Protein NMR Spectroscopy

, by Cavanagh; Skelton; Fairbrother; Rance; Palmer, III

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ISBN: 9780121644918 | 012164491X
Cover: Hardcover
Copyright: 11/20/2006

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Protein NMR Spectroscopy combines a comprehensive theoretical treatment of NMR spectroscopy with an extensive exposition of the experimental techniques applicable to proteins and other biological macromolecules in solution. Beginning with simple theoretical models and experimental techniques, Protein NMR Spectroscopy develops the complete repertoire of theoretical principles and experimental techniques necessary for understanding and implementing the most sophisticated NMR experiments. Important new techniques and applications of NMR spectroscopy have emerged since the first edition of this extremely successful book was published in 1996. The second edition includes new sections describing measurement and use of residual dipolar coupling constants for structure determination, TROSY and deuterium labeling for application to large macromolecules, and experimental techniques for characterizing conformational dynamics. In addition, the treatments of instrumentation and signal acquisition, field gradients, multidimensional spectroscopy, and structure calculation are updated and enhanced. Protein NMR Spectroscopy is written as a graduate-level textbook and will be of interest to biochemists, chemists, biophysicists, and structural biologists who utilize NMR spectroscopy or who wish to understand the latest developments in this field. Provides an understanding of the theoretical principles important for biological NMR spectroscopy Demonstrates how to implement, optimize and troubleshoot modern multi-dimensional NMR experiments Allows for the capability of designing effective experimental protocols for investigations of protein structures and dynamics Includes a comprehensive set of example NMR spectra of ubiquitin provides a reference for validation of experimental methods

Preface

Preface to the First Edition

vii

Acknowledgements

CHAPTER 1 CLASSICAL NMR SPECTROSCOPY

1.1 Nuclear Magnetism

(5)

1.2 The Bloch Equations

(9)

1.3 The One-Pulse NMR Experiment

(2)

1.4 Linewidth

(3)

1.5 Chemical Shift

(2)

1.6 Scalar Coupling and Limitations of the Bloch Equations

(4)

References

(2)

CHAPTER 2 THEORETICAL DESCRIPTION OF NMR SPECTROSCOPY

2.1 Postulates of Quantum Mechanics

(8)

2.1.1 THE SCHRODINGER EQUATION

(1)

2.1.2 EIGENVALUE EQUATIONS

(3)

2.1.3 SIMULTANEOUS EIGENFUNCTIONS

(1)

2.1.4 EXPECTATION VALUE OF THE MAGNETIC MOMENT

(2)

2.2 The Density Matrix

(13)

2.2.1 DIRAC NOTATION

(3)

2.2.2 QUANTUM STATISTICAL MECHANICS

(1)

2.2.3 THE LIOUVILLE-VON NEUMANN EQUATION

(2)

2.2.4 THE ROTATING FRAME TRANSFORMATION

(3)

2.2.5 MATRIX REPRESENTATIONS OF THE SPIN OPERATORS

(4)

2.3 Pulses and Rotation Operators

(4)

2.4 Quantum Mechanical NMR Spectroscopy

(4)

2.4.1 EQUILIBRIUM AND OBSERVATION OPERATORS

(1)

2.4.2 THE ONE-PULSE EXPERIMENT

(2)

2.5 Quantum Mechanics of Multispin Systems

(12)

2.5.1 DIRECT PRODUCT SPACES

(2)

2.5.2 SCALAR COUPLING HAMILTONIAN

(4)

2.5.3 ROTATIONS IN PRODUCT SPACES

(3)

2.5.4 ONE-PULSE EXPERIMENT FOR A TWO-SPIN SYSTEM

(2)

2.6 Coherence

(7)

2.7 Product Operator Formalism

(25)

2.7.1 OPERATOR SPACES

(2)

2.7.2 BASIS OPERATORS

(4)

2.7.3 EVOLUTION IN THE PRODUCT OPERATOR FORMALISM

(4)

2.7.3.1 FREE PRECESSION

(1)

2.7.3.2 PULSES

(1)

2.7.3.3 PRACTICAL POINTS

(2)

2.7.4 SINGLE-QUANTUM COHERENCE AND OBSERVABLE OPERATORS

(2)

2.7.5 MULTIPLE-QUANTUM COHERENCE

(2)

2.7.6 COHERENCE TRANSFER AND GENERATION OF MULTIPLE-QUANTUM COHERENCE

(1)

2.7.7 EXAMPLES OF PRODUCT OPERATOR CALCULATIONS

(31)

2.7.7.1 THE SPIN ECHO

(3)

2.7.7.2 INSENSITIVE NUCLEI ENHANCED BY POLARIZATION TRANSFER

(2)

2.7.7.3 REFOCUSED INEPT

(1)

2.7.7.4 SPIN-STATE SELECTIVE POLARIZATION TRANSFER

(3)

2.8 Averaging of the Spin Hamiltonians and Residual Interactions

102

(10)

References

112

(2)

CHAPTER 3 EXPERIMENTAL ASPECTS OF NMR SPECTROSCOPY

3.1 NMR Instrumentation

114

(10)

3.2 Data Acquisition

124

(12)

3.2.1 SAMPLING

124

(2)

3.2.2 OVERSAMPLING AND DIGITAL FILTERS

126

(6)

3.2.3 QUADRATURE DETECTION

132

(4)

3.3 Data Processing

136

(29)

3.3.1 FOURIER TRANSFORMATION

136

(6)

3.3.2 DATA MANIPULATIONS

142

(16)

3.3.2.1 ZERO-FILLING

142

(1)

3.3.2.2 APODIZATION

143

(8)

3.3.2.3 PHASING

151

(7)

3.3.3 SIGNAL-TO-NOISE RATIO

158

(1)

3.3.4 ALTERNATIVES TO FOURIER TRANSFORMATION

159

(6)

3.3.4.1 LINEAR PREDICTION

160

(1)

3.3.4.2 MAXIMUM ENTROPY RECONSTRUCTION

161

(4)

3.4 Pulse Techniques

165

(36)

3.4.1 OFF-RESONANCE EFFECTS

165

(7)

3.4.2 B1 INHOMOGENEITY

172

(2)

3.4.3 COMPOSITE PULSES

174

(5)

3.4.4 SELECTIVE PULSES

179

(2)

3.4.5 PHASE-MODULATED PULSES

181

(8)

3.4.6 ADIABATIC PULSES

189

(12)

3.5 Spin Decoupling

201

(16)

3.5.1 SPIN DECOUPLING THEORY

201

(3)

3.5.2 COMPOSITE PULSE DECOUPLING

204

(5)

3.5.3 ADIABATIC SPIN DECOUPLING

209

(3)

3.5.4 CYCLING SIDEBANDS

212

(4)

3.5.5 RECOMMENDATIONS FOR SPIN DECOUPLING

216

(1)

3.6 B0 Field Gradients

217

(4)

3.7 Water Suppression Techniques

221

(13)

3.7.1 PRESATURATION

223

(1)

3.7.2 JUMP-RETURN AND BINOMIAL SEQUENCES

224

(3)

3.7.3 SPIN LOCK AND FIELD GRADIENT PULSES

227

(5)

3.7.4 POSTACQUISITION SIGNAL PROCESSING

232

(2)

3.8 One-Dimensional ¹H NMR Spectroscopy

234

(33)

3.8.1 SAMPLE PREPARATION

234

(2)

3.8.2 INSTRUMENT SETUP

236

(26)

3.8.2.1 TEMPERATURE CALIBRATION

236

(1)

3.8.2.2 TUNING

237

(1)

3.8.2.3 SHIMMING

238

(14)

3.8.2.4 PULSE WIDTH CALIBRATION

252

(5)

3.8.2.5 RECYCLE DELAY

257

(2)

3.8.2.6 LIN EWIDTH MEASUREMENT

259

(3)

3.8.3 REFERENCING

262

(1)

3.8.4 ACQUISITION AND DATA PROCESSING

263

(17)

3.8.4.1 ONE-PULSE EXPERIMENT

263

(2)

3.8.4.2 HAHN ECHO EXPERIMENT

265

(2)

References

267

(6)

CHAPTER 4 MULTIDIMENSIONAL NMR SPECTROSCOPY

4.1 Two-Dimensional NMR Spectroscopy

273

(7)

4.2 Coherence Transfer and Mixing

280

(12)

4.2.1 THROUGH-BOND COHERENCE TRANSFER

280

(9)

4.2.1.1 COSY-TYPE COHERENCE TRANSFER

281

(3)

4.2.1.2 TOCSY TRANSFER THROUGH-BONDS

284

(5)

4.2.2 THROUGH-SPACE COHERENCE TRANSFER

289

(1)

4.2.3 HETERONUCLEAR COHERENCE TRANSFER

290

(1)

4.2.4 COHERENCE TRANSFER UNDER RESIDUAL DIPOLAR COUPLING HAMILTONIANS

291

(1)

4.3 Coherence Selection, Phase Cycling, and Field Gradients

292

(34)

4.3.1 COHERENCE LEVEL DIAGRAMS

293

(2)

4.3.2 PHASE CYCLES

295

(16)

4.3.2.1 SELECTION OF A COHERENCE TRANSFER PATHWAY

298

(7)

4.3.2.2 SAVING TIME

305

(2)

4.3.2.3 ARTIFACT SUPPRESSION

307

(3)

4.3.2.4 LIMITATIONS OF PHASE CYCLING

310

(1)

4.3.3 PULSED FIELD GRADIENTS

311

(4)

4.3.3.1 SELECTION OF A COHERENCE TRANSFER PATHWAY

311

(2)

4.3.3.2 ARTIFACT SUPPRESSION

313

(1)

4.3.3.3 LIMITATIONS OF PULSED FIELD GRADIENTS

314

(1)

4.3.4 FREQUENCY DISCRIMINATION

315

(19)

4.3.4.1 FREQUENCY DISCRIMINATION BY PHASE CYCLING

320

(2)

4.3.4.2 FREQUENCY DISCRIMINATION BY PULSED FIELD GRADIENTS

322

(1)

4.3.4.3 ALIASING, FOLDING, AND PHASING IN MULTIDIMENSIONAL NMR SPECTROSCOPY

323

(3)

4.4 Resolution and Sensitivity

326

(1)

4.5 Three- and Four-Dimensional NMR Spectroscopy

327

(4)

References

331

(3)

CHAPTER 5 RELAXATION AND DYNAMIC PROCESSES

5.1 Introduction and Survey of Theoretical Approaches

334

(17)

5.1.1 RELAXATION IN THE BLOCH EQUATIONS

337

(1)

5.1.2 THE SOLOMON EQUATIONS

338

(8)

5.1.3 RANDOM-PHASE MODEL FOR TRANSVERSE RELAXATION

346

(4)

5.1.4 BLOCH, WANGSNESS, AND REDFIELD THEORY

350

(1)

5.2 The Master Equation

351

(14)

5.2.1 INTERFERENCE EFFECTS

359

(1)

5.2.2 LIKE SPINS, UNLIKE SPINS, AND THE SECULAR APPROXIMATION

360

(3)

5.2.3 RELAXATION IN THE ROTATING FRAME

363

(2)

5.3 Spectral Density Functions

365

(5)

5.4 Relaxation Mechanisms

370

(18)

5.4.1 INTRAMOLECULAR DIPOLAR RELAXATION FOR IS SPIN SYSTEM

371

(7)

5.4.2 INTRAMOLECULAR DIPOLAR RELAXATION FOR SCALAR-COUPLED IS SPIN SYSTEM

378

(3)

5.4.3 INTRAMOLECULAR DIPOLAR RELAXATION FOR IS SPIN SYSTEM IN THE ROTATING FRAME

381

(2)

5.4.4 CHEMICAL SHIFT ANISOTROPY AND QUADRUPOLAR RELAXATION

383

(2)

5.4.5 RELAXATION INTERFERENCE

385

(2)

5.4.6 SCALAR RELAXATION

387

(1)

5.5 Nuclear Overhauser Effect

388

(3)

5.6 Chemical Exchange Effects in NMR Spectroscopy

391

(11)

5.6.1 CHEMICAL EXCHANGE FOR ISOLATED SPINS

392

(9)

5.6.2 QUALITATIVE EFFECTS OF CHEMICAL EXCHANGE IN SCALAR-COUPLED SYSTEMS

401

(1)

References

402

(4)

CHAPTER 6 EXPERIMENTAL ¹H NMR METHODS

6.1 Assessment of the 1D ¹H Spectrum

406

(3)

6.2 COSY-Type Experiments

409

(28)

6.2.1 COSY

410

(19)

6.2.1.1 PRODUCT OPERATOR ANALYSIS

410

(2)

6.2.1.2 EXPERIMENTAL PROTOCOL

412

(3)

6.2.1.3 PROCESSING

415

(3)

6.2.1.4 INFORMATION CONTENT

418

(2)

6.2.1.5 QUANTITATION OF SCALAR COUPLING CONSTANTS IN COSY SPECTRA

420

(6)

6.2.1.6 EXPERIMENTAL VARIANTS

426

(3)

6.2.2 RELAYED COSY

429

(4)

6.2.2.1 PRODUCT OPERATOR ANALYSIS

430

(2)

6.2.2.2 EXPERIMENTAL PROTOCOL

432

(1)

6.2.2.3 PROCESSING

432

(1)

6.2.2.4 INFORMATION CONTENT

432

(1)

6.2.3 DOUBLE-RELAYED COSY

433

(4)

6.3 Multiple-Quantum Filtered COSY

437

(26)

6.3.1 2QF-COSY

440

(9)

6.3.1.1 PRODUCT OPERATOR ANALYSIS

440

(4)

6.3.1.2 EXPERIMENTAL PROTOCOL

444

(1)

6.3.1.3 PROCESSING

445

(1)

6.3.1.4 INFORMATION CONTENT

446

(3)

6.3.2 3QF-COSY

449

(6)

6.3.2.1 PRODUCT OPERATOR ANALYSIS

449

(2)

6.3.2.2 EXPERIMENTAL PROTOCOL AND PROCESSING

451

(1)

6.3.2.3 INFORMATION CONTENT

452

(3)

6.3.3 E.COSY

455

(8)

6.3.3.1 PRODUCT OPERATOR ANALYSIS

457

(3)

6.3.3.2 EXPERIMENTAL PROTOCOL

460

(1)

6.3.3.3 PROCESSING

461

(1)

6.3.3.4 INFORMATION CONTENT

462

(1)

6.3.3.5 EXPERIMENTAL VARIANTS

463

(1)

6.4 Multiple-Quantum Spectroscopy

463

(23)

6.4.1 2Q SPECTROSCOPY

465

(16)

6.4.1.1 PRODUCT OPERATOR ANALYSIS

466

(7)

6.4.1.2 EXPERIMENTAL PROTOCOL

473

(1)

6.4.1.3 PROCESSING

474

(1)

6.4.1.4 INFORMATION CONTENT

474

(7)

6.4.2 3Q SPECTROSCOPY

481

(5)

6.4.2.1 PRODUCT OPERATOR ANALYSIS

481

(2)

6.4.2.2 EXPERIMENTAL PROTOCOL AND PROCESSING

483

(1)

6.4.2.3 INFORMATION CONTENT

484

(2)

6.5 TOCSY

486

(16)

6.5.1 PRODUCT OPERATOR ANALYSIS

486

(7)

6.5.2 EXPERIMENTAL PROTOCOL

493

(3)

6.5.3 PROCESSING

496

(2)

6.5.4 INFORMATION CONTENT

498

(1)

6.5.5 EXPERIMENTAL VARIANTS

499

(3)

6.6 Cross-Relaxation NMR Experiments

502

(23)

6.6.1 NOESY

502

(15)

6.6.1.1 PRODUCT OPERATOR ANALYSIS

503

(3)

6.6.1.2 EXPERIMENTAL PROTOCOL

506

(4)

6.6.1.3 PROCESSING

510

(1)

6.6.1.4 INFORMATION CONTENT

510

(1)

6.6.1.5 EXPERIMENTAL VARIANTS

511

(6)

6.6.2 ROESY

517

(8)

6.6.2.1 PRODUCT OPERATOR ANALYSIS

517

(3)

6.6.2.2 EXPERIMENTAL PROTOCOL AND PROCESSING

520

(2)

6.6.2.3 INFORMATION CONTENT

522

(2)

6.6.2.4 EXPERIMENTAL VARIANTS

524

(1)

6.7 ¹H 3D Experiments

525

(4)

6.7.1 EXPERIMENTAL PROTOCOL

526

(1)

6.7.2 PROCESSING

527

(1)

6.7.3 INFORMATION CONTENT

527

(1)

6.7.4 EXPERIMENTAL VARIANTS

528

(1)

References

529

(6)

CHAPTER 7 HETERONUCLEAR NMR EXPERIMENTS

7.1 Heteronuclear Correlation NMR Spectroscopy

535

(46)

7.1.1 BASIC HMQC AND HSQC EXPERIMENTS

536

(10)

7.1.1.1 THE HMQC EXPERIMENT

536

(4)

7.1.1.2 THE HSQC EXPERIMENT

540

(3)

7.1.1.3 THE CONSTANT-TIME HSQC EXPERIMENT

543

(1)

7.1.1.4 COMPARISON OF HMQC AND HSQC SPECTRA

544

(2)

7.1.2 ADDITIONAL CONSIDERATIONS IN HETERONUCLEAR CORRELATION EXPERIMENTS

546

(6)

7.1.2.1 PHASE CYCLING AND ARTIFACT SUPPRESSION

546

(2)

7.1.2.2 ¹³C SCALAR COUPLING AND MULTIPLET STRUCTURE

548

(1)

7.1.2.3 FOLDING AND ALIASING

549

(3)

7.1.2.4 PROCESSING HETERONUCLEAR CORRELATION EXPERIMENTS

552

(1)

7.1.3 DECOUPLED HSQC, SENSITIVITY-ENHANCED HSQC, AND TROSY EXPERIMENTS

552

(21)

7.1.3.1 THE DECOUPLED HSQC EXPERIMENT

553

(7)

7.1.3.2 SENSITIVITY-ENHANCED HSQC

560

(6)

7.1.3.3 TROSY EXPERIMENT

566

(4)

7.1.3.4 COMPARISON OF DECOUPLED HSQC, PEP-HSQC, AND TROSY EXPERIMENTS

570

(1)

7.1.3.5 RELAXATION INTERFERENCE AND TROSY SPECTRA OF LARGER PROTEINS

570

(3)

7.1.4 WATER SUPPRESSION AND GRADIENT ENHANCEMENT OF HETERONUCLEAR CORRELATION SPECTRA

573

(5)

7.1.4.1 SOLVENT SUPPRESSION

573

(1)

7.1.4.2 GRADIENT-ENHANCED HSQC AND TROSY NMR SPECTROSCOPY

574

(4)

7.1.5 THE CONSTANT-TIME ¹H-¹³C HSQC EXPERIMENT

578

(3)

7.2 Heteronuclear-Edited NMR Spectroscopy

581

(20)

7.2.1 3D NOESY–HSQC SPECTROSCOPY

582

(7)

7.2.1.1 3D ¹H-15N NOESY–HSQC

585

(3)

7.2.1.2 3D ¹H-¹³C NOESY–HSQC

588

(1)

7.2.2 3D TOCSY–HSQC SPECTROSCOPY

589

(2)

7.2.3 3D HSQC–NOESY AND HSQC–TOCSY EXPERIMENTS

591

(2)

7.2.4 HMQC–NOESY–HMQC EXPERIMENTS

593

(7)

7.2.4.1 3D 15N/15N HMQC–NOESY–HMQC

594

(1)

7.2.4.2 4D ¹³C/15N HMQC–NOESY–HMQC

595

(2)

7.2.4.3 4D ¹³C/¹³C HMQC–NOESY–HMQC

597

(2)

7.2.4.4 PROCESSING 4D HMQC–NOESY–HMQC SPECTRA

599

(1)

7.2.5 RELATIVE MERITS OF 3D AND 4D HETERONUCLEAR-EDITED NOESY SPECTROSCOPY

600

(1)

7.3 ¹³C-¹³C Correlations: The HCCH–COSY and HCCH–TOCSY Experiments

601

(12)

7.3.1 HCCH–COSY

603

(4)

7.3.2 CONSTANT-TIME HCCH–COSY

607

(1)

7.3.3 HCCH–TOCSY

608

(5)

7.4 3D Triple-Resonance Experiments

613

(43)

7.4.1 A PROTOTYPE TRIPLE-RESONANCE EXPERIMENT: HNCA

614

(15)

7.4.1.1 A SIMPLE HNCA EXPERIMENT

618

(7)

7.4.1.2 THE CT-HNCA EXPERIMENT

625

(1)

7.4.1.3 THE DECOUPLED CT-HNCA EXPERIMENT

626

(1)

7.4.1.4 THE GRADIENT-ENHANCED HNCA EXPERIMENT

627

(1)

7.4.1.5 THE GRADIENT-ENHANCED TROSY–HNCA EXPERIMENT

628

(1)

7.4.2 A COMPLEMENTARY APPROACH: THE HN(CO)CA EXPERIMENT

629

(3)

7.4.3 A STRAIGHT-THROUGH TRIPLE-RESONANCE EXPERIMENT: H(CA)NH

632

(5)

7.4.4 BACKBONE CORRELATIONS WITH THE ¹³CO SPINS

637

(4)

7.4.4.1 HNCO

637

(1)

7.4.4.2 HN(CA)CO

638

(3)

7.4.5 CORRELATIONS WITH THE Cβ/Hβ SPINS

641

(13)

7.4.5.1 CBCA(CO)NH

642

(3)

7.4.5.2 CBCANH

645

(5)

7.4.5.3 HNCACB

650

(4)

7.4.6 ADDITIONAL CONSIDERATIONS FOR TRIPLE-RESONANCE EXPERIMENTS

654

(2)

7.5 Measurement of Scalar Coupling Constants

656

(9)

7.5.1 HNCA-J EXPERIMENT

656

(4)

7.5.2 HNHA EXPERIMENT

660

(5)

7.6 Measurement of Residual Dipolar Coupling Constants

665

(8)

References

673

(7)

CHAPTER 8 EXPERIMENTAL NMR RELAXATION METHODS

8.1 Pulse Sequences and Experimental Methods

680

(5)

8.2 Picosecond–Nanosecond Dynamics

685

(17)

8.2.1 EXPERIMENTAL METHODS FOR 15N LABORATORY-FRAME RELAXATION

686

(6)

8.2.2 EXPERIMENTAL METHODS FOR 15N RELAXATION INTERFERENCE

692

(1)

8.2.3 EXPERIMENTAL METHODS FOR ¹³CH2D METHYL LABORATORY-FRAME RELAXATION

693

(6)

8.2.4 EXPERIMENTAL METHODS FOR ¹³CO LABORATORY-FRAME RELAXATION

699

(3)

8.3 Microsecond–Second Dynamics

702

(19)

8.3.1 LINESHAPE ANALYSIS

704

(2)

8.3.2 ZZ-EXCHANGE SPECTROSCOPY

706

(1)

8.3.3 R17rho;, ROTATING-FRAME RELAXATION METHODS

707

(4)

8.3.4 CPMG RELAXATION METHODS

711

(4)

8.3.5 CHEMICAL EXCHANGE IN MULTIPLE-QUANTUM SPECTROSCOPY

715

(3)

8.3.6 TROSY-BASED APPROACHES

718

(3)

References

721

(4)

CHAPTER 9 LARGER PROTEINS AND MOLECULAR INTERACTIONS

9.1 Larger Proteins

725

(28)

9.1.1 PROTEIN DEUTERATION

726

(2)

9.1.2 RELAXATION IN PERDEUTERATED AND RANDOM FRACTIONALLY DEUTERATED PROTEINS

728

(1)

9.1.3 SENSITIVITY FOR PERDEUTERATED PROTEINS

729

(3)

9.1.4 ²H ISOTOPE SHIFTS

732

(1)

9.1.5 EXPERIMENTS FOR ¹HN, 15N, ¹³Cα, ¹³Cβ, AND ¹³CO ASSIGNMENTS IN DEUTERATED PROTEINS

733

(7)

9.1.5.1 CONSTANT-TIME HNCA FOR DEUTERATED PROTEINS

735

(2)

9.1.5.2 HN(CA)CB FOR DEUTERATED PROTEINS

737

(2)

9.1.5.3 OTHER EXPERIMENTS FOR RESONANCE ASSIGNMENTS

739

(1)

9.1.6 SIDE CHAIN ¹³C ASSIGNMENTS IN DEUTERATED PROTEINS

740

(3)

9.1.7 SIDE CHAIN ¹H ASSIGNMENTS

743

(2)

9.1.8 NOE RESTRAINTS FROM DEUTERATED PROTEINS

745

(4)

9.1.8.1 4D HN-HN 15N15N-SEPARATED NOESY EXPERIMENT

745

(2)

9.1.8.2 ¹³C/15N-, ¹³C/¹³C-, AND 15N/15N- SEPARATED NOESY EXPERIMENTS ON RANDOM FRACTIONALLY DEUTERATED PROTEINS

747

(2)

9.1.9 SELECTIVE PROTONATION

749

(4)

9.2 Intermolecular Interactions

753

(16)

9.2.1 EXCHANGE REGIMES

753

(2)

9.2.2 PROTEIN-LIGAND BINDING INTERFACES

755

(5)

9.2.2.1 CHEMICAL SHIFT MAPPING

756

(1)

9.2.2.2 CROSS-SATURATION

757

(2)

9.2.2.3 TRANSVERSE RELAXATION AND AMIDE PROTON SOLVENT EXCHANGE

759

(1)

9.2.3. RESONANCE ASSIGNMENTS AND STRUCTURAL RESTRAINTS FOR PROTEIN COMPLEXES

760

(9)

9.2.3.1 ASSIGNMENTS AND STRUCTURES OF PROTEINS IN PROTEIN-LIGAND COMPLEXES

761

(1)

9.2.3.2 ISOTOPE-EDITED/FILTERED NOESY TO DEFINE INTERMOLECULAR INTERFACES

762

(7)

9.3 Methods for Rapid Data Acquisition

769

(6)

9.3.1 NONUNIFORM SAMPLING

770

(1)

9.3.2 GFT-NMR SPECTROSCOPY

771

(2)

9.3.3 PROJECTION-RECONSTRUCTION

773

(2)

References

775

(7)

CHAPTER 10 SEQUENTIAL ASSIGNMENT, STRUCTURE DETERMINATION, AND OTHER APPLICATIONS

10.1 Resonance Assignment Strategies

782

(14)

10.1.1 ¹H RESONANCE ASSIGNMENTS FOR UNLABELED PROTEINS

782

(10)

10.1.2 HETERONUCLEAR RESONANCE ASSIGNMENTS FOR ISOTOPICALLY LABELED PROTEINS

792

(4)

10.2 Three-Dimensional Solution Structures

796

(17)

10.2.1 NM R-DERIVED STRUCTURAL RESTRAINTS

796

(10)

10.2.1.1 NOE DISTANCE RESTRAINTS

797

(1)

10.2.1.2 DIHEDRAL ANGLE RESTRAINTS FROM SCALAR COUPLING CONSTANTS

798

(6)

10.2.1.3 DIHEDRAL ANGLE RESTRAINTS FROM ISOTROPIC CHEMICAL SHIFTS

804

(1)

10.2.1.4 RESTRAINTS FROM RESIDUAL DIPOLAR COUPLING CONSTANTS

804

(1)

10.2.1.5 HYDROGEN BOND RESTRAINTS FROM AMIDE PROTON-SOLVENT EXCHANGE

805

(1)

10.2.1.6 HYDROGEN BOND RESTRAINTS FROM TRANS-HYDROGEN BOND SCALAR COUPLING CONSTANTS

806

(1)

10.2.2 STRUCTURE DETERMINATION

806

(7)

10.3 Conclusion

813

(1)

References

814

(5)

Table of Symbols

819

(6)

List of Figures

825

(12)

List of Tables

837

(2)

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Protein NMR Spectroscopy

Summary

Table of Contents

Supplemental Materials

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