|
Member of the Editorial Board |
5 |
|
|
Preface |
6 |
|
|
Acknowledgements |
8 |
|
|
Contents |
9 |
|
|
Methodology |
11 |
|
|
1 Protein Studies by High-Pressure NMR |
12 |
|
|
Abstract |
12 |
|
|
1.1 Introduction |
12 |
|
|
1.1.1 The NMR Spectroscopy and Its Limitation |
13 |
|
|
1.1.2 Overcoming the Limitation with Pressure |
15 |
|
|
1.1.3 Turning NMR “Invisible” Conformers into NMR “Visible” with Pressure |
16 |
|
|
1.2 The Thermodynamic Background |
19 |
|
|
1.2.1 Effect of Pressure on the Protein Conformational Equilibrium |
19 |
|
|
1.2.2 “Volume” Decreases as “Cavity” Hydration Increases |
21 |
|
|
1.2.3 The “Volume ??Theorem”?? of Protein and the High-Pressure NMR Experiment |
23 |
|
|
1.3 Apparatus for High-Pressure NMR Experiments |
24 |
|
|
1.3.1 The Autoclave Method |
25 |
|
|
1.3.2 The Pressure-Resisting Cell Method |
25 |
|
|
1.4 Application to Protein Studies |
28 |
|
|
1.4.1 Fluctuations within the Basic Folded Ensemble |
29 |
|
|
1.4.1.1 Fluctuation in Individual Hydrogen Bonds Detected by 1H Pressure Shifts |
30 |
|
|
1.4.1.2 Residue-Specific Fluctuations of the Polypeptide Chain Conformation Detected by 15N/1H Pressure Shifts |
32 |
|
|
1.4.1.3 Slow Cooperative Fluctuations Detected by Ring-Flip Motions |
34 |
|
|
1.4.2 Fluctuations into Alternately Folded Conformer |
35 |
|
|
1.4.3 Conformational Fluctuations Involving Fibril Formation and Dissociation |
35 |
|
|
1.4.3.1 Cause for Familial Amyloidotic Polyneuropathy |
36 |
|
|
1.4.3.2 Conformational Fluctuations in Prion Protein and Drugs to Prevent Fibrillation |
37 |
|
|
1.4.3.3 Amyloid Fibril Is a High-Volume State |
39 |
|
|
1.4.3.4 Fibril Formation Is Part of the Intrinsic Conformational Fluctuation of Proteins |
39 |
|
|
1.4.4 Exploring the Protein Folding Pathway with High-Pressure NMR |
40 |
|
|
1.5 Summary: Perspectives of High-Pressure NMR Spectroscopy |
41 |
|
|
References |
42 |
|
|
2 Isotope-Aided Methods for Biological NMR Spectroscopy: Past, Present, and Future |
46 |
|
|
Abstract |
46 |
|
|
2.1 Historical Background of Our Research to Develop Isotope-Aided NMR Methods |
47 |
|
|
2.1.1 Stereo-Specific Deuteration of Prochiral Methylene Protons—Conformational Analysis of Amino Acids and Peptides |
48 |
|
|
2.1.2 Selective 13C, 15N Double-Labeling Method for the Sequential Assignment of Backbone Amide NMR Signals in Large Proteins |
49 |
|
|
2.1.3 Revisiting the Stereo-Specific Isotope-Labeling Approach for Studying Proteins: A Long March to the SAIL Method |
51 |
|
|
2.2 The SAIL Method: An Optimized Isotope-Labeling Strategy for the Structural Study of Proteins by NMR Spectroscopy |
51 |
|
|
2.2.1 Cell-Free Expression and NMR Spectra of SAIL Proteins |
53 |
|
|
2.2.2 Structural Determination of SAIL Proteins |
56 |
|
|
2.3 Recent Trends in the Isotope-Aided NMR Methods for Studying Proteins |
58 |
|
|
2.3.1 Residue- and Stereo-Specific Labeling Method: The Case for Leu and Val Methyl Labeling of Larger Proteins |
59 |
|
|
2.3.2 Large-Amplitude Dynamics of Proteins as Probed by Aromatic Ring-Flipping Motions—The Case for the Interface Between FKBP and Drug Complexes |
61 |
|
|
2.3.3 Deuterium-Induced Isotope Shifts for Measuring Hydrogen Exchange Rates of Polar Side-Chain Groups in Proteins: Facile Screening of the Polar Groups Involved in Hydrogen Bond Networks |
64 |
|
|
2.4 Future Perspectives of the Isotope-Aided NMR Method |
66 |
|
|
Acknowledgements |
66 |
|
|
References |
67 |
|
|
3 Advances in NMR Data Acquisition and Processing for Protein Structure Determination |
71 |
|
|
Abstract |
71 |
|
|
3.1 Advances in Processing of Multi-dimensional NMR Spectra, and Their Application to Rapid NMR Measurements |
72 |
|
|
3.1.1 Multi-dimensional NMR Takes Time |
72 |
|
|
3.1.2 Processing of Multi-dimensional NMR Spectra |
73 |
|
|
3.1.3 Rapid Measurement of Multi-dimensional NMR Spectra |
75 |
|
|
3.1.4 Non-uniform Sampling |
76 |
|
|
3.1.5 NUS Sampling Schemes |
77 |
|
|
3.1.6 Semi-constant-Time Evolution Periods |
79 |
|
|
3.1.7 Conclusions |
82 |
|
|
3.2 Data Analysis for Protein Structure Determination |
82 |
|
|
3.2.1 Chemical Shift Data Analysis |
82 |
|
|
3.2.2 NOE Data Analysis |
85 |
|
|
3.2.3 NMR Protein Structure Determination Based on Bayesian Inference |
88 |
|
|
3.2.4 Hybrid Method with Small-Angle Scattering (SAS) |
92 |
|
|
3.2.5 Conclusions |
94 |
|
|
Acknowledgements |
94 |
|
|
References |
95 |
|
|
4 Advances in High-Field DNP Methods |
99 |
|
|
Abstract |
99 |
|
|
4.1 Introduction |
100 |
|
|
4.2 Overview of a DNP-NMR System |
101 |
|
|
4.3 DNP Mechanisms and Polarizing Agents |
101 |
|
|
4.4 SMMW Sources and Transmission Systems |
107 |
|
|
4.4.1 Various Light Sources and Gyrotron |
107 |
|
|
4.4.2 Principles of Gyrotron |
109 |
|
|
4.4.3 Operation of Gyrotron |
112 |
|
|
4.4.4 Transmission of SMMW |
116 |
|
|
4.4.5 Feedback Regulation of SMMW |
117 |
|
|
4.4.6 Double SMMW Irradiation |
119 |
|
|
4.5 DNP-NMR Probes and Low-Temperature Facilities |
120 |
|
|
4.5.1 MAS at Cryogenic Temperatures |
120 |
|
|
4.5.2 SMMW Irradiation of Sample |
122 |
|
|
4.5.3 Production of Cryogenic Spinner Gas |
125 |
|
|
4.6 DNP Samples and Recent Applications |
128 |
|
|
4.6.1 Basic Setup |
128 |
|
|
4.6.2 Sample Preparation and DNP Efficiency |
130 |
|
|
4.6.3 DNP Enhancement Factor and Temperature |
134 |
|
|
4.7 Summary and Outlook |
135 |
|
|
Acknowledgements |
136 |
|
|
References |
136 |
|
|
5 Photoirradiation and Microwave Irradiation NMR Spectroscopy |
143 |
|
|
Abstract |
143 |
|
|
5.1 Introduction |
144 |
|
|
5.1.1 Photoirradiation Solid-State NMR Spectroscopy |
144 |
|
|
5.1.2 Microwave Irradiation NMR Spectroscopy |
145 |
|
|
5.2 Experimental Details for Photoirradiation Solid-State NMR Spectroscopy |
146 |
|
|
5.2.1 Photoirradiation System for Solid-State NMR |
146 |
|
|
5.2.2 Photoirradiation NMR Measurements |
146 |
|
|
5.2.3 Detection of Photo-Intermediates in the Photoreaction Cycles |
147 |
|
|
5.3 Photoreaction Cycle for SRI as Revealed by In Situ Photoirradiation Solid-State NMR |
148 |
|
|
5.4 The Photoreaction Cycle of Pharaonis Phoborhodopsin (SRII) as Revealed by Photoirradiation Solid-State NMR Spectroscopy |
152 |
|
|
5.5 The Photoreaction Pathway for the Bacteriorhodopsin Y185F Mutant |
154 |
|
|
5.6 Experimental Details for Microwave Irradiation NMR Spectroscopy |
156 |
|
|
5.6.1 In Situ Microwave Irradiation NMR Spectrometer |
156 |
|
|
5.6.2 Temperature Measurements |
157 |
|
|
5.6.3 Microwave Temperature Jump Experiments |
158 |
|
|
5.7 Microwave Heating Effect of MBBA |
159 |
|
|
5.7.1 Microwave Heating Effect of MBBA in the Liquid Crystalline State |
159 |
|
|
5.7.2 Microwave Heating Effect of MBBA in the Isotropic State |
160 |
|
|
5.7.3 Mechanism for Microwave Heating of Liquid Crystalline MBBA |
162 |
|
|
5.7.4 Mechanism for Microwave Heating of Isotropic Phase MBBA |
163 |
|
|
5.8 Experimental Details for SC-2D NMR Spectroscopy |
164 |
|
|
5.9 SC-2D NMR Spectra of Liquid Crystalline Samples |
165 |
|
|
5.9.1 SC-2D NMR Measurements of APAPA |
165 |
|
|
5.9.2 Interpretation of the Cross-sectional Spectra from SC-2D NMR Experiments |
168 |
|
|
5.9.3 Interpretation of the Dipolar Patterns of the Aromatic and Methyl Protons |
170 |
|
|
5.9.4 Interpretation of the Cross-Sectional Patterns |
171 |
|
|
5.10 Conclusions |
173 |
|
|
Acknowledgements |
174 |
|
|
References |
174 |
|
|
6 Solid-State NMR Under Ultrafast MAS Rate of 40–120 kHz |
179 |
|
|
Abstract |
179 |
|
|
6.1 Overview |
179 |
|
|
6.2 Setup of Sample-independent Factors |
182 |
|
|
6.2.1 Shimming |
182 |
|
|
6.2.2 Magic-Angle Adjustment |
184 |
|
|
6.2.3 rf Field Strength Calibration |
185 |
|
|
6.2.4 Reference |
187 |
|
|
6.3 Sample-Dependent Setup |
188 |
|
|
6.3.1 Relaxation Delay |
188 |
|
|
6.3.2 Hardware Treatment |
191 |
|
|
6.4 Setup of 2D Measurements |
192 |
|
|
6.4.1 1H DQ/SQ Correlation |
192 |
|
|
6.4.2 1H-detected 1H/X CP-HSQC |
196 |
|
|
6.5 Conclusions |
198 |
|
|
Acknowledgements |
199 |
|
|
References |
199 |
|
|
7 Elucidating Functional Dynamics by R1? and R2 Relaxation Dispersion NMR Spectroscopy |
204 |
|
|
Abstract |
204 |
|
|
7.1 Relaxation Dispersion |
205 |
|
|
7.2 Accessible Information |
206 |
|
|
7.3 R1? Relaxation Dispersion |
207 |
|
|
7.3.1 General Aspects |
207 |
|
|
7.3.2 Pulse Sequence of the R1? Relaxation Dispersion Experiment |
208 |
|
|
7.3.3 Automation of R1? Relaxation Dispersion Measurements and Data Processing |
211 |
|
|
7.3.3.1 Experimental Setup |
211 |
|
|
7.3.3.2 Screening |
212 |
|
|
7.3.3.3 Processing |
213 |
|
|
7.4 R2 Relaxation Dispersion |
214 |
|
|
7.4.1 General Aspects |
214 |
|
|
7.4.2 Quantifying Protein–Ligand Interactions by R2 Relaxation Dispersion |
215 |
|
|
7.4.2.1 Theory |
216 |
|
|
7.4.2.2 Example 1: Interaction Between the pKID Domain of CREB and the KIX Domain of CBP/p300 |
217 |
|
|
7.4.2.3 Example 2: Interaction Between the Transactivation Domain of c-Myb and KIX |
219 |
|
|
7.5 Fitting of the Relaxation Rates to a Theoretical Model |
219 |
|
|
7.5.1 Least-Squares Fitting in GLOVE |
219 |
|
|
7.5.2 Monte Carlo Minimization Algorithm in GLOVE |
221 |
|
|
7.5.3 Two-State Exchange |
221 |
|
|
7.5.4 Workflow for Processing Relaxation Dispersion Data in GLOVE |
223 |
|
|
7.5.5 Examples of Relaxation Dispersion Curve Fitting by GLOVE |
224 |
|
|
7.6 Outlook |
226 |
|
|
References |
227 |
|
|
8 Structural Study of Proteins by Paramagnetic Lanthanide Probe Methods |
233 |
|
|
Abstract |
233 |
|
|
8.1 Introduction |
234 |
|
|
8.2 Structural Information Obtained from Paramagnetic Lanthanide Probe Methods |
234 |
|
|
8.2.1 Pseudocontact Shift (PCS) |
235 |
|
|
8.2.2 Residual Dipolar Coupling (RDC) |
235 |
|
|
8.2.3 Paramagnetic Relaxation Enhancement (PRE) |
237 |
|
|
8.3 Various Magnetic Properties of Lanthanide Ions |
238 |
|
|
8.4 Application of the Paramagnetic Lanthanide Probe in Protein Structural Studies |
239 |
|
|
8.4.1 Caged Lanthanide NMR Probe 5 (CLaNP-5) |
240 |
|
|
8.4.2 Two-Point Anchored Lanthanide-Binding Peptide Tag (LBT) |
241 |
|
|
8.5 Measurement and Analysis of Anisotropic Paramagnetic Effects |
245 |
|
|
8.6 Use of Paramagnetic Effects in Protein Structural Studies |
246 |
|
|
8.6.1 PCS-Based Docking for Protein–Protein Complexes |
246 |
|
|
8.6.2 Evaluation of the Conformational Changes in a Multi-domain Protein |
248 |
|
|
8.6.3 Further Applications of Paramagnetic Lanthanide Probe Methods |
249 |
|
|
8.7 Concluding Remarks |
251 |
|
|
Acknowledgements |
252 |
|
|
References |
252 |
|
|
9 Structure Determination of Membrane Peptides and Proteins by Solid-State NMR |
259 |
|
|
Abstract |
259 |
|
|
9.1 Introduction |
260 |
|
|
9.2 Experimental Approaches Used in Solid-State NMR Spectroscopy |
260 |
|
|
9.2.1 Experimental Details for Obtaining the Structures of Membrane-Associated Peptides and Proteins Using Anisotropic Interactions |
261 |
|
|
9.2.1.1 Orientation Dependence of Chemical-Shift Interaction |
261 |
|
|
9.2.1.2 Orientation Dependence of Nuclear Dipolar Interactions |
266 |
|
|
9.2.1.3 Interatomic Distance Measurements by REDOR |
267 |
|
|
Simple Description of the REDOR Experiment |
267 |
|
|
Rotational Echo Amplitude by the Density Operator Approach |
269 |
|
|
Echo Amplitude in Three-Spin System (S1-I1-S2) |
271 |
|
|
Practical Aspects of a REDOR Experiment |
272 |
|
|
9.2.2 Magic-Angle Spinning NMR |
274 |
|
|
9.2.2.1 CP-MAS NMR |
274 |
|
|
9.2.2.2 Correlation NMR Spectroscopy |
275 |
|
|
9.2.2.3 PDSD and DARR 2D NMR Spectroscopy |
275 |
|
|
9.3 Structure Determination of Membrane-Bound Peptides |
277 |
|
|
9.3.1 Melittin |
277 |
|
|
9.3.2 Alamethicin |
283 |
|
|
9.3.3 Bovine Lactoferrampin |
284 |
|
|
9.4 Structure Determination of Membrane Proteins |
287 |
|
|
9.5 Conclusion |
291 |
|
|
Acknowledgements |
293 |
|
|
References |
293 |
|
|
Application to Life Science and Materials Science |
300 |
|
|
10 NMR Studies on Silk Materials |
301 |
|
|
Abstract |
301 |
|
|
10.1 Introduction |
301 |
|
|
10.2 Results and Discussion |
302 |
|
|
10.2.1 Dynamics of Silk Fibroin Stored in Living Silkworm |
302 |
|
|
10.2.2 Solution Structure of Silk Fibroin at Atomic Level |
304 |
|
|
10.2.3 Dynamics of Water Molecules Interacted with Silk Fibroin |
305 |
|
|
10.2.4 Dynamics of Hydrated Silk Cocoon, Sericin, and Fibroin |
307 |
|
|
10.2.5 Fraction of Several Conformations of Silk Fibroin |
308 |
|
|
10.2.6 Domain of Silk Fibroin |
309 |
|
|
10.2.7 Inter-molecular Arrangement of Alanine Oligopeptide |
310 |
|
|
10.2.8 Complex between Silk Fibroin and Glycerin |
310 |
|
|
10.2.9 Use of Chemical Shift Calculation for Verification of Silk Fibroin Structural Model |
312 |
|
|
10.3 Conclusion |
313 |
|
|
References |
314 |
|
|
11 NMR Studies on Polymer Materials |
317 |
|
|
Abstract |
317 |
|
|
11.1 Introduction |
318 |
|
|
11.2 Polymer Blends and Alloys |
318 |
|
|
11.2.1 Miscibility and Mobile Heterogeneity |
318 |
|
|
11.2.1.1 PS/PVME Blends |
320 |
|
|
11.2.1.2 PMAA/PVAc Blends |
323 |
|
|
11.2.1.3 PK/PA Alloys |
325 |
|
|
11.2.2 Phase Separation |
328 |
|
|
11.2.2.1 PS/PVME Blends |
328 |
|
|
11.2.2.2 P3HT/PCBM Blends |
330 |
|
|
11.3 Polymer Nanocomposites |
332 |
|
|
11.3.1 Paramagnetic Effect on Relaxation |
332 |
|
|
11.3.1.1 PVA/Montmorillonite Clay Nanocomposites |
332 |
|
|
11.3.1.2 Nylon-6/mmt Nanocomposites |
333 |
|
|
11.3.2 Interaction Between Polymers and Fillers |
334 |
|
|
11.3.2.1 Nylon-6/Montmorillonite Clay Nanocomposites |
334 |
|
|
11.3.2.2 PS-PEO Block Copolymer/Hectorite Clay Nanocomposites |
335 |
|
|
11.3.3 Morphology |
336 |
|
|
11.3.3.1 PVIBE/?-PL/Saponite Clay Blends |
336 |
|
|
11.3.3.2 Nylon-6/Montmorillonite Clay Nanocomposites |
337 |
|
|
11.4 Rubbers and Elastomers |
339 |
|
|
11.5 Conclusion |
340 |
|
|
References |
341 |
|
|
12 Solid-State 2H NMR Studies of Molecular Motion in Functional Materials |
344 |
|
|
Abstract |
344 |
|
|
12.1 Introduction |
345 |
|
|
12.2 Measurements of Solid-State 2H NMR Spectrum |
345 |
|
|
12.3 Simulation Methods of Solid-State 2H NMR Spectrum |
347 |
|
|
12.4 Analysis of MOF/PCP |
354 |
|
|
12.5 Analysis of Solid Proton-Conducting Material |
356 |
|
|
12.6 Analysis of Spin-Crossover Material |
361 |
|
|
12.7 Summary |
365 |
|
|
References |
366 |
|
|
13 NMR Spectral Observations of the Gases in Polymer Materials |
368 |
|
|
Abstract |
368 |
|
|
13.1 Introduction |
368 |
|
|
13.2 Basics of the NMR Analysis of Gas–Polymer Systems |
369 |
|
|
13.2.1 Apparatus for the Preparation of NMR Sample Tubes Containing High-Pressure Gas Samples |
369 |
|
|
13.2.2 Gas Sorption Properties of Polymers |
370 |
|
|
13.3 Characterization of the High-Order Structure of a Glassy Polymer Based on 129Xe NMR Chemical Shifts |
372 |
|
|
13.4 Characterization of the High-Order Structure of Rubbery Polymers from 129Xe NMR Chemical Shifts |
374 |
|
|
13.5 Analysis of Gas Diffusion Characteristics in Polymers Based on NMR Peak Width |
376 |
|
|
13.6 Characterization of Oriented Structures by Pulsed Field Gradient NMR |
379 |
|
|
13.7 Summary |
382 |
|
|
References |
382 |
|
|
14 NMR Studies on Natural Product—Stereochemical Determination and Conformational Analysis in Solution and in Membrane |
385 |
|
|
Abstract |
385 |
|
|
14.1 Stereochemical Determination of Natural Products |
386 |
|
|
14.1.1 JBCA Method |
387 |
|
|
14.1.2 UDB Method |
392 |
|
|
14.1.3 Calculations |
394 |
|
|
14.1.4 RDCs |
398 |
|
|
14.2 NMR Methods for Examining the Conformation and Intermolecular Interactions of Natural Products in Membranes |
401 |
|
|
14.2.1 Amphotericin B |
402 |
|
|
14.2.2 Erythromycin A |
406 |
|
|
14.2.3 Theonellamide A |
407 |
|
|
14.3 Summary and Outlook |
412 |
|
|
Acknowledgements |
412 |
|
|
References |
412 |
|
|
15 Technical Basis for Nuclear Magnetic Resonance Approach for Glycoproteins |
417 |
|
|
Abstract |
417 |
|
|
15.1 Introduction |
418 |
|
|
15.2 Enigmatic Aspects of Carbohydrate Structures |
418 |
|
|
15.3 Expression of Isotope-Labeled Glycoproteins |
420 |
|
|
15.4 Glycosylation Profiling |
425 |
|
|
15.5 Remodeling of Glycoprotein Glycoforms |
426 |
|
|
15.6 Spectral Observations and Assignments |
430 |
|
|
15.7 NMR Analyses of Dynamic Conformations and Interactions of Oligosaccharides |
432 |
|
|
15.8 Perspectives |
434 |
|
|
Acknowledgements |
435 |
|
|
References |
435 |
|
|
16 NMR Studies on RNA |
441 |
|
|
Abstract |
441 |
|
|
16.1 Design of RNA Sequences |
441 |
|
|
16.2 Sample Preparation |
442 |
|
|
16.2.1 In Vitro Transcription |
444 |
|
|
16.2.2 Chemical Synthesis |
444 |
|
|
16.2.3 Enzymatic Ligation |
445 |
|
|
16.2.4 Artificial Base Pair System |
445 |
|
|
16.2.5 Stable Isotopic Labelling |
446 |
|
|
16.2.6 Purification |
446 |
|
|
16.3 Measurements |
447 |
|
|
16.3.1 Exchangeable Protons |
447 |
|
|
16.3.2 Non-exchangeable Protons |
449 |
|
|
16.3.3 Residual Dipolar Coupling |
449 |
|
|
16.4 Signal Assignments |
451 |
|
|
16.4.1 Exchangeable Protons |
451 |
|
|
16.4.2 Non-exchangeable Protons |
451 |
|
|
16.5 Structural Calculation |
455 |
|
|
16.6 Interaction Analysis and Structure Screening |
457 |
|
|
16.7 Perspective |
459 |
|
|
References |
459 |
|
|
17 NMR Analysis of Molecular Complexity |
462 |
|
|
Abstract |
462 |
|
|
17.1 Introduction |
463 |
|
|
17.2 Metabolomics and Metabolic Profiling for Small Molecular Complexity |
463 |
|
|
17.2.1 Basic Knowledge for Small Molecular Profiling |
463 |
|
|
17.2.2 Experimental Aspects of Sample Preparation |
464 |
|
|
17.2.3 NMR Measurements and Data Processing |
466 |
|
|
17.2.3.1 Useful Pulse Sequences |
466 |
|
|
17.2.3.2 Databases and Tools for NMR Analysis |
467 |
|
|
17.2.3.3 Signal Assignments and Structure Elucidation |
467 |
|
|
17.2.3.4 Spectral Pretreatment for Data Science |
470 |
|
|
17.2.3.5 Practical Aspects of Data Science |
471 |
|
|
17.2.4 Applications to Plant, Animal, and Microbial Systems |
471 |
|
|
17.2.4.1 Application to Plant Systems |
471 |
|
|
17.2.4.2 Application to Animal Systems |
472 |
|
|
17.2.4.3 Application to Microbial Systems |
473 |
|
|
17.3 Biomass Profiling for Macromolecular Complexity |
474 |
|
|
17.3.1 Basic Knowledge for Macromolecular Profiling |
474 |
|
|
17.3.2 Experimental Aspects of Sample Preparation |
474 |
|
|
17.3.3 NMR Measurements and Data Processing |
476 |
|
|
17.3.3.1 Useful Pulse Sequences |
476 |
|
|
Peak Separation for Broad Macromolecular Spectra |
478 |
|
|
17.3.4 Applications to Material, Biological, and Geochemical Systems |
479 |
|
|
17.3.4.1 Application to Cellulosic Material Systems |
479 |
|
|
17.3.4.2 Application to Biological Systems |
480 |
|
|
17.3.4.3 Application to Geochemical Samples |
482 |
|
|
17.4 Future Perspectives |
483 |
|
|
References |
483 |
|
|
18 NMR of Paramagnetic Compounds |
491 |
|
|
Abstract |
491 |
|
|
18.1 Introduction |
491 |
|
|
18.2 Paramagnetic Effects |
494 |
|
|
18.2.1 Paramagnetic Shifts |
494 |
|
|
18.2.2 Paramagnetic Relaxation |
495 |
|
|
18.3 1H NMR Spectra of Myoglobin with 0, 1, 4, or 5 Unpaired Electrons |
498 |
|
|
18.3.1 Overview |
498 |
|
|
18.3.2 Diamagnetic Carbonmonoxy Form [Mb(CO)] |
499 |
|
|
18.3.3 Paramagnetic Deoxy Form (Deoxy Mb) with S = 2 |
499 |
|
|
18.3.4 Paramagnetic Met-Cyano Form [MetMb(CN?)] with S = ½ |
502 |
|
|
18.3.5 Paramagnetic Met-Azido Form [MetMb(N3?)] with Mainly S = ½ |
504 |
|
|
18.3.6 Paramagnetic Met-Aquo Form [MetMb(H2O)] with S = 5/2 |
505 |
|
|
18.4 NMR Measurements |
506 |
|
|
18.4.1 NOEs in Paramagnetic Compounds |
506 |
|
|
18.4.2 Hydrogen Exchange Rates |
509 |
|
|
18.5 Concluding Remarks |
512 |
|
|
Acknowledgements |
513 |
|
|
References |
513 |
|
|
19 NMR of Quadrupole Nuclei in Organic Compounds |
519 |
|
|
Abstract |
519 |
|
|
19.1 Introduction |
519 |
|
|
19.2 Theoretical Background of Quadrupole Interactions |
520 |
|
|
19.3 Simulating Solid-State NMR of Quadrupole Nuclei Based on the Perturbation Method |
522 |
|
|
19.3.1 Stationary NMR Spectra Under the Influence of Second-Order Quadrupole Interactions |
524 |
|
|
19.3.2 Fast MAS NMR Conditions Under the Influence of Second-Order Quadrupole and CS Interactions |
527 |
|
|
19.3.3 Stationary NMR Spectra Under the Influence of Second-Order Quadrupole and CS Interactions |
530 |
|
|
19.4 Solid-State NMR of Quadrupole Nuclei Based on Direct Calculation Methods |
534 |
|
|
19.5 Conclusions |
541 |
|
|
References |
542 |
|
|
20 Quadrupole Nuclei in Inorganic Materials |
544 |
|
|
Abstract |
544 |
|
|
20.1 Introduction |
545 |
|
|
20.2 Anisotropy of Quadrupolar Interaction |
546 |
|
|
20.3 Orientation Dependence of Quadrupolar Interaction |
552 |
|
|
20.4 Signal Separation Through Quadrupolar Coupling |
557 |
|
|
20.4.1 MQMAS |
558 |
|
|
20.4.2 STMAS |
561 |
|
|
20.5 Signal Separation Through Correlations to Other Nuclei |
561 |
|
|
20.6 Sensitivity Enhancement Through Population Transfer |
565 |
|
|
20.7 Confronting the Real World, Real Materials |
567 |
|
|
Acknowl?edge??ments |
572 |
|
|
References |
572 |
|
|
21 Protein–Ligand Interactions Studied by NMR |
577 |
|
|
Abstract |
577 |
|
|
21.1 Overview |
578 |
|
|
21.2 Ligand-Based Approach |
578 |
|
|
21.2.1 Ligand Screening |
581 |
|
|
21.2.1.1 Saturation Transfer Difference (STD) |
581 |
|
|
21.2.1.2 WaterLOGSY |
581 |
|
|
21.2.1.3 STD Versus WaterLOGSY |
582 |
|
|
21.2.2 Pharmacophore Determination |
582 |
|
|
21.2.2.1 DIRECTION |
583 |
|
|
21.2.2.2 INPHARMA |
583 |
|
|
21.2.3 Structural Information-Driven Ligand Design |
584 |
|
|
21.2.3.1 Inter-ligand Nuclear Overhauser Effect (ILOE) |
585 |
|
|
21.2.3.2 Transferred Nuclear Overhauser Effect (trNOE) |
585 |
|
|
21.2.3.3 Technical Comments on INPHARMA, ILOE and trNOE Experiments |
586 |
|
|
21.3 Protein-Based Approach for Protein–Ligand Interactions |
586 |
|
|
21.3.1 Ligand Screening and NMR-Assisted Fragment-Based Drug Discovery |
588 |
|
|
21.3.1.1 HSQC-Based Ligand Screening |
588 |
|
|
21.3.1.2 SAR-by-NMR |
589 |
|
|
21.3.2 Determination of the Molecular Interface and Exploring the Mode of Action |
589 |
|
|
21.3.2.1 Chemical Shift Mapping |
589 |
|
|
21.3.2.2 KD Determination by the NMR Titration |
590 |
|
|
21.4 Experimental Aspects of the NMR Study of Protein–Ligand Interactions |
591 |
|
|
21.4.1 Stable Isotope Labeling |
591 |
|
|
21.4.2 Tips for the NMR Titration Experiment |
592 |
|
|
21.4.2.1 Sample Handling |
592 |
|
|
21.4.2.2 Data Acquisition and Analysis |
594 |
|
|
21.5 Other Complementary Methods for Protein–Ligand Interactions |
594 |
|
|
21.6 Perspective |
595 |
|
|
References |
595 |
|
|
22 Protein Structure and Dynamics Determination by Residual Anisotropic Spin Interactions |
599 |
|
|
Abstract |
599 |
|
|
22.1 Why Do We Need Residual Anisotropic Nuclear Spin Interactions in Solution NMR? |
600 |
|
|
22.2 Theoretical Backgrounds of the Residual Anisotropies |
602 |
|
|
22.2.1 Residual Dipolar Coupling, RDC |
603 |
|
|
22.2.2 Theoretical Description on RDC |
605 |
|
|
22.2.3 Residual Chemical Shift Anisotropy, RCSA |
608 |
|
|
22.3 Practical Procedures to Use the Residual Anisotropies |
611 |
|
|
22.3.1 Magnetically Aligning Liquid Crystalline Media |
611 |
|
|
22.3.2 Naturally Occurring Materials that Spontaneously Align in a Magnetic Field |
613 |
|
|
22.3.3 Compressed Acryl Amide Gel |
613 |
|
|
22.3.4 Protein Structures in Weakly Aligned Media |
615 |
|
|
22.4 RDC-Based Domain Orientation Analysis |
616 |
|
|
22.4.1 Collecting the RDC Data |
617 |
|
|
22.4.2 Domain Orientation Analysis Based on the RDC Data |
617 |
|
|
22.4.3 Significance of the Domain Orientation Analysis by RDCs |
619 |
|
|
22.4.4 Molecular Size Limitation in the RDC-Based Approach |
619 |
|
|
22.4.5 Existing Remedy for Overcoming the Size Limitation in the RDC-Based Approach |
621 |
|
|
22.5 Alignment Tensor Determination Using Only TROSY |
622 |
|
|
22.5.1 Alignment-Induced TROSY Shift Changes |
622 |
|
|
22.5.2 CSA Tensor Parameters Used in DIORITE |
624 |
|
|
22.5.3 DIORITE Analysis Using Different Magnetic Field Strengths |
625 |
|
|
22.5.4 Practical Aspects of the DIORITE Data Collection |
627 |
|
|
22.5.5 DIORITE Analyses on MBP in Different Ligand Bound States |
628 |
|
|
22.6 Conclusion |
630 |
|
|
References |
631 |
|