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NMR of biomolecules : towards mechanistic systems biology / edited by Ivano Bertini, Kathleen S. McGreevy, and Giacomo Parigi. — Weinheim, Germany : Wiley-VCH, c2012.—(58.178/N964) |
Contents
Contents
Preface
List of Contributors XXIII
List of Abbreviations XXIX
Part One Introduction
1 NMR and its Place in Mechanistic Systems Biology 3
2 Structure of Biomolecules: Fundamentals 7
2.1 Structural Features of Proteins 7
2.2 Nucleic Acids 21
3 What Can be Learned About the Structure and Dynamics of Biomolecules from NMR
3.1 Proteins Studied by NMR 33
3.2 Nucleic Acids Studied by NMR 47
Part Two Role of NMR in the Study of the Structure and Dynamics of Biomolecules 51
4 Determination of Protein Structure and Dynamics 53
4.1 Determination of Protein Structures 53
4.2 NMR Restraints 58
4.3 Structure Calculations 65
4.4 Validation of Protein Structures 72
4.5 Protein Dynamics and NMR Observables 76
4.6 Protocols 83
4.7 Troubleshooting 92
Further Reading 94
5 DNA 97
5.1 NMR Spectroscopy of DNA 97
5.2 Assessment of the Folding Topology 99
5.3 Resonance Assignment through Sequential and Interstrand Interactions 100
5.4 Pseudorotation of 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 of Three-Dimensional Structure 107
5.11 Search for Transient Structures 109
5.12 Protocols 110
5.13 Example Experiments and Troubleshooting 114
Further Reading 115
6 RNA 119
6.1 NMR Spectroscopy of RNA 119
6.2 Preparation of RNA Samples for NMR 120
6.3 Probing of the RNA Fold 121
6.4 Assessment of the Spectral Resolution 122
6.5 Strategy for the Resonance Assignment 123
6.6 Collection of Structural Information 126
6.7 Structural Calculation of RNA 128
6.8 Assessment of Quality of NMR Structures 129
6.9 Protocols 129
6.10 Troubleshooting 135
Further Reading 135
7 Intrinsically Disordered Proteins 137
7.1 Intrinsically Disordered Proteins 137
7.2 Importance of NMR to Study IDPs 140
7.3 Structural and Dynamic Information on IDPs - NMR Observables 141
7.4 Protocols 146
7.5 Troubleshooting 150
Further Reading 152
8 Paramagnetic Molecules 155
8.1 Paramagnetism-Assisted NMR 155
8.2 Scalar and Dipolar Electron Spin-Nuclear Spin Interactions: Hyperfine Shift 157
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
8.9 Troubleshooting 169
Further Reading 170
Part Three Role of NMR in the Study of the Structure and Dynamics of Biomolecular Interactions 173
9 NMR Methodologies for the Analysis of Protein-Protein Interactions 175
9.1 Introduction 175
9.2 Dynamics and Ligand Binding 176
9.3 General Strategy 177
9.4 Overview of Methods 178
9.5 Outlook 186
9.6 Protocols for the Analysis of Protein Complexes 186
9.7 Troubleshooting 194
Further Reading 194
10 Metal-Mediated Interactions 197
10.1 Theoretical Background 197
10.2 Protocol for the Structural Determination of a Metal-Mediated Complex 200
10.3 Example Experiment 202
10.4 Troubleshooting 202
Further Reading 203
11 Protein-Paramagnetic Protein Interactions 205
11.1 Paramagnetic Sources in Protein Complexes 205
11.2 Types of NMR Restraints Obtained from Paramagnetic Centers 206
11.3 Protein Complexes 207
11.4 Protocols 211
11.5 Example Experiment 215
11.6 Troubleshooting 215
Further Reading 217
12 Protein-RNA Interactions 219
12.1 Introduction 219
12.2 NMR Methodology 221
12.3 Protocols and Troubleshooting 228
13 Protein-DNA Interactions 239
13.1 State of the Art 239
13.2 Conclusions and Perspectives 242
13.3 Protocols 243
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
14.1 High-Throughput Screening and Fragment-Based Design 255
14.2 General Aspects of NMR Spectroscopy in 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
15.1 Ligand-Observed NMR Spectroscopy 265
15.2 On the Transient Binding of Small Molecules to the Protein 266
15.3 Questions Asked by Ligand-Based Fragment Screening 267
15.4 Summary 274
15.5 Protocols 274
15.6 Example Experiments 276
15.7 Troubleshooting 278
Further Readings 280
16 Interactions of Metallodrugs with DNA 283
16.1 Metallodrugs and DNA Interactions 283
16.2 Coordinative Binding 286
16.3 Groove Binding 289
16.4 Intercalation and Insertion 290
16.5 Dual Binding (Coordination and Intercalation) 291
16.6 Protocols 293
16.7 Tricks and Troubleshooting 294
Further Reading 295
17 RNA as a Drug Target 299
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 of RNA 304
17.5 Ligand-Based Methods 305
17.6 Protocols 306
17.7 Troubleshooting 312
Further Reading 313
18 Fluorine NMR Spectroscopy for Biochemical Screening in Drug Discovery 315
18.1 Enzymatic Inhibition Mechanisms 316
18.2 n-FABS 317
18.3 Comparison of n-FABS with Other Biophysical Techniques 322
18.4 Outlook 323
18.5 Protocols 323
18.6 Troubleshooting 326
Further Reading 327
19 NMR of Peptides 329
19.1 Introduction 329
19.2 Resonance Assignment 330
19.3 Stereostructure and Conformational Restraints 330
19.4 Structure Calculation 333
19.5 Importance of Peptide Conformations for Biological Activity 334
19.6 Protocols 334
19.7 Troubleshooting 342
Further Reading 343
Part Five Solid-State NMR 345
20 Biomolecular Solid-State NMR/Basics 347
20.1 Introduction 347
20.2 NMR Hamiltonian 347
20.3 Magic Angle Spinning 349
20.4 Cross-Polarization 350
20.5 Heteronuclear 1H Decoupling 350
20.6 Dipolar Recoupling 351
20.7 Recent Progress: New Probes - Ultrafast MAS - High Magnetic Fields 354
20.8 Protocols 355
20.9 Troubleshooting 362
Further Reading 364
21 Protein Dynamics in the Solid State 367
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 of Dynamics 371
21.5 15N and 13C T1 - Spin-Lattice Relaxation 372
21.6 Protocols 373
22 Microcrystalline Proteins - An Ideal Benchmark for Methodology Development 377
22.1 Microcrystalline Protein Sample Preparation 377
22.2 Sequential Assignment of Proteins 378
22.3 Structural Restraints 380
22.4 Paramagnetic Systems 384
22.5 Benchmarking of the Solid-State NMR Structure Determination Methodology:. Comparison of Structure Calculation Protocols and Accuracy of Structures 386
22.6 Protocols 389
22.7 Troubleshooting 391
Further Reading 392
23 Structural Studies of Protein Fibrils by Solid-State NMR 395
23.1 Background 395
23.2 NMR Spectra of Fibrils 396
23.3 Outlook 397
23.4 Protocols and Examples 398
23.5 Troubleshooting 404
Further Reading 405
24 Solid-State NMR on Membrane Proteins: Methods and Applications 407
24.1 Solid-State NMR of Membrane Proteins 407
24.2 MAS Applied to Ion Channels and Retinal Proteins 411
24.3 Protocols 413
24.4 Troubleshooting 417
Further Reading 417
Part Six Frontiers in NMR Spectroscopy 419
25 Dynamic Nuclear Polarization 421
25.1 Dynamic Nuclear Polarization at High Magnetic Fields 421
25.2 Theoretical Background 422
25.3 Protocols 427
25.4 Example Experiment 429
25.5 Perspectives 430
Further Reading 431
26 13C Direct Detection NMR 433
26.1 13C Direct Detection NMR for Biomolecular Applications 433
26.2 Protocols for Experimental Setup 439
26.3 Troubleshooting 442
Further Reading 442
27 Speeding Up Multidimensional NMR Data Acquisition 445
27.1 Multidimensional NMR: Basic Concepts and Features 445
27.2 Fast Methods in N-Dimensional NMR 447
27.3 Protocols for Fast N-Dimensional NMR and Troubleshooting 457
Further Reading 465
28 Metabolomics 467
28.1 Metabolomics in Systems Biology 467
28.2 NMR and Metabolomics 469
28.3 Data Analysis 471
28.4 Success in the Application of Metabolomics 472
28.5 Protocols 473
28.6 Troubleshooting 477
Further Reading 477
29 In-Cell Protein NMR Spectroscopy 479
29.1 Background 479
29.2 Specific Applications 480
29.3 Conclusions and Future Directions 485
29.4 Protocols and Example Experiments 486
29.5 Troubleshooting 492
Further Reading 493
30 Structural Investigation of Cell-Free Expressed Membrane Proteins 497
30.1 Introduction 497
30.2 Cell-Free Expression of 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
30.9 Troubleshooting 507
Further Reading 508
Part Seven Computational Aspects 509
31 Grid Computing 511
31.1 Grid Infrastructure 511
31.2 e-NMR Web Platform 512
31.3 Protocols 515
31.4 Troubleshooting 517
Further Reading 518
32 Protein-Protein Docking with HADDOCK 521
32.1 Protein-Protein Docking: General Concepts 521
32.2 Gathering Experimental Information for Data-Driven Docking 522
32.3 How Does HADDOCK Use the Information? 526
32.4 Protocol: A Guided Tour of the HADDOCK Web Interface 530
32.5 Troubleshooting 534
Further Reading 535
33 Automated Protein Structure Determination Methods 537
33.1 NMR Experiment-Driven Protein Modeling 537
33.2 NOE-Based Structure Determination 538
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
Further Reading 546
34 NMR Structure Determination of Protein-Ligand Complexes 549
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
35.1 Introduction 563
35.2 Invariants 566
35.3 Ab Initio Shape Determination 567
35.4 Validation of Atomic Models 568
35.5 Rigid-Body Modeling of Quaternary Structure 568
35.6 Equilibrium Mixtures and Flexible Systems 569
35.7 Protocols 570
35.8 Troubleshooting 573
Further Reading 574
References 575
Index 609
