Biological Magnetic Resonance
Volume 16
Modern Techniques in
Protein NMR
Edited by
N. Rama Krishna
University of Alabama at Birmingham
Birmingham, Alabama
and
Lawrence J. Berliner
Ohio State University
Columbus, Ohio
Contents
Section I. Large Proteins, Complexes, and Membrane Proteins
Chapter 1
Determining Structures of Large Proteins and Protein
Complexes by NMR
G. Marius Clore and Angela M. Gronenborn
1. Introduction ..................................................................................... 3
2. Basic Principles of Multidimensional NMR ................................... 4
3. The Nuclear Overhauser Effect ....................................................... 5
4. General Strategy for the Structure Determination of Proteins and
Protein Complexes by NMR ........................................................... 6
4.1. Sample Requirements for NMR Spectroscopy ..................... 6
4.2. Sequential Assignment .......................................................... 8
4.3. Stereospecific Assignments and Torsion-Angle
Restraints ............................................................................... 11
4.4. Assignment of Through-Space Proton– Proton Interactions
within a Protein ..................................................................... 14
4.5. Protein– Ligand and Protein– Protein Complexes ................ 15
5. Additional Methods of Structure Refinement ................................. 19
6. Long-Range Structural Restraints ................................................... 19
7. Perspectives and Concluding Remarks .......................................... 23
References ............................................................................................. 23
1. Introduction ....................................................................................................................... 27
1.1. Background: Deuteration prior to 1993 .................................................................. 27
1.2. Scope of This Review: Deuteration since 1993 ..................................................... 29
2. Deuterium Labeling Methods ............................................................................................ 32
2.1. Uniform Deuteration .............................................................................................. 33
2.2. Site-Specific Protonation in a Highly Deuterated
Environment ........................................................................................................... 34
2.3. Practical Aspects of Producing Deuterated Proteins in
E. coli ...................................................................................................................... 40
3. Triple-Resonance Methods ................................................................................................ 42
3.1. General Comments ................................................................................................. 42
3.2. Backbone Chemical Shift Assignment ................................................................... 44
3.3. Sidechain Chemical Shift Assignment ................................................................... 49
3.4. Deuterium Decoupling ........................................................................................... 50
3.5. The Use of Enhanced Sensitivity Pulsed Field Gradient
Coherence Transfer Methods for Experiments on Large
Deuterated Proteins ................................................................................................ 50
3.6. Deuterium Isotope Effects on 13C and 15N Chemical
Shifts ....................................................................................................................... 52
4. Impact of Deuteration on Structure Determination ........................................................... 55
4.1. Structure Determination of Perdeuterated Proteins ................................................ 55
4.2. Improving the Quality of Structures from Perdeuterated
Systems: Additional Distance Restraints ............................................................... 57
4.3. Improving the Quality of Structures from Highly
Deuterated Systems ................................................................................................ 62
5. Use of Deuteration to Study Protein Dynamics ................................................................ 66
6. Concluding Remarks ......................................................................................................... 69
References ................................................................................................................................ 69
1.1. Assignment and Structural Studies of Larger Proteins ............................................ 75
1.2. Deuteration .............................................................................................................. 77
2. Isotopic Labeling ................................................................................................................ 81
2.1. Perdeuteration Using Acetate .................................................................................. 81
2.2. Selective Protonation ............................................................................................... 85
3. Protein Assignment ............................................................................................................ 86
3.1. Backbone Assignment Using Perdeuterated Proteins..... ........................................ 86
3.2. Sidechain Assignments .......................................................................................... 101
3.3. 2H Isotope Shifts .................................................................................................... 104
3.4. Secondary Structure .............................................................................................. 105
4. Global Fold Determination ............................................................................................... 106
4.1. 4D 1HN–1HN NOESY .......................................................................................... 106
4.2. Structure Calculations ........................................................................................... 111
4.3. Selective Protonation ............................................................................................. 114
5. Concluding Remarks ........................................................................................................ 116
References ............................................................................................................................... 117
Chapter 4
Recent Developments in Multidimensional NMR Methods for Structural
Studies of Membrane Proteins
Francesca M. Marassi, Jennifer J. Gesell, and Stanley J. Opella
1. Introduction to the Structural Biology of Membrane Proteins ......................................... 121
2. Biological Expression and Chemical Synthesis of Proteins and
Peptides ............................................................................................................................ 123
3. Solution NMR Spectroscopy ............................................................................................ 125
3.1. Sample Preparation ................................................................................................ 125
3.2. Multidimensional Experiments for Spectral Resolution and
Resonance Assignment .......................................................................................... 126
3.3. Structure Determination from Distance and Torsion Angle
Constraints ............................................................................................................. 130
4. Solid-State NMR Spectroscopy ........................................................................................ 131
4.1. Solid-State NMR of Oriented Samples ................................................................. 131
4.2. Multidimensional Experiments for Spectral Resolution and
Resonance Assignment Strategies ......................................................................... 133
4.3. Structure Determination from Angular Constraints .............................................. 139
5. Summary and Future Prospects ........................................................................................ 141
References ............................................................................................................................... 143
Section II. Pulse Methods
Chapter 5
Homonuclear Decoupling in Proteins
Eriks Kupce, Hiroshi Matsuo, and Gerhard Wagner
1. Introduction ...................................................................................................................... 149
2. Basic Aspects of Spin Decoupling ................................................................................... 150
2.1. Coherent Decoupling ............................................................................................. 151
2.2. Band-Selective and Wide-Band Decoupling ........................................................ 153
2.3. Supercycles ............................................................................................................ 154
2.4. Decoupling Sidebands ......... ................................................................................. 155
2.5. Relaxation Effects ................................................................................................. 157
2.6. Decoupling at Several Frequencies ....................................................................... 159
3. Homonuclear Decoupling ................................................................................................. 160
3.1. Bloch– Siegert Effect .............................................................................................. 161
3.2. Modulation Sidebands ........................................................................................... 162
3.3. Decoupling Noise .................................................................................................. 165
3.4. Time-Shared Decoupling ....................................................................................... 166
4. Adiabatic Decoupling Waveforms .................................................................................... 168
4.1. The Adiabatic Condition ....................................................................................... 168
4.2. Constant-Adiabaticity Pulses ................................................................................ 169
5. Applications ...................................................................................................................... 172
5.1. H– H Decoupling .................................................................................................... 172
5.2. C– C Decoupling .................................................................................................... 174
6. Conclusions ...................................................................................................................... 191
References ............................................................................................................................... 192
Chapter 6
Pulse Sequences for Measuring Coupling Constants
Geerten W. Vuister, Marco Tessari,
Yasmin Karimi-Nejad, and Brian Whitehead
1. Introduction ...................................................................................................................... 195
2. Direct Methods for Measuring J Couplings ..................................................................... 196
3. The E.COSY Methods ...................................................................................................... 198
3.1. Explanation of the E.COSY Principle ................................................................... 198
3.2. Extraction of the J Value and Accuracy of the Method ......................................... 201
4. The Quantitative J Correlation Methods .......................................................................... 204
4.1. Spin-Echo-Based Quantitative J Correlation Schemes ......................................... 204
4.2. HMQC-Based Quantitative J Correlation Schemes .............................................. 206
4.3. COSY-Based Quantitative J Correlation Schemes ................................................ 208
4.4. Sources of Systematic Errors ................................................................................ 209
5. The Backbone Angle φ ...................................................................................................... 212
5.1. J Couplings Related to φ ........................................................................................ 213
5.2. The HNHA Experiment ......................................................................................... 216
5.3. The J-Modulated {1H– 15N}-COSY Experiment ................................................. 219
5.4. The HNCA[H α] Experiment ................................................................................. 220
5.5. The HN(CO)CO Experiment ................................................................................. 223
6. The Backbone Angle ψ ..................................................................................................... 225
7. The Sidechain Angles χ1 and χ2 ........................................................................................ 227
7.1. The HSQC-NOESY[N] Experiment ..................................................................... 228
7.2. The HNHB Experiment ......................................................................................... 232
7.3. The {13C’} and {15N} Spin-Echo Difference 13C CT-HSQC ..................................
Experiments ..................................................................................................... 233
7.4. The HACAHB Experiment ................................................................................... 237
7.5. The LRCC and LRCH Experiments ...................................................................... 240
8. Usage of J Couplings ....................................................................................................... 242
8.1. Parametrization of Karplus Curves ........................................................................ 243
8.2. Analysis of J Couplings in Proteins ...................................................................... 244
8.3. Application to the Photoactive Yellow Protein ...................................................... 249
9. Concluding Remarks ........................................................................................................ 252
References ............................................................................................................................... 254
Chapter 7
Methods for the Determination of Torsion Angle Restraints in
Biomacromolecules
C. Griesinger, M. Hennig, J. P. Marino, B. Reif, C. Richter, and H. Schwalbe
1. Introduction ...................................................................................................................... 259
1.1. Angular Dependence of NMR Observables ........................................................ 263
2. Determination of Torsion Angle Restraints in RNA......................................................... 272
2.1. Description of Conformations of Oligonucleotides .............................................. 274
2.2. Determination of Pseudorotation Phase P and Amplitude νmax
from 3J(H,H) Couplings ........................................................................................ 275
2.3. Determination of Exocyclic Torsion Angles ......................................................... 286
2.4. 19F-Labeled RNA Oligonucleotides ...................................................................... 298
3. Measurement of Scalar Coupling Constants in Perdeuterated
Proteins ........................................................................................................... 304
3.1. Determination of the Backbone Angle φ in Perdeuterated
Proteins ................................................................................................. 306
3.2. Determination of the Backbone Angle ψ in Perdeuterated
Proteins ................................................................................................. 317
3.3. Determination of the Sidechain Angle χl in Perdeuterated
Proteins ................................................................................................. 318
3.4. Determination of the Sidechain Angle χ2 in Perdeuterated
Proteins ................................................................................................. 330
4. Cross-Correlated Relaxation for the Measurement of Angles Between
Bond Vectors .................................................................................................. 334
4.1. Theoretical Description ......................................................................... 334
4.2. Application of Cross-Correlated Relaxation to High-Resolution
NMR as a Tool to Obtain Structural Information ................................. 340
4.3. Cross-Correlated Relaxation of Zero and Double Quantum
Coherences ............................................................................................ 341
4.4. Practical Extraction Procedure .............................................................. 348
4.5. Constant-Time versus Real-Time Evolution ......................................... 350
4.6. Nonsecular Terms in the DQ/ZQ Relaxation Matrix ............................ 351
4.7. Experimental Implementation ............................................................... 354
References ............................................................................................................ 362
Contents of Previous Volumes ..................................................................................... 369
Index .............................................................................................................................. 383
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