING 194
10 METAL-MEDIATED INTERACTIONS 197 SIMONE CIOFI-BAFFONI 10.1 THEORETICAL
BACKGROUND 197 10.2 PROTOCOL FOR THE STRUCTURAL DETERMINATION O F A
METAL-MEDIATED COMPLEX 200 10.2.1 OPTIMIZATION O F EXPERIMENTAL
CONDITIONS TO OBTAIN THE PROTEIN-PROTEIN COMPLEX 200 10.2.2 TITRATIONS
TO MAP PROTEIN-PROTEIN INTERFACES AND OBTAIN
BINDING CHARACTERISTICS 201 10.2.3 MODELING 201 10.2.4 DEFINITION O F
METAL COORDINATION 201 10.2.5 DETERMINATION O F THREE-DIMENSIONAL
STRUCTURE 202
IMAGE 6
10.3 EXAMPLE EXPERIMENT 202
10.4 TROUBLESHOOTING 202
FURTHER READING 203
11 PROTEIN-PARAMAGNETIC PROTEIN INTERACTIONS 205 PETER H.J. KEIZERS,
YOSHITAKA HIRUMA, A N D MARCELLUS UBBINK 11.1 PARAMAGNETIC SOURCES IN
PROTEIN COMPLEXES 205 11.2 TYPES O F NMR RESTRAINTS OBTAINED FROM
PARAMAGNETIC CENTERS 206 11.3 PROTEIN COMPLEXES 207
11.3.1 STRUCTURES O F PROTEIN COMPLEXES 207 11.3.2 DYNAMICS IN PROTEIN
COMPLEXES 208 11.3.2.1 PLASTOCYANIN AND CYTOCHROME / 209 11.3.2.2
CYTOCHROME C A N D CYTOCHROME C PEROXIDASE 209 11.3.2.3 HISTIDINE
PHOSPHOCARRIER PROTEIN AND ENZYME I 209
11.3.2.4 ADRENODOXIN AND CYTOCHROME C 210 11.3.2.5 CALMODULIN DOMAIN
DYNAMICS 211 11.4 PROTOCOLS 211
11.4.1 PROTEIN TITRATIONS TO OBTAIN THE KJ AND A BINDING MAP 211 11.4.2
PARAMAGNETIC TAGGING AND USE O F PARAMAGNETS I N NMR 212 11.4.3 ENSEMBLE
MODELING 214 11.5 EXAMPLE EXPERIMENT 215
11.6 TROUBLESHOOTING 215
FURTHER READING 217
12 PROTEIN-RNA INTERACTIONS 219
VIJAYALAXMI MANOHARAN, JOSE MANUEL PEREZ-CANADILLAS, AND ANDRES RAMOS
12.1 INTRODUCTION 219
12.1.1 POST-TRANSCRIPTIONAL REGULATION AND RNA RECOGNITION DOMAINS 219
12.1.2 PROTEIN-RNA INTERFACES 219 12.2 NMR METHODOLOGY 221
12.2.1 USING NMR TO INVESTIGATE PROTEIN-RNA INTERACTIONS 221 12.2.2
MAPPING INTERACTION SITES 222 12.2.2.1 CHEMICAL SHIFT PERTURBATION 222
12.2.2.2 CROSS-SATURATION 223 12.2.2.3 PARAMAGNETIC RELAXATION
ENHANCEMENT 224 12.2.3 AFFINITY AND SPECIFICITY 226
12.2.3.1 DETERMINING DISSOCIATION CONSTANTS 226 12.2.3.2 DETERMINING
STOICHIOMETRY 226 12.2.3.3 SCAFFOLD-INDEPENDENT ANALYSIS 2 2 7 12.2.4
HIGH-RESOLUTION STRUCTURE DETERMINATION AND DYNAMICS 2 2 7 12.3
PROTOCOLS AND TROUBLESHOOTING 228
12.3.1 PREPARATION O F PROTEIN-RNA COMPLEXES 228 12.3.1.1 MATERIALS AND
SAMPLE PREPARATION 229 12.3.1.2 TROUBLESHOOTING 229 12.3.2 PROTOCOL AND
EXAMPLE EXPERIMENT 1: CALCULATING THE AFFINITY O F A
PROTEIN-RNA INTERACTION 230 12.3.2.1 MATERIALS AND SAMPLE PREPARATION
230 12.3.2.2 TROUBLESHOOTING 231 12.3.3 PROTOCOL AND EXAMPLE EXPERIMENT
2: PARAMAGNETIC LABELING 232 12.3.3.1 MATERIALS AND SAMPLE PREPARATION
233 T
12.3.3.2 TROUBLESHOOTING 233
12.3.4 PROTOCOL AND EXAMPLE EXPERIMENT 3: SIA 234 12.3.4.1 MATERIALS AND
SAMPLE PREPARATION 234 12.3.4.2 TROUBLESHOOTING 235 FURTHER READING 235
IMAGE 7
CONTENTS | X I
13 PROTEIN-DNA INTERACTIONS 239
LIDIJA KOVACIC AND ROLF BOELENS 13.1 STATE O F THE ART 239
13.2 CONCLUSIONS AND PERSPECTIVES 242 13.3 PROTOCOLS 243
13.3.1 SAMPLE PREPARATION 243 13.3.2 NMR METHODOLOGY 244 13.3.3
IDENTIFICATION O F THE INTERACTION SURFACES 247 13.3.4 STRUCTURE
CALCULATIONS 250
13.4 TROUBLESHOOTING 251
FURTHER READING 252
PART FOUR NMR IN DRUG DISCOVERY 253
14 HIGH-THROUGHPUT SCREENING AND FRAGMENT-BASED DESIGN: GENERAL
CONSIDERATIONS FOR LEAD DISCOVERY AND OPTIMIZATION 255 MAURIZIO
PELLECCHIA 14.1 HIGH-THROUGHPUT SCREENING AND FRAGMENT-BASED DESIGN 255
14.2 GENERAL ASPECTS O F NMR SPECTROSCOPY I N HIT IDENTIFICATION AND
OPTIMIZATION PROCESSES 257 14.3 CHEMICAL SHIFT PERTURBATION AS A
SCREENING METHOD 261 FURTHER READING 263
15 LIGAND-OBSERVED NMR IN FRAGMENT-BASED APPROACHES 265 PAWEI SLEDZ,
CHRIS ABELL, AND ALESSIO CIULLI 15.1 LIGAND-OBSERVED NMR SPECTROSCOPY
265 15.2 ON THE TRANSIENT BINDING O F SMALL MOLECULES TO THE PROTEIN 266
15.3 QUESTIONS ASKED BY LIGAND-BASED FRAGMENT SCREENING 267 15.3.1
DIRECT YES/NO BINDING EXPERIMENTS 268
15.3.1.1 STD 269 15.3.1.2 WATERLOGSY 270 15.3.1.3 RELAXATION-EDITED
ONE-DIMENSIONAL EXPERIMENTS 271 15.3.2 AFFINITY MEASUREMENTS AND
AFFINITY-ORIENTED SCREENING 271 15.3.3 INFORMATION O N THE BINDING MODE
272
15.4 SUMMARY 274
15.5 PROTOCOLS 274
15.5.1 GENERAL ASPECTS O F SAMPLE PREPARATION 274 15.5.2 PREPARING
SAMPLES 275 15.5.3 PULSE SEQUENCES 276 15.5.4 AUTOMATION 276
15.6 EXAMPLE EXPERIMENTS 276
15.6.1 ONE-DIMENSIONAL DIRECT BINDING EXPERIMENTS 276 15.6.2 COMPETITION
NMR SCREENING EXPERIMENTS 277 15.6.3 TWO-DIMENSIONAL ILOE BINDING
EXPERIMENTS 278 15.7 TROUBLESHOOTING 278
15.7.1 SAMPLE PREPARATION 278 15.7.2 EXPERIMENTAL SETUP 280 FURTHER
READINGS 280
16 INTERACTIONS O F METALLODRUGS WITH DNA 283 HONG-KE LIU AND PETER J.
SADLER 16.1 METALLODRUGS AND DNA INTERACTIONS 283 16.1.1 METALLODRUGS
283
16.1.2 GENERAL FEATURES O F METALLODRUG-DNA INTERACTIONS 284 16.1.3 NMR
TECHNIQUES AND METALLODRUG-DNA INTERACTIONS 285 16.2 COORDINATIVE
BINDING 286
16.3 GROOVE BINDING 289
IMAGE 8
XII CONTENTS
16.3.1 MAJOR GROOVE BINDING 289
16.3.2 MINOR GROOVE BINDING 289 16.4 INTERCALATION AND INSERTION 290
16.4.1 METALLO-INTERCALATORS 290 16.4.2 DNA INSERTION AND
METALLO-INSERTERS 291 16.5 DUAL BINDING (COORDINATION AND INTERCALATION)
291 16.5.1 INTERCALATION BY METALLODRUG WITH A-BONDED INTERCALATOR 291
16.5.2 INTERCALATION BY METALLODRUG WITH JI-BONDED INTERCALATOR 292
16.6 PROTOCOLS 293
16.6.1 DETERMINATION O F THE COORDINATIVE BINDING SITES 293 16.6.2
DETECTION O F INTERCALATION AND INSERTION 294 16.6.3 DETECTION O F
METALLODRUG-DNA GROOVE-BINDING INTERACTIONS 294
16.6.4 EXAMPLE EXPERIMENT 294 16.7 TRICKS AND TROUBLESHOOTING 294
FURTHER READING 295
17 RNA AS A DRUG TARGET 299
JAN-PETER FERNER, ELKE DUCHARDT FERNER, JORG RINNENTHAL, JANINA BUCK,
JENS WOHNERT, AND HARALD SCHWALBE 17.1 RNA AS A TARGET FOR SMALL
MOLECULES 299
17.2 CHEMICAL SHIFT PERTURBATION AND PARAMAGNETIC RELAXATION ENHANCEMENT
301 17.3 NUCLEAR OVERHAUSER EFFECT-BASED METHODS 304 17.4 FLUORINE
LABELING O F RNA 304
17.5 LIGAND-BASED METHODS 305
17.6 PROTOCOLS 306
17.6.1 DETERMINATION O F THE COOPERATIVITY BETWEEN MG 2 + BINDING SITES
IN RNA BY CSP ANALYSIS 306 17.6.2 LIGAND-BINDING SITE MAPPING BY CSP
TRACKING 308 17.6.3 MAPPING MG2 + - B I N D I N G SITES IN RNA USING
MNCL 2
PRE EXPERIMENTS 308
17.6.4 LIGAND-BINDING SITE MAPPING BY NOE METHODS 308 17.6.5 MAPPING
OUTER SPHERE MG 2 + - B I N D I N G SITES BY CO (NH 3) 3 + 6 N O E S Y
EXPERIMENTS 311 17.7 TROUBLESHOOTING 312
FURTHER READING 313
18 FLUORINE NMR SPECTROSCOPY FOR BIOCHEMICAL SCREENING IN DRUG DISCOVERY
315 CLAUDIO DALVIT 18.1 ENZYMATIC INHIBITION MECHANISMS 316 18.2 II-EABS
317
18.2.1 ONE SUBSTRATE AND ONE ENZYME 318 18.2.2 ONE SUBSTRATE A N D ONE
ENZYME I N THE PRESENCE O F SERUM ALBUMIN AND/ OR ENZYMES O F THE
CYTOCHROME P450 SUPERFAMILY 318 18.2.3 ONE SUBSTRATE WITH MULTIPLE
ENZYMES 319 18.2.4 MULTIPLE SUBSTRATES WITH ONE ENZYME 320 18.2.5
MULTIPLE SUBSTRATES WITH MULTIPLE ENZYMES 320 18.2.6 APPLICATION TO
FUNCTIONAL GENOMICS 321
18.3 COMPARISON O F N-FABS WITH OTHER BIOPHYSICAL TECHNIQUES 322 18.4
OUTLOOK 323
18.5 PROTOCOLS 323
18.5.1 PROTOCOL FOR SETUP O F THE N-FABS ASSAY 323 18.5.2 PROTOCOL FOR A
SCREENING RUN WITH RZ-FABS 324 18.5.3 PROTOCOL FOR MEASURING THE IC 50 O
F IDENTIFIED INHIBITORS 325
18.5.4 EXAMPLE EXPERIMENT 326
IMAGE 9
CONTENTS XIII
18.6 TROUBLESHOOTING 326
FURTHER READING 327
19 N MR O F PEPTIDES 329
JOHANNES C. BECK, ANDREAS O. FRANK, AND HORST KESSLER 19.1 INTRODUCTION
329
19.2 RESONANCE ASSIGNMENT 330
19.3 STEREOSTRUCTURE AND CONFORMATIONAL RESTRAINTS 330 19.3.1 NOES AND
ROES 331
19.3.2 3 / COUPLING CONSTANTS 332 19.3.3 RESIDUAL DIPOLAR COUPLINGS 332
19.4 STRUCTURE CALCULATION 333
19.5 IMPORTANCE O F PEPTIDE CONFORMATIONS FOR BIOLOGICAL ACTIVITY 334
19.6 PROTOCOLS 334
19.6.1 RESONANCE ASSIGNMENT 334 19.6.2 ROESY: EXTRACTION O F ACCURATE
DISTANCES 336 19.6.3 3 / COUPLINGS: USE IN STRUCTURE DETERMINATION AND
USEFUL EXPERIMENTS 337 19.6.4 MODELING O F THE STRUCTURE 339
19.6.4.1 DISTANCE GEOMETRY 340 19.6.4.2 MD 340 19.7 TROUBLESHOOTING 342
FURTHER READING 343
PART FIVE SOLID-STATE NMR 345
20 BIOMOLECULAR SOLID-STATE NMR/BASICS 347 EMELINE BARBET-MASSIN AND
CUIDO PINTACUDA 20.1 INTRODUCTION 347
20.2 NMR HAMILTONIAN 347
20.3 MAGIC ANGLE SPINNING 349
20.4 CROSS-POLARIZATION 350
20.5 HETERONUCLEAR 1 H DECOUPLING 350
20.6 DIPOLAR RECOUPLING 351
20.7 RECENT PROGRESS: NEW PROBES - ULTRAFAST MAS - HIGH MAGNETIC FIELDS
354 20.8 PROTOCOLS 355
20.8.1 HARDWARE SETUP 355 20.8.2 MAGIC ANGLE SETTING 356 20.8.3
ADAMANTANE 356 20.8.3.1 MAS SPINNING 356
20.8.3.2 CALIBRATE THE 1 H CHANNEL 357 20.8.4 CALIBRATE THE 13C CHANNEL
357 20.8.4.1 REFERENCE THE SPECTRA 358 20.8.5 CROSS-POLARIZATION 358
20.8.5.1 SET THE SPINNING 358 20.8.5.2 CALIBRATE THE 1 H CHANNEL 358
20.8.5.3 SETUP A CROSS-POLARIZATION EXPERIMENT 358 20.8.5.4 CALIBRATE
THE 13C/15N FIELDS 360
20.8.6 HETERONUCLEAR DECOUPLING SEQUENCES 360 20.8.7 DCP 360
20.8.8 RECOUPLING SEQUENCES 361 20.8.9 EXAMPLE O F AN EXPERIMENT 362
20.9 TROUBLESHOOTING 362 20.9.1 TIPS TO OPTIMIZE SIGNAL ACQUISITION AND
SENSITIVITY 362
20.9.2 NARROWING THE 13C OR 15N LINEWIDTHS 363 20.9.3 RECOUPLING
OPTIMIZATION 363 FURTHER READING 364
IMAGE 10
21 PROTEIN DYNAMICS IN THE SOLID STATE 367
J O Z E F R. LEWANDOWSKI A N D LYNDON EMSLEY 21.1 INTRODUCTION 367
21.2 BASIC CONCEPTS 369
21.3 COHERENT VERSUS INCOHERENT PROCESSES: DECAY IS NOT ALWAYS
RELAXATION 370 21.4 DEUTERIUM AS A PROBE O F DYNAMICS 371
21.5 15N AND 13C TI - SPIN-LATTICE RELAXATION 372
21.6 PROTOCOLS 373
21.6.1 MEASURING 15N TI RELAXATION 373 21.6.2 MEASURING 13C T X
RELAXATION 373 21.6.3 HETERONUCLEAR NOE 373 21.6.4 MEASURING 15N
DIPOLAR-CSA CROSS-CORRELATED RELAXATION 374 21.6.5 MEASURING 15N R L E
374
21.6.6 MEASURING MOTIONALLY AVERAGED SECULAR INTERACTIONS 374 21.6.7
SLOW CONFORMATIONAL EXCHANGE 374 21.6.8 IDENTIFICATION O F HIGHLY MOBILE
SITES 374 FURTHER READING 375
22 MICROCRYSTALLINE PROTEINS - AN IDEAL BENCHMARK FOR METHODOLOGY
DEVELOPMENT 377 W. TRENT FRANKS, BARTH-JAN VAN ROSSUM, BENJAMIN
BARDIAUX, ENRICO RAVERA, CIACOMO PARIGI, CLAUDIO LUCHINAT, AND HARTMUT
OSCHKINAT 22.1 MICROCRYSTALLINE PROTEIN SAMPLE PREPARATION 377 22.2
SEQUENTIAL ASSIGNMENT O F PROTEINS 378
22.3 STRUCTURAL RESTRAINTS 380
22.3.1 DISTANCE MEASUREMENTS: CROSS-RELAXATION-LIKE TRANSFER 380
22.3.1.1 PDSD/DARR/RAD 380 22.3.1.2 CHHC AND NHHC EXPERIMENTS 381
22.3.1.3 LH-DETECTED NOE 381
22.3.2 DISTANCE MEASUREMENTS: MULTIPLE-PULSE DIPOLAR RECOUPLING 382
22.3.2.1 RFDR 382 22.3.2.2 TSAR, PAR, AND PAIN 382 22.3.2.3 REDOR 382
22.3.2.4 TEDOR 382 22.3.2.5 PROTON DIPOLAR RECOUPLING: TMREV AND LG-CP
383 22.3.3 PARAMETERS ENCODING TORSION ANGLES 383
22.3.3.1 CHEMICAL SHIFTS 383 22.3.3.2 DOUBLE DIP-SHIFT SPECTROSCOPY 383
22.3.3.3 CSA-DIPOLAR INTERACTIONS 384 22.4 PARAMAGNETIC SYSTEMS 384
22.4.1 PRE 384
22.4.2 PCS 386
22.5 BENCHMARKING O F THE SOLID-STATE NMR STRUCTURE DETERMINATION
METHODOLOGY: COMPARISON O F STRUCTURE CALCULATION PROTOCOLS AND ACCURACY
O F STRUCTURES 386 22.6 PROTOCOLS 389
22.6.1 THREE-DIMENSIONAL NANOCRYSTALLINE SAMPLE PREPARATION 389 22.6.2
SEQUENTIAL ASSIGNMENTS O F SOLID-STATE NMR SPECTRA 389 22.6.3 DISTANCE
RESTRAINT ASSIGNMENTS WITH SOLID-STATE NMR 389 22.6.4 SECONDARY
STRUCTURE PREDICTION BY TALOS 390 (
22.6.5 DIPOLAR TENSOR, CSA, AND VECTOR ANGLE FITTING 390
22.6.6 USE O F PCS FOR STRUCTURAL RESTRAINTS: STRUCTURE O F THE
CATALYTIC DOMAIN O F MMP-12 AS A N EXAMPLE 390 1 1 1 TROUBLESHOOTING 391
FURTHER READING 392
IMAGE 11
CONTENTS XV
23 STRUCTURAL STUDIES O F PROTEIN FIBRILS BY SOLID-STATE NMR 395
ANJA BOCKMANN AND BEAT H. MEIER 23.1 BACKGROUND 395
23.2 NMR SPECTRA O F FIBRILS 396
23.3 OUTLOOK 397
23.4 PROTOCOLS AND EXAMPLES 398
23.4.1 SAMPLE PREPARATION 398 23.4.2 EXPERIMENTS FOR THE RESONANCE
ASSIGNMENT 398 23.4.3 EXPERIMENTS TO OBTAIN STRUCTURAL RESTRAINTS 400
23.4.4 FLEXIBLE ELEMENTS 401
23.4.5 STRUCTURE CALCULATION IN FIBRILS 402 23.5 TROUBLESHOOTING 404
FURTHER READING 405
24 SOLID-STATE NMR ON MEMBRANE PROTEINS: METHODS AND APPLICATIONS 407
A.A. CUKKEMANE, M. RENAULT, AND M. BALDUS 24.1 SOLID-STATE NMR O F
MEMBRANE PROTEINS 407 24.1.1 MAGIC ANGLE SPINNING 407 24.1.2 METHODS FOR
HIGH-RESOLUTION STRUCTURAL INVESTIGATION O F MEMBRANE PROTEINS 408
24.1.3 INVESTIGATION O F MEMBRANE PROTEIN TOPOLOGY 409 24.1.4
SENSITIVITY AND RESOLUTION 410 24.2 MAS APPLIED TO ION CHANNELS AND
RETINAL PROTEINS 411
24.2.1 RETINAL PROTEINS 411 24.2.2 CHIMERIC POTASSIUM CHANNEL KCSA-KVL.3
411 24.3 PROTOCOLS 413
24.3.1 SAMPLE PREPARATION 413 24.3.2 ISOTOPE LABELING 414 24.3.3
RESONANCE ASSIGNMENT 415 24.3.4 COLLECTING NMR RESTRAINTS 415 24.3.5 A
REAL EXPERIMENT 416 24.4 TROUBLESHOOTING 417
24.4.1 TIPS AND TRICKS IN OPTIMIZING SAMPLE PREPARATION 417 24.4.2
IMPROVING SENSITIVITY 417 FURTHER READING 417
PART SIX FRONTIERS IN NMR SPECTROSCOPY 419
25 DYNAMIC NUCLEAR POLARIZATION 421
THOMAS F. PRISNER
25.1 DYNAMIC NUCLEAR POLARIZATION AT HIGH MAGNETIC FIELDS 421 25.2
THEORETICAL BACKGROUND 422 25.2.1 OVERHAUSER EFFECT 423 25.2.2 SOLID
EFFECT 425
25.2.3 THREE-SPIN CROSS-POLARIZATION: CROSS-EFFECT 425 25.2.4 MANY-SPIN
CROSS-POLARIZATION: THERMAL MIXING 426 25.3 PROTOCOLS 427
25.3.1 HF LIQUID DNP SPECTROMETERS 427 25.3.2 SHUTTLE DNP 428
25.3.3 SS MAS DNP 428
25.3.4 LOW-TEMPERATURE DISSOLUTION POLARIZER 429 25.4 EXAMPLE EXPERIMENT
429
25.5 PERSPECTIVES 430 V
25.5.1 HF LIQUID DNP 430
25.5.2 SHUTTLE DNP 430
25.5.3 SS MAS DNP 430
25.5.4 DISSOLUTION DNP 431 FURTHER READING 431
IMAGE 12
26 13C DIRECT DETECTION NMR 433
ISABELLA C. FELLI AND ROBERTA PIERATTELLI 26.1 13C DIRECT DETECTION NMR
FOR BIOMOLECULAR APPLICATIONS 433 26.1.1 13C NMR PROPERTIES AND
APPLICATION AREAS 433 26.1.2 PROBLEM O F HOMONUCLEAR DECOUPLING IN THE
DIRECT ACQUISITION
DIMENSION 436
26.1.3 EXPERIMENTS FOR HIGH-RESOLUTION NMR 438 26.2 PROTOCOLS FOR
EXPERIMENTAL SETUP 439
26.3 TROUBLESHOOTING 442
FURTHER READING 442
27 SPEEDING UP MULTIDIMENSIONAL NMR DATA ACQUISITION 445 BERNHARD
BRUTSCHER, DOMINIQUE MARION, AND LUCIO FRYDMAN 27.1 MULTIDIMENSIONAL
NMR: BASIC CONCEPTS AND FEATURES 445 27.1.1 DISCRETE DATA SAMPLING,
ALIASING, AND TRUNCATION ARTIFACTS 446 27.1.2 TIME REQUIREMENTS IN
N-DIMENSIONAL NMR 447 27.2 FAST METHODS I N N-DIMENSIONAL NMR 447
27.2.1 SPARSE TIME-DOMAIN DATA SAMPLING AND PROCESSING 447 27.2.1.1
SAMPLING SCHEME AND THE POINT SPREAD FUNCTION 448 27.2.1.2 SPARSE
SAMPLING SCHEMES 448
27.2.1.3 ALTERNATIVE DATA PROCESSING METHODS 449 27.2.2 FAST-PULSING
METHODS 451 27.2.2.1 REPETITION RATE AND EXPERIMENTAL SENSITIVITY 452
27.2.2.2 LONGITUDINAL RELAXATION ENHANCEMENT 452 27.2.2.3 ERNST ANGLE
EXCITATION 453 27.2.2.4 BEST AND SOFAST EXPERIMENTS 453 27.2.3
SINGLE-SCAN "ULTRAFAST" TWO-DIMENSIONAL NMR 454 27.2.3.1 GENERAL
PRINCIPLES 454 27.2.3.2 SPATIOTEMPORAL ENCODING PROCESS 455 27.2.3.3
SPATIOTEMPORAL DECODING: TWO-DIMENSIONAL NMR IN ONE SCAN 455 27.3
PROTOCOLS FOR FAST JV-DIMENSIONAL NMR AND TROUBLESHOOTING 457
27.3.1 SETTING UP A N APPROPRIATE SAMPLING GRID 457 27.3.1.1
INFORMATION-DRIVEN SPECTRAL ALIASING 458 27.3.1.2 RANDOM SPARSE SAMPLING
AND MAXENT PROCESSING 458 27.3.2 PRACTICAL CONSIDERATIONS FOR THE SETUP
O F FAST-PULSING
EXPERIMENTS 459
27.3.3 SETTING UP A SINGLE-SCAN TWO-DIMENSIONAL EXPERIMENT 460 27.3.3.1
PROPERTIES O F DIFFERENT ENCODING SCHEMES 460 27.3.3.2 SINGLE-SCAN
TWO-DIMENSIONAL NMR SPECTRUM: CHARACTERISTICS 461 27.3.4 FAST
TWO-DIMENSIONAL NMR FOR
SAMPLE QUALITY SCREENING AND MOLECULAR INTERACTION STUDIES 462 27.3.5
REAL-TIME TWO-DIMENSIONAL NMR MEASUREMENTS 463 FURTHER READING 465
28 METABOLOMICS 467
LEONARDO TENORI
28.1 METABOLOMICS I N SYSTEMS BIOLOGY 467 28.2 NMR AND METABOLOMICS 469
28.3 DATA ANALYSIS 471
28.4 SUCCESS IN THE APPLICATION O F METABOLOMICS 472 28.5 PROTOCOLS 473
28.5.1 SERUM EXTRACTION 473 '
28.5.2 PLASMA EXTRACTION 473 28.5.3 URINE COLLECTION 474
28.5.4 TIP ON SAMPLES LABELING 474 28.5.5 SAMPLE PREPARATION FOR NMR
ANALYSIS 474 28.5.5.1 URINE 474
IMAGE 13
28.5.5.2 SERUM/PLASMA 475
28.5.6 BUFFER RECIPES 475
28.5.7 NMR ANALYSIS (WORKING WITH A 600-MHZ BRUKER SPECTROMETER) 475
28.5.7.1 URINE 475
28.5.7.2 SERUM/PLASMA 475 28.5.8 SPECTRAL PROCESSING 476 28.5.9
BUCKETING 476
28.5.10 DATA MINING 476 28.5.11 EXAMPLE EXPERIMENT 477 28.6
TROUBLESHOOTING 477
FURTHER READING 477
29 IN-CELL PROTEIN NMR SPECTROSCOPY 479 DAVID S. BURZ, DAVID COWBURN,
KAUSHIK DUTTA, AND ALEXANDER SHEKHTMAN 29.1 BACKGROUND 479
29.2 SPECIFIC APPLICATIONS 480
29.2.1 STRUCTURE DETERMINATION 481 29.2.2 PERTURBATIONS WITHIN THE CELL
- H O W IN-CELL AND IN VITRO ARE DIFFERENT ENVIRONMENTS 481 29.2.3
SPECIFIC PROTEIN-PROTEIN INTERACTIONS: STINT-NMR 483
29.2.4 OTHER PROTEIN-LIGAND INTERACTIONS 484 29.2.5 POST-TRANSLATIONAL
MODIFICATION - IN-CELL BIOCHEMISTRY 484 29.2.5.1 OTHER IN-CELL
BIOCHEMICAL STUDIES 485 29.2.6 NUCLEIC ACIDS IN-CELL 485
29.3 CONCLUSIONS AND FUTURE DIRECTIONS 485 29.4 PROTOCOLS AND EXAMPLE
EXPERIMENTS 486 29.4.1 EXPERIMENTAL DESIGN O F MULTIPLE EXPRESSION
SYSTEMS IN-CELL 486 29.4.2 DETAILED STINT PROTOCOL 487
29.4.2.1 DATA ACQUISITION AND ANALYSIS 488 29.4.2.2 EXAMPLE EXPERIMENT
489 29.4.3 DETAILED SMILI-NMR PROTOCOL 489 29.4.3.1 EXAMPLE EXPERIMENT
489
29.4.4 DETAILED PROTOCOL FOR POST-TRANSLATIONAL MODIFICATION 491
29.4.4.1 EXAMPLE EXPERIMENT 491 29.5 TROUBLESHOOTING 492
29.5.1 NO SIGNAL 492
29.5.2 WEAK SIGNAL 493 29.5.3 SIGNAL IS EXTRACELLULAR 493 29.5.3.1
CONTROL EXPERIMENTS FOR PROTEIN LEAKAGE/CELL LYSIS 493 29.5.3.2 CELL
VIABILITY 493
29.5.4 CELL GROWTH 493 FURTHER READING 493
30 STRUCTURAL INVESTIGATION O F CELL-FREE EXPRESSED MEMBRANE PROTEINS
497 SOLMAZ SOBHANIFAR, SINA RECKEL, FRANK LOHR, FRANK BERN HARD, AND
VOLKER DOTSCH 30.1 INTRODUCTION 497
30.2 CELL-FREE EXPRESSION O F MEMBRANE PROTEINS 498 30.3 CELL-FREE
EXPRESSION IN MEMBRANE-MIMETIC ENVIRONMENTS 499 30.4 STRATEGIES FOR
FUNCTIONAL PROTEIN EXPRESSION 500 30.5 CELL-FREE APPROACHES FOR
STRUCTURAL STUDIES 501 30.6 CELL-FREE LABELING STRATEGIES FOR BACKBONE
ASSIGNMENT 502
30.7 STRUCTURE DETERMINATION WITH LIMITED NUCLEAR OVERHAUSER EFFECT
LONG-DISTANCE RESTRAINTS 502 30.8 PROTOCOLS 504
30.8.1 EXTRACT 504
30.8.2 REACTION DEVICES 505 30.8.3 DNA TEMPLATE PREPARATION 506
IMAGE 14
30.8.4 DIFFERENT MODES FOR THE CELL-FREE PRODUCTION O F MEMBRANE
PROTEINS 506
30.8.5 EXAMPLE EXPERIMENT 507 30.9 TROUBLESHOOTING 507
FURTHER READING 508
PART SEVEN COMPUTATIONAL ASPECTS 509
31 GRID COMPUTING 511
ANTONIO ROSATO
31.1 GRID INFRASTRUCTURE 511
31.2 E-NMR WEB PLATFORM 512
31.3 PROTOCOLS 515
31.3.1 HOW TO REGISTER WITH THE E-NMR/WENMR VO 515 31.3.2 PERFORMING A
CYANA CALCULATION 516 31.3.3 REFINING A STRUCTURE WITH AMBER 516 31.4
TROUBLESHOOTING 517
FURTHER READING 518
32 PROTEIN-PROTEIN DOCKING WITH HADDOCK 521 CHRISTOPHE SCHMITZ, ADRIEN
S.J. MELQUIOND, SJOERDJ. DE VRIES, EZGI KARACA, MARC FAN DIJK,
PANAGIOTIS L. KASTRITIS, A N D ALEXANDRE M.J.J. BONVIN 32.1
PROTEIN-PROTEIN DOCKING: GENERAL CONCEPTS 521 32.1.1 WHY PROTEIN-PROTEIN
DOCKING? 521 32.1.2 GENERAL METHODS FOR PROTEIN-PROTEIN DOCKING 522 32.2
GATHERING EXPERIMENTAL INFORMATION FOR DATA-DRIVEN DOCKING 522 32.2.1
CHEMICAL SHIFT PERTURBATIONS 523 32.2.2 CROSS-SATURATION EXPERIMENTS 524
32.2.3 HYDROGEN/DEUTERIUM EXCHANGE 524 32.2.4 INTERMOLECULAR NOES 524
32.2.5 PARAMAGNETIC RELAXATION ENHANCEMENT 524 32.2.6 PSEUDOCONTACT
SHIFT 525 32.2.7 RESIDUAL DIPOLAR COUPLING 525 32.2.8 DIFFUSION
ANISOTROPY 526 32.2.9 NON-NMR INFORMATION 526 32.3 HOW DOES HADDOCK USE
THE INFORMATION? 526 32.3.1 INCORPORATION O F AMBIGUOUS DISTANCE
RESTRAINTS 527 32.3.2 INCORPORATION O F UNAMBIGUOUS DISTANCE RESTRAINTS
527 32.3.3 INCORPORATION O F SHAPE RESTRAINTS 528 32.3.4 INCORPORATION O
F ORIENTATION RESTRAINTS 528 32.3.5 SYMMETRY RESTRAINTS 528 32.3.6
ADDITIONAL DOCKING MODE 528 32.3.7 OVERVIEW O F A HADDOCK RUN 529 32.4
PROTOCOL: A GUIDED TOUR O F THE HADDOCK WEB INTERFACE 530 32.4.1
PREREQUISITE: REGISTRATION 530 32.4.2 DESCRIPTION O F THE WEB INTERFACE
531 32.4.3 ANALYSIS O F THE DOCKING RUN 533 32.5 TROUBLESHOOTING 534
32.5.1 GENERAL CONSIDERATIONS 534 32.5.2 PROBLEMS RELATED TO THE PDB
FILE 534 32.5.3 PROBLEMS ENCOUNTERED DURING DOCKING 535 FURTHER READING
535
S
33 AUTOMATED PROTEIN STRUCTURE DETERMINATION METHODS 537 PAUL GUERRY AND
TORSTEN HERRMANN 33.1 NMR EXPERIMENT-DRIVEN PROTEIN MODELING 537 33.2
NOE-BASED STRUCTURE DETERMINATION 538 33.2.1 CHEMICAL SHIFT AMBIGUITY
539
IMAGE 15
CONTENTS XIX
33.2.2 AMBIGUOUS DISTANCE RESTRAINTS 539
33.2.3 USING INTERMEDIATE STRUCTURES AND ELIMINATION O F ARTIFACTS 540
33.2.4 STRUCTURE CALCULATION AND ENERGY REFINEMENT 540 33.2.5 STRUCTURE
VALIDATION 541 33.3 SEQUENCE-SPECIFIC RESONANCE ASSIGNMENT 541 33.4 NMR
SIGNAL IDENTIFICATION 542 33.5 PERSPECTIVES 542
33.6 PROTOCOLS 543
33.7 EXAMPLE STRUCTURE DETERMINATION AND TROUBLESHOOTING 544 33.7.1
SEQUENCE-SPECIFIC RESONANCE ASSIGNMENT 545 33.7.2 AMINO ACID SEQUENCE,
CIS/TRANS ISOMERIZATION, AND REDOX STATE 545 33.7.3 NOE ASSIGNMENT,
STRUCTURE CALCULATION, AND STRUCTURE VALIDATION 545
FURTHER READING 546
34 NMR STRUCTURE DETERMINATION O F PROTEIN-LIGAND COMPLEXES 549 ULRICH
SCHIEBORR, SRIDHAR SREERAMULU, AND HAROLD SCHWALBE 34.1 PROTEIN-LIGAND
COMPLEX STRUCTURE DETERMINATION BY NMR 549 34.2 METHODS FOR
HIGH-AFFINITY BINDERS 550 34.3 METHODS FOR LOW-AFFINITY BINDERS 552 34.4
PROTOCOLS AND TROUBLESHOOTING 558
FURTHER READING 561
35 SMALL ANGLE X-RAY SCATTERING/SMALL ANGLE NEUTRON SCATTERING AS
METHODS COMPLEMENTARY TO NMR 563 M.V. PETOUKHOV AND D.I. SVERGUN 35.1
INTRODUCTION 563
35.2 INVARIANTS 566
35.3 A B INITIO SHAPE DETERMINATION 567
35.4 VALIDATION O F ATOMIC MODELS 568 35.5 RIGID-BODY MODELING O F
QUATERNARY STRUCTURE 568 35.6 EQUILIBRIUM MIXTURES AND FLEXIBLE SYSTEMS
569 35.7 PROTOCOLS 570
35.7.1 VALIDATION O F HIGH-RESOLUTION MODELS BY SOLUTION SCATTERING 570
35.7.2 UNRESTRAINED RIGID-BODY MODELING O F A COMPLEX 571 35.7.3
RIGID-BODY MODELING WITH CONTACT RESTRAINTS FROM NMR CHEMICAL SHIFTS 572
35.7.4 RIGID-BODY MODELING O F A COMPLEX WITH ORIENTATIONAL CONSTRAINTS
FROM NMR RDCS 572 35.7.5 CHARACTERIZATION O F FLEXIBLE SYSTEMS 573 35.8
TROUBLESHOOTING 573
FURTHER READING 574
REFERENCES 575
INDEX 609 |
| any_adam_object | 1 |
| author2 | Bertini, Ivano |
| author2_role | edt |
| author2_variant | i b ib |
| author_facet | Bertini, Ivano |
| building | Verbundindex |
| bvnumber | BV039877353 |
| classification_rvk | VG 9500 WC 2600 WC 3460 |
| classification_tum | CHE 808f CHE 244f |
| ctrlnum | (OCoLC)794523456 (DE-599)DNB1013615476 |
| dewey-full | 572.36 |
| dewey-hundreds | 500 - Natural sciences and mathematics |
| dewey-ones | 572 - Biochemistry |
| dewey-raw | 572.36 |
| dewey-search | 572.36 |
| dewey-sort | 3572.36 |
| dewey-tens | 570 - Biology |
| discipline | Chemie / Pharmazie Biologie Chemie |
| format | Book |
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| id | DE-604.BV039877353 |
| illustrated | Illustrated |
| indexdate | 2024-11-25T17:37:10Z |
| institution | BVB |
| isbn | 9783527328505 |
| language | English |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-024736553 |
| oclc_num | 794523456 |
| open_access_boolean | |
| owner | DE-11 DE-703 DE-91G DE-BY-TUM DE-20 DE-355 DE-BY-UBR DE-19 DE-BY-UBM |
| owner_facet | DE-11 DE-703 DE-91G DE-BY-TUM DE-20 DE-355 DE-BY-UBR DE-19 DE-BY-UBM |
| physical | XXXVIII, 612 S. Ill., graph. Darst. |
| publishDate | 2012 |
| publishDateSearch | 2012 |
| publishDateSort | 2012 |
| publisher | Wiley-Blackwell |
| record_format | marc |
| spellingShingle | NMR of biomolecules towards mechanistic systems biology NMR-Spektroskopie (DE-588)4075421-2 gnd Biomolekül (DE-588)4135124-1 gnd Systembiologie (DE-588)4809615-5 gnd |
| subject_GND | (DE-588)4075421-2 (DE-588)4135124-1 (DE-588)4809615-5 |
| title | NMR of biomolecules towards mechanistic systems biology |
| title_auth | NMR of biomolecules towards mechanistic systems biology |
| title_exact_search | NMR of biomolecules towards mechanistic systems biology |
| title_full | NMR of biomolecules towards mechanistic systems biology ed. by Ivano Bertini ... |
| title_fullStr | NMR of biomolecules towards mechanistic systems biology ed. by Ivano Bertini ... |
| title_full_unstemmed | NMR of biomolecules towards mechanistic systems biology ed. by Ivano Bertini ... |
| title_short | NMR of biomolecules |
| title_sort | nmr of biomolecules towards mechanistic systems biology |
| title_sub | towards mechanistic systems biology |
| topic | NMR-Spektroskopie (DE-588)4075421-2 gnd Biomolekül (DE-588)4135124-1 gnd Systembiologie (DE-588)4809615-5 gnd |
| topic_facet | NMR-Spektroskopie Biomolekül Systembiologie |
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| work_keys_str_mv | AT bertiniivano nmrofbiomoleculestowardsmechanisticsystemsbiology |