Recent Developments in Biomolecular Nmr

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ISBN: 9781849731201 | 1849731209
Cover: Hardcover
Copyright: 8/30/2012

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NMR spectroscopy is widely used in biomolecular science particularly for structure determination of proteins, nucleic acids and carbohydrates. Much of the innovation within NMR spectroscopy has been within the field of protein NMR spectroscopy, an important technique in structural biology. Filling a gap in the literature, this book will draw together experts in the field to discuss the real advances in NMR methods that have occurred or have an impact on the biomolecular field in the last few years. The coverage will include recent developments in using NMR for determination of protein structures, membrane proteins, the dynamics of RNA and advances in NMR in drug discovery. Edited by leading biological NMR spectroscopists, the book will be an essential reference for researchers in industry and academia interested in or joining this bioanalytical field.

Isotope-Labelling of Methyl Groups for NMR Studies of Large Proteins	p. 1
Introduction-Large Proteins and Solution NMR Spectroscopy	p. 1
Isotope-Labelling and Protein NMR Spectroscopy	p. 1
General Considerations for NMR Studies of Larger Proteins	p. 2
NMR Experiments Designed for Larger Systems	p. 4
Using Methyl Groups as Probes for NMR Spectroscopy	p. 6
Why the Methyl Group?	p. 6
Strategies for Selective Protonation of Methyl Groups in Perdeuterated Proteins	p. 6
Strategies for Sequence-Specific Resonance Assignment in High Molecular Weight Proteins	p. 13
Resonance Assignment of Large Proteins by 'Divide and Conquer'	p. 14
Resonance Assignment by Mutagenesis	p. 16
Time Frames for Resonance Aassignment of Methyl Groups in Very Large Proteins	p. 17
High Molecular Weight Protein Applications of Methyl-Specific Isotope-Labelling	p. 18
Conclusions and Future Directions	p. 18
Acknowledgements	p. 21
References	p. 22
Low-¿ Nuclei Detection Experiments for Biomolecular NMR	p. 25
Introduction	p. 25
Relaxation Properties of Low-¿ Nuclei	p. 28
Management of One-Bond Couplings in Low-¿ Detection Experiments	p. 31
C^¿-Detection Experiments for Main-Chain Resonance Assignments	p. 35
¹⁵N_H-Detection Experiments for Main-Chain Resonance Assignments	p. 43
Low-¿ Detection in Interaction Studies and Structure Determination	p. 46
Conclusion	p. 47
Acknowledgements	p. 48
References	p. 49
Making the Most of Chemical Shifts	p. 53
Introduction	p. 53
The Chemical Shift Tensor	p. 54
Referencing, Databases and Re-referencing	p. 56
Reference States and Secondary Chemical Shifts	p. 58
Detecting Structure and Flexibility	p. 60
Predicting Dihedral Angles	p. 63
Predicting Isotropic Chemical Shifts from Atomic Coordinates	p. 66
Predicting Tertiary Structure from Chemical Shifts	p. 69
Predicting Quaternary Structure from Chemical Shifts	p. 72
Conclusions	p. 76
Acknowledgements	p. 76
References	p. 76
Protein Structure Determination using Sparse NMR Data	p. 84
Introduction	p. 84
Force-Fields	p. 88
Introduction to Force-Fields	p. 88
Hybrid Molecular Mechanics Force-Fields	p. 88
The ROSETTA All-Atom Force-Field	p. 88
Relaxing the Structure	p. 90
ROSETTA All-Atom Force-Field Accuracy	p. 90
NMR Restraints	p. 92
Nuclear Overhauser Effect	p. 92
Residual Dipolar Coupling	p. 96
Paramagnetic Relaxation Enhancement	p. 97
Pseudo-Contact Chemical Shifts	p. 98
Chemical Shift	p. 99
Optimization Methods	p. 101
Challenges for Optimisation Methods	p. 101
Top-Down vs. Bottom-Up	p. 102
Resolution-Adapted Structural Recombination	p. 103
Concluding Remarks	p. 104
Acknowledgements	p. 105
References	p. 105
NMR Studies of Disordered but Functional Proteins	p. 111
Introduction	p. 111
NMR Methods Used for Disordered Proteins	p. 112
Coupled Folding and Binding	p. 112
Folded and Unfolded CBP Domains Bind IDP Partners	p. 113
The NF¿B-I¿B¿ Interaction: Fold/Unfold Symphony	p. 117
Binding Without Folding	p. 121
Partly Folded and Molten Globule-Like States	p. 121
Ankyrin Repeat Proteins	p. 121
Binding-Induced Molten Globule-Like States	p. 122
Functional Disorder in Folded States	p. 122
Sequence Specificity of Zinc-Finger Proteins	p. 122
Effects of Alternative Splicing	p. 124
Conclusions	p. 125
References	p. 125
Paramagnetic NMR Spectroscopy and Lowly Populated States	p. 130
Introduction	p. 130
Lowly Populated States and Paramagnetic NMR Spectroscopy	p. 130
Paramagnetic Centers	p. 131
Ensemble Modelling	p. 133
Residual Dipolar Coupling and Pseudo-Contact Shifts	p. 133
RDC Theory	p. 133
PCS Theory	p. 134
Applications for Studying Lowly Populated States	p. 135
Paramagnetic Relaxation Enhancement	p. 135
PRE Theory	p. 135
Applications for Studying Lowly Populated States	p. 138
Relaxation Dispersion	p. 142
RD Theory	p. 142
Applications for Studying Lowly Populated States	p. 144
Conclusion and Future Perspectives	p. 145
References	p. 145
NMR Relaxation Dispersion Studies of Large Enzymes in Solution	p. 151
Introduction	p. 151
Conformational Exchange	p. 152
The Benefits of TROSY	p. 155
¹H-¹⁵N TROSY	p. 155
Methyl-TROSY	p. 157
Isotopic Labelling Strategies	p. 159
Applications	p. 159
Imidazole Glycerol Phosphate Synthase	p. 159
Triosephosphate Isomerase	p. 161
Conclusions	p. 162
Acknowledgements	p. 162
References	p. 162
Residual Dipolar Couplings as a Tool for the Study of Protein Conformation and Conformational Flexibility	p. 166
Introduction	p. 166
Residual Dipolar Couplings as Probes of Protein Conformation	p. 168
Residual Dipolar Couplings for Structure Determination	p. 169
Residual Dipolar Couplings for the Study of Protein Dynamics	p. 170
Domain Dynamics	p. 171
Local Backbone Dynamics	p. 171
Conclusions	p. 180
References	p. 180
Characterising RNA Dynamics using NMR Residual Dipolar Couplings	p. 184
Introduction	p. 184
Residual Dipolar Coupling Theory	p. 185
The Dipolar Interaction	p. 185
The Alignment Tensor	p. 187
Partial Alignment of Nucleic Acids	p. 188
Ordering Media-Induced Alignment	p. 189
Magnetic-Field-Induced Alignment	p. 192
Measurement of RDCs in Nucleic Acids	p. 193
Dynamic Interpretation of RDCs Measured in RNA	p. 197
Dynamics Information Contained Within RDCs	p. 197
Decoupling Internal and Overall Motions by Domain Elongation	p. 199
Inter-Helical Motions from Order Tensor Analysis of RDCs	p. 201
Constructing Dynamic Ensembles	p. 202
Explicit Treatment of Motional Couplings	p. 204
Example Applications in Studies of RNA Dynamics From RDCs	p. 205
Summary and Future Perspectives	p. 208
Acknowledgements	p. 209
References	p. 209
Non-Canonical Ligand-Binding Events as Detected by NMR	p. 216
A Brief Refresher on NMR-Focussed Ligand Binding	p. 216
Ligand Binding Thermodynamics and Kinetics	p. 216
Ligand Binding and NMR	p. 218
The Proton Ligands to Inositol Hexakis Phosphate Take Five Instead of Three Log Units to Complete Binding	p. 221
The Binding of Inositol Hexakis Phosphate to Hemoglobin: Fast-Exchange Kinetics for Nanomolar Affinity	p. 226
Non-Canonical Line Broadening in Slow Exchange after Equivalence is Reached	p. 235
Binding of a 10 kDa Ligand to a 70 kDa Protein Does not Result in Significant Line Broadening of the NMR Signals of the 10 kDa Ligand	p. 242
A View From the DnaJ Perspective	p. 242
A View from the DnaK Perspective	p. 247
Relevance of the J-Domain-DnaK Complex	p. 248
Acknowledgements	p. 251
References	p. 252
Recent Advances in Biomolecular NMR for Drug Discovery	p. 254
Introduction	p. 254
NMR for Ligand Discovery	p. 255
Protein-Observed NMR	p. 255
Ligand-Observed NMR	p. 257
Hit Prioritisation	p. 261
Protein-Ligand Structures	p. 262
In-Cell NMR Spectroscopy	p. 266
Perspectives	p. 267
References	p. 267
NMR of Membrane Proteins	p. 271
Introduction	p. 271
Protein Expression	p. 273
Escherichia coli	p. 273
Yeast	p. 274
Baculovirus/Insect Expression	p. 275
Mammalian	p. 276
Cell-Free Expression	p. 276
Directed Evolution	p. 278
Membrane Mimics	p. 278
Detergents	p. 278
Fluorinated Surfactants	p. 283
Amphipols	p. 284
Problems with Micelles	p. 285
Nanolipoprotein Particles	p. 286
NMR Studies using Nanodiscs	p. 287
Bicelles	p. 287
Isotope-Labelling Strategies	p. 289
Structure Determination	p. 292
Paramagnetic Effects	p. 293
Residual Dipolar Couplings	p. 295
Chemical Shift Prediction	p. 297
NMR Method Development	p. 298
¹³C Direct Detection	p. 298
Alternative Sampling	p. 299
Functional Information	p. 300
Dynamics	p. 300
Variation of Experimental Conditions	p. 301
Ligand-Binding Studies	p. 301
Conclusions	p. 303
References	p. 304
Recent Developments in Biomolecular Solid-State NMR	p. 318
Introduction	p. 318
Samples	p. 319
Assignment Strategies	p. 322
Labelling Strategies	p. 322
Structure Determination	p. 323
Dynamics	p. 324
Static Solid-State NMR	p. 325
Proton Detection	p. 325
Ultra-Fast Spinning	p. 326
Dynamic Nuclear Polarisation	p. 326
Approaches Using Complementary Techniques	p. 328
Conclusions and Perspectives	p. 328
References	p. 329
Subject Index	p. 335
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Recent Developments in Biomolecular Nmr

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