Nuclear magnetic resonance (NMR) is an analytical tool used by chemists and physicists to study the structure and dynamics of molecules. In recent years, no other technique has gained such significance as NMR spectroscopy. It is used in all branches of science in which precise structural determination is required and in which the nature of interactions and reactions in solution is being studied. Annual Reports on NMR Spectroscopy has established itself as a premier means for the specialist and non-specialist alike to become familiar with new techniques and applications of NMR spectroscopy. - This volume of Annual Reports on NMR Spectroscopy focuses on the analytical tools used by chemists and physicists, taken together with other volumes of this series, an excellent account of progress in NMR and its many applications is provided and anyone using NMR will find interest in this Serial
Front Cover 1
Annual Reports on NMR Spectroscopy 4
Copyright 5
Contents 6
Contributors 8
Preface 10
Chapter One: Dynamic Pictures of Proteins by NMR 12
1. Introduction 13
2. Pico- to Nanosecond Motions 15
2.1. Generalized Order Parameters from the Relaxation Parameters [8-10,30-33] 16
2.2. Moiety of Membrane Proteins Protruding from Membrane Surfaces 20
3. Micro- to Milliseconds Motions: Solution NMR 22
3.1. CPMG R2 Relaxation Rate Dispersion 23
3.2. R1. Relaxation Rate Dispersion 27
3.3. Differential ZQC/DQC Decay Rates 30
3.4. ZZ-Exchange 30
3.5. Residual Dipolar Couplings 31
4. Micro- to Millisecond Motions: Solid State NMR 35
4.1. Dynamic Interference: SRI 35
4.2. CODEX and Chemical Exchange 38
4.3. Order Parameters Based on DCs 40
4.4. Relaxation Rate parameters: R1, R2, and R1. 41
4.5. Lineshape Analysis 45
5. Very Slow Motions: 1D MAS Exchange 46
6. Globular Proteins 48
6.1. Comparison of Protein Dynamics Between Solution and Solid 48
6.2. Pico- to Nanosecond motions: Conformational Entropy and Allostery 48
6.3. ms-µs Motions: Biological Function 51
6.3.1. Protein Folding 51
6.3.2. Catalysis and Allosteric Regulation 52
7. Membrane Proteins 54
7.1. Retinal Proteins 54
7.1.1. Bacteriorhodopsin (bR) 54
7.1.2. Sensory Rhodopsin and Proteorhodopsin 58
7.2. Other Proteins 60
8. Conclusion 61
Acknowledgements 62
References 62
Chapter Two: Recent Progress in the Solid-State NMR Studies of Short Peptides: Techniques, Structure and Dynamics 78
1. Introduction 79
2. Development of the New Solid-State NMR Techniques Useful in Structural Studies of Peptides 81
2.1. 1H Solid-State NMR 81
2.2. 13C and 15N Sensitivity under Fast and Medium Magic-Angle Spinning 83
2.3. Two-Dimensional Correlations under F-MAS 89
2.3.1. 1H-13C and 1H-15N HETCOR Correlations 89
2.3.2. 13C-13C and 15N-15N HOMCOR Correlations 91
2.4. Quadrupolar Nuclei 93
3. Molecular Dynamics of Peptides in the Solid State 94
3.1. Probing the Dynamics in Different Time Scales 95
3.2. Tools for Analysis of the Local Molecular Motions of Peptides in the Solid State 98
3.2.1. Relaxation Times 98
3.2.2. Chemical Shift Anisotropy 102
3.2.3. Investigation of the Dynamics by Deuterium Solid-State NMR: Line-Shape Analysis 106
3.2.4. Heteronuclear Dipolar Recoupling Sequences 112
4. Polymorphism and Solvatomorphism of Peptides 116
4.1. Solid-State NMR Study of Polymorphs and Solvatomorphs 117
4.1.1. Ala-Ala-Ala Tripeptide-The Case Study 122
5. Complementarity of Theoretical and NMR Methods in Assignment of the Solid-State Structure of Peptides 126
5.1. Techniques Used for Calculations of NMR Parameters in the Solid State 129
5.2. Theoretical Methods as a Tool for Structure Assignment of Peptides in the Solid State 130
5.3. Fine Refinement of Peptide Crystals with Molecular Disorder 135
5.4. Theoretical Methods Versus Molecular Motion 140
6. Concluding Remarks 142
Acknowledgement 143
References 143
Chapter Three: Solid-State 17O NMR Studies of Biomolecules 156
1. Introduction 157
2. NMR Tensor Parameters 160
3. NMR Methodologies 163
3.1. Site-Specific Spectral Resolution 164
3.1.1. Single-Crystal NMR 164
3.1.2. Magic-Angle Spinning 165
3.1.3. MQMAS and STMAS 166
3.1.4. Dynamic Angle Spinning and Double Rotation 168
3.2. Detection Sensitivity Enhancement 169
3.2.1. Isotopic Enrichment and High Magnetic Field 169
3.2.2. Spin Population Transfer Experiments 170
3.2.3. Dynamic Nuclear Polarization 171
3.2.4. Cryo-MAS 172
3.2.5. Cross-polarization 173
3.3. Correlation NMR Experiments 174
3.4. Quantum Chemical Calculations 178
3.4.1. Molecular Cluster Model 179
3.4.2. Periodic Crystal Lattice 180
3.5. Basic NMR Experimental Considerations 180
3.6. General Schemes for Determining the Tensor Parameters 182
3.6.1. Single Oxygen 183
3.6.2. Multiple Oxygens 183
4. 17O NMR Studies of Biomolecules 186
4.1. Proteins 189
4.1.1. Amino Acids 189
4.1.2. Peptides 191
4.1.3. Proteins 195
4.2. Nucleic Acids 197
4.3. Carbohydrates 198
4.4. Recent Progress on Organic Molecules of Biological Relevance 201
4.4.1. Carboxylic Acids and Carboxylates 201
4.4.2. C-Nitroso Compounds 204
4.4.3. Keto Acids 204
4.4.4. Sulfonic Acids 205
5. Concluding Remarks 206
Acknowledgements 207
Appendix 208
References 224
Chapter Four: Solid-State Nuclear Magnetic Resonance in Pharmaceutical Compounds 232
1. Introduction 233
2. SSNMR Techniques 236
2.1. 1D High-Resolution SSNMR Experiments 236
2.1.1. Diluted Spins 236
2.1.2. High-Resolution 1H NMR MAS 238
2.2. 2D SSNMR Experiments 240
2.3. First Principles Calculations 241
2.4. Relaxation Time Measurements 241
2.5. Multinuclear SSNMR 242
3. SSNMR of Pharmaceutical Compounds 243
3.1. API Characterization 243
3.2. Polymorphism 248
3.3. Pharmaceutical Complexes with Cyclodextrins 257
3.4. Salts and Cocrystals 261
3.5. NMR Crystallography 267
3.6. Tablet Characterization 270
4. Conclusions 271
5. Table of Compounds 271
Acknowledgements 273
References 273
Chapter Five: Covariance NMR and Small Molecule Applications 282
1. Introduction 283
2. On the Theory of Covariance NMR 284
2.1. The General Description 284
2.2. Types of Covariance Transformations in NMR 289
2.2.1. The Classification of Covariance NMR 289
2.2.2. Some Aspects of the Workings of 4D NMR 291
2.2.3. Matrix Regularization in Covariance NMR 292
2.2.4. The Transition from Indirect to Unsymmetrical Indirect Covariance 292
2.2.5. The Workings of Generalized Indirect Covariance NMR 293
2.3. Examples of Covariance Transformations 295
2.4. Artefacts in Covariance NMR Spectra 300
2.5. The Determination of the Non-Linear Signal-to-Noise Ratio 301
2.6. Asynchronous Spectra-The Neglected Imaginary Part 302
2.6.1. General Aspects of Asynchronous Spectra 302
2.6.2. Applications of Asynchronous Spectra 304
2.7. Heterospectroscopy 305
3. Software for Covariance NMR Processing 307
4. Covariance and NUS-The Combination of Two Approaches to Fast Methods 311
5. Applications of Covariance NMR to Small Molecules 317
5.1. Direct Covariance 317
5.1.1. Solution State 317
5.1.2. Solid State 320
5.2. Indirect Covariance 321
5.2.1. Solution State 321
5.2.2. Solid State 327
5.3. Unsymmetrical and Generalized Indirect Covariance 329
5.4. Multidimensional Covariance 344
5.4.1. Triple Rank 344
5.4.2. 4D NMR 345
5.5. Synchronous and Asynchronous Spectra 346
5.6. Statistical Analysis of NMR Spectra in the Field of Metabolomics 347
5.7. Other Covariance Applications in NMR Spectroscopy 349
6. Conclusion 351
Acknowledgements 352
References 352
Index 362
References
[1] Gurd FRN, Rothgeb TM. Motions in protein. Adv. Protein Chem. 1979;33:73–165.
[2] Creighton TE. Proteins. Structures and Molecular Properties. second ed. New York, NY: W. H. Freeman and Company; 1993.
[3] Abragam A. The Principles of Nuclear Magnetism. Oxford: Claredon Press; 1961.
[4] Ernst RR, Bodenhausen G, Wokaun A. Principles of Nuclear Magnetic Resonance in One and Two Dimensions. Oxford: Clarendon Press; 1987.
[5] Evans JNS. Biomolecular NMR Spectroscopy. Oxford: Oxford University Press; 1995.
[6] Becker ED. High Resolution NMR, Theory and Chemical Applications. third ed. San Diego, CA: Academic Press; 2000.
[7] Slichter CP. Principles of Magnetic Resonance. third enlarged and updated ed. Berlin: Springer Verlag; 1989.
[8] Lipari G, Szabo A. Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 1. Theory and range of validity. J. Am. Chem. Soc. 1982;104:4546–4559.
[9] Lipari G, Szabo A. Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 2. Analysis of experimental results. J. Am. Chem. Soc. 1982;104:4559–4570.
[10] Clore GM, Szabo A, Bax A, Kay LE, Driscoll PC, Gronenborn AM. Deviations from the simple two-parameter model-free approach to the interpretation of nitrogen-15 nuclear magnetic relaxation of proteins. J. Am. Chem. Soc. 1990;112:4989–4991.
[11] Palmer III AG. Probing molecular motion by NMR. Curr. Opin. Struct. Biol. 1997;7:732–737.
[12] Palmer III AG, Kroenke CD, Loria JP. Nuclear magnetic resonance methods for quantifying microsecond-to-millisecond motions in biological macromolecules. Methods Enzymol. 2001;339:204–238.
[13] Akke M. NMR methods for characterizing microsecond to millisecond dynamics in recognition and catalysis. Curr. Opin. Struct. Biol. 2002;12:642–647.
[14] Palmer III AG. NMR characterization of the dynamics of biomacromolecules. Chem. Rev. 2004;104:3623–3640.
[15] Palmer III AG, Grey MJ, Wang C. Solution NMR spin relaxation methods for characterizing chemical exchange in high-molecular-weight systems. Methods Enzymol. 2005;394:430–465.
[16] Boehr DD, Dyson HJ, Wright PE. An NMR perspective on enzyme dynamics. Chem. Rev. 2006;106:3055–3079.
[17] Kleckner IR, Foster MP. An introduction to NMR-based approaches for measuring protein dynamics. Biochim. Biophys. Acta. 2011;1814:942–968.
[18] Carr HY, Purcell EM. Effects of diffusion on free precession in nuclear magnetic resonance experiments. Phys. Rev. 1954;94:630–638.
[19] Meiboom S, Gill D. Modified spin-echo method for measuring nuclear relaxation times. Rev. Sci. Instrum. 1958;29:688–691.
[20] Deverell C, Morgan RE, Strange JH. Studies of chemical exchange by nuclear magnetic relaxation in the rotating frame. Mol. Phys. 1970;18:553–559.
[21] Saitô H, Tuzi S, Tanio M, Naito A. Dynamic aspect of membrane proteins and membrane associated peptides as revealed by 13C NMR: lessons from bacteriorhodopsin as an intact protein. Annu. Rep. NMR Spectrosc. 2002;47:39–108.
[22] Saitô H, Mikami J, Yamaguchi S, Tanio M, Kira A, Arakawa T, Yamamoto K, Tuzi S. Site-directed 13C solid-state NMR studies on membrane proteins: strategy and goals toward revealing conformation and dynamics as illustrated for 13C-labeled bacteriorhodopsin. Magn. Reson. Chem. 2004;42:218–230.
[23] Saitô H. Site-directed solid-state NMR on membrane proteins. Annu. Rep. NMR Spectrosc. 2006;57:100–171.
[24] Saitô H, Ando I, Naito A. Solid State NMR Spectroscopy for Biopolymers, Principles and Applications. Berlin: Springer; 2006.
[25] Sarkar SK, Sullivan CE, Torchia DA. Solid state 13C NMR study of collagen molecular dynamics in hard and soft tissues. J. Biol. Chem. 1983;258:9762–9767.
[26] Jelinski LW, Sullivan CE, Torchia DA. 2H NMR study of molecular motion in collagen fibrils. Nature. 1980;284:531–534.
[27] Suwelack D, Rothwell WP, Waugh JS. Slow molecular motion detected in the NMR spectra of rotating solids. J. Chem. Phys. 1980;73:2559–2569.
[28] Rothwell WP, Waugh JS. Transverse relaxation of dipolar coupled spin systems under rf irradiation: detecting motions in solids. J. Chem. Phys. 1981;74:2721–2732.
[29] Naito A, Fukutani A, Uitdehaag M, Tuzi S, Saitô H. Backbone dynamics of polycrystalline peptides studied by measurements of 15N NMR lineshapes and 13C transverse relaxation times. J. Mol. Struct. 1998;441:231–241.
[30] Palmer III AG. Dynamic properties of proteins from NMR spectroscopy. Curr. Opin. Biotechnol. 1993;4:385–391.
[30a] Palmer III AG. NMR characterization of the dynamics of biomacromolecules. Chem. Rev. 2004;104:3623–3640.
[31] Jarymowycz VA, Stone MJ. Fast time scale dynamics of protein backbones: NMR relaxation methods, applications, and functional consequences. Chem. Rev. 2006;106:1624–1671.
[32] Igumenova TI, Frederick KK, Wand AJ. Characterization of the fast dynamics of protein amino acid side chains using NMR relaxation in solution. Chem. Rev. 2006;106:1672–1699.
[32a] Kleckner IR, Foster MP. An introduction to NMR-based approaches for measuring protein dynamics. Biochim. Biophys. Acta. 2011;1814:942–968.
[33] Daragan VA, Mayo KH. Motional model analyses of protein and peptide dynamics using 13C and 15N NMR relaxation. Prog. Nucl. Magn. Reson. Spectrosc. 1997;31:63–105.
[34] Woessner DE. Spin relaxation processes in a two‐proton system undergoing anisotropic reorientation. J. Chem. Phys. 1962;36:1–4.
[35] Richarz R, Nagayama K, Wüthrich K. Carbon-13 nuclear magnetic resonance relaxation studies of internal mobility of the polypeptide chain in basic pancreatic trypsin inhibitor and a selectively reduced analog. Biochemistry. 1980;19:5189–5196.
[36] Peng JW, Wagner G. Mapping of spectral density functions using heteronuclear NMR relaxation measurements. J. Magn. Reson. 1992;98:308–332.
[37] Peng JW, Wagner G. Mapping of the spectral densities of nitrogen-hydrogen bond motions in eglin c using heteronuclear relaxation experiments. Biochemistry. 1992;31:8571–8586.
[38] Kay LE, Torchia DA, Bax A. Backbone dynamics of proteins as studied by 15N inverse detected heteronuclear NMR Spectroscopy: application to staphylococcal nuclease. Biochemistry. 1989;28:8972–8979.
[39] Palmer III AG, Rance M, Wright PE. Intramolecular motions of a zinc finger DNA-binding domain from Xfin characterized by proton-detected natural abundance 13C heteronuclear NMR spectroscopy. J. Am. Chem. Soc. 1991;113:4371–4380.
[40] Akke M, Skelton NJ, Kördel J, Palmer III AG, Chazin WJ. Effects of ion binding on the backbone dynamics of calbindin D9k determined by 15N NMR relaxation. Biochemistry. 1993;32:9832–9844.
[41] Mandel AM, Akke M, Palmer III AG. Backbone dynamics of Escherichia coli ribonuclease HI: correlations with structure and function in an active enzyme. J. Mol. Biol. 1995;246:144–163.
[42] Pang Y, Buck M, Zuiderweg ER. Backbone dynamics of the ribonuclease binase active site area using multinuclear (15N and 13CO) NMR relaxation and computational molecular dynamics. Biochemistry. 2002;41:2655–2666.
[43] Muhandiram DR, Yamazaki T, Sykes BD, Kay LE. Measurement of 2H T1 and T1ρ relaxation times in uniformly 13C-labeled and fractionally 2H-labeled proteins in solution. J. Am. Chem. Soc. 1995;117:11536–11544.
[44] Kay LE, Muhandiram DR, Farrow NA, Aubin Y, Forman-Kay JD. Correlation between dynamics and high affinity binding in an SH2 domain interaction. Biochemistry. 1996;35:361–368.
[45] Akke M, Brüschweiler R, Palmer III AG. NMR order parameters and free energy: an analytical approach and its application to cooperative calcium(2 +) binding by calbindin D9k. J. Am. Chem. Soc. 1993;115:9832–9833.
[46] Yang D, Kay LE. Contributions to conformational entropy arising from bond vector fluctuations measured from NMR-derived order parameters: application to protein folding. J. Mol. Biol. 1996;263:369–382.
[47] Li Z, Raychaudhuri S, Wand AJ. Insights into local residual entropy of proteins provided by NMR relaxlation. Protein Sci. 1996;5:2647–2650.
[48] Spyracopoulos L, Sykes BD. Thermodynamic insights into proteins from NMR spin relaxation studies. Curr. Opin. Struct. Biol. 2001;11:555–559.
[49] Tuzi S, Naito A, Saitô H. 13C NMR study on conformation and dynamics of the transmembrane...
| Erscheint lt. Verlag | 22.7.2014 |
|---|---|
| Sprache | englisch |
| Themenwelt | Naturwissenschaften ► Chemie ► Analytische Chemie |
| Naturwissenschaften ► Physik / Astronomie ► Elektrodynamik | |
| Technik | |
| ISBN-10 | 0-12-800327-8 / 0128003278 |
| ISBN-13 | 978-0-12-800327-5 / 9780128003275 |
| Haben Sie eine Frage zum Produkt? |
PDF (Adobe DRM)Größe: 17,2 MB
Kopierschutz: Adobe-DRM
Adobe-DRM ist ein Kopierschutz, der das eBook vor Mißbrauch schützen soll. Dabei wird das eBook bereits beim Download auf Ihre persönliche Adobe-ID autorisiert. Lesen können Sie das eBook dann nur auf den Geräten, welche ebenfalls auf Ihre Adobe-ID registriert sind.
Details zum Adobe-DRM
Dateiformat: PDF (Portable Document Format)
Mit einem festen Seitenlayout eignet sich die PDF besonders für Fachbücher mit Spalten, Tabellen und Abbildungen. Eine PDF kann auf fast allen Geräten angezeigt werden, ist aber für kleine Displays (Smartphone, eReader) nur eingeschränkt geeignet.
Systemvoraussetzungen:
PC/Mac: Mit einem PC oder Mac können Sie dieses eBook lesen. Sie benötigen eine
eReader: Dieses eBook kann mit (fast) allen eBook-Readern gelesen werden. Mit dem amazon-Kindle ist es aber nicht kompatibel.
Smartphone/Tablet: Egal ob Apple oder Android, dieses eBook können Sie lesen. Sie benötigen eine
Geräteliste und zusätzliche Hinweise
Buying eBooks from abroad
For tax law reasons we can sell eBooks just within Germany and Switzerland. Regrettably we cannot fulfill eBook-orders from other countries.
EPUB (Adobe DRM)Größe: 18,7 MB
Kopierschutz: Adobe-DRM
Adobe-DRM ist ein Kopierschutz, der das eBook vor Mißbrauch schützen soll. Dabei wird das eBook bereits beim Download auf Ihre persönliche Adobe-ID autorisiert. Lesen können Sie das eBook dann nur auf den Geräten, welche ebenfalls auf Ihre Adobe-ID registriert sind.
Details zum Adobe-DRM
Dateiformat: EPUB (Electronic Publication)
EPUB ist ein offener Standard für eBooks und eignet sich besonders zur Darstellung von Belletristik und Sachbüchern. Der Fließtext wird dynamisch an die Display- und Schriftgröße angepasst. Auch für mobile Lesegeräte ist EPUB daher gut geeignet.
Systemvoraussetzungen:
PC/Mac: Mit einem PC oder Mac können Sie dieses eBook lesen. Sie benötigen eine
eReader: Dieses eBook kann mit (fast) allen eBook-Readern gelesen werden. Mit dem amazon-Kindle ist es aber nicht kompatibel.
Smartphone/Tablet: Egal ob Apple oder Android, dieses eBook können Sie lesen. Sie benötigen eine
Geräteliste und zusätzliche Hinweise
Buying eBooks from abroad
For tax law reasons we can sell eBooks just within Germany and Switzerland. Regrettably we cannot fulfill eBook-orders from other countries.
aus dem Bereich
