Protein NMR Spectroscopy
Practical Techniques and Applications
1. Edition July 2011
366 Pages, Hardcover
Practical Approach Book
Nuclear Magnetic Resonance (NMR) spectroscopy is a powerful technique in structural biology for obtaining high resolution 3-D structures of proteins, second only, and complementary to X-ray crystallography. Molecules are studied in solution, where conditions are closer to what is found in the cell. It is the primary technique used to obtain information on intrinsically disordered (unfolded) proteins, since these proteins will not crystallize easily.
The aim of this book is to provide the newcomer to NMR techniques with practical guidance on how to choose the right experiment, how to carry out the experiment, and how to analyse the resulting spectra. Those who are familiar with the chemical applications of NMR will also find it helpful in describing the special requirements of proteins.
Introduction 1
Lu-Yun Lian and Gordon Roberts
References 4
1 Sample Preparation, Data Collection and Processing 5
Frederick W. Muskett
1.1 Introduction 5
1.2 Sample Preparation 5
1.3 Data Collection 11
1.4 Data Processing 17
2 Isotope Labelling 23
Mitsuhiro Takeda and Masatsune Kainosho
2.1 Introduction 23
2.2 Production Methods for Isotopically Labelled Proteins 24
2.3 Uniform Isotope Labelling of Proteins 29
2.4 Selective Isotope Labelling of Proteins 32
2.5 Segmental Labelling 37
2.6 SAIL Methods 38
2.7 Concluding Remarks 45
3 Resonance Assignments 55
Lu-Yun Lian and Igor L. Barsukov
3.1 Introduction 55
3.2 Resonance Assignment of Unlabelled Proteins 56
3.3 15N-Edited Experiments 60
3.4 Triple Resonance 62
3.5 Side-Chain Assignments 77
4 Measurement of Structural Restraints 83
Geerten W. Vuister, Nico Tjandra, Yang Shen, Alex Grishaev and Stephan Grzesiek
4.1 Introduction 83
4.2 NOE-Based Distance Restraints 84
4.3 Dihedral Restraints Derived from J-Couplings 96
4.4 Hydrogen Bond Restraints 103
4.5 Orientational Restraints 107
4.6 Chemical Shift Structural Restraints 129
4.7 Solution Scattering Restraints 137
5 Calculation of Structures from NMR Restraints 159
Peter Guntert
5.1 Introduction 159
5.2 Historical Development 161
5.3 Structure Calculation Algorithms 164
5.4 Automated NOE Assignment 173
5.5 Nonclassical Approaches 178
5.6 Fully Automated Structure Analysis 181
6 Paramagnetic Tools in Protein NMR 193
Peter H.J. Keizers and Marcellus Ubbink
6.1 Introduction 193
6.2 Types of Restraints 194
6.3 What Metals to Use? 200
6.4 Paramagnetic Probes 203
6.5 Examples 209
6.6 Conclusions and Perspective 212
7 Structural and Dynamic Information on Ligand Binding 221
Gordon Roberts
7.1 Introduction 221
7.2 Fundamentals of Exchange Effects on NMR Spectra 222
7.3 Measurement of Equilibrium and Rate Constants 229
7.4 Detecting Binding - NMR Screening 238
7.5 Mechanistic Information 241
7.6 Structural Information 246
8 Macromolecular Complexes 269
Paul C. Driscoll
8.1 Introduction 269
8.2 Spectral Simplification through Differential Isotope Labelling 270
8.3 Basic NMR Characterisation of Complexes 273
8.4 3D Structure Determination of Macromolecular Protein-Ligand Complexes 277
8.5 Literature Examples 297
9 Studying Partially Folded and Intrinsically Disordered Proteins Using NMR Residual Dipolar Couplings 319
Malene Ringkjøbing Jensen, Valery Ozenne, Loic Salmon, Gabrielle Nodet, Phineus Markwick, Pau Bernado´ and Martin Blackledge
9.1 Introduction 319
9.2 Ensemble Descriptions of Unfolded Proteins 320
9.3 Experimental Techniques for the Characterisation of IDPs 320
9.4 NMR Spectroscopy of Intrinsically Disordered Proteins 321
9.5 Residual Dipolar Couplings 323
9.6 Conclusions 340
References 340
Index 347
