Cavanagh / Skelton / Fairbrother Protein NMR Spectroscopy

Principles and Practice
2. Auflage 2010
ISBN: 978-0-08-047103-7
Verlag: Elsevier Science & Techn.
Format: EPUB
Kopierschutz: 6 - ePub Watermark

E-Book, Englisch, 912 Seiten

Protein NMR Spectroscopy, Second Edition combines a comprehensive theoretical treatment of NMR spectroscopy with an extensive exposition of the experimental techniques applicable to proteins and other biological macromolecules in solution. Beginning with simple theoretical models and experimental techniques, the book develops the complete repertoire of theoretical principles and experimental techniques necessary for understanding and implementing the most sophisticated NMR experiments. Important new techniques and applications of NMR spectroscopy have emerged since the first edition of this extremely successful book was published in 1996. This updated version includes new sections describing measurement and use of residual dipolar coupling constants for structure determination, TROSY and deuterium labeling for application to large macromolecules, and experimental techniques for characterizing conformational dynamics. In addition, the treatments of instrumentation and signal acquisition, field gradients, multidimensional spectroscopy, and structure calculation are updated and enhanced. The book is written as a graduate-level textbook and will be of interest to biochemists, chemists, biophysicists, and structural biologists who utilize NMR spectroscopy or wish to understand the latest developments in this field. - Provides an understanding of the theoretical principles important for biological NMR spectroscopy - Demonstrates how to implement, optimize and troubleshoot modern multi-dimensional NMR experiments - Allows for the capability of designing effective experimental protocols for investigations of protein structures and dynamics - Includes a comprehensive set of example NMR spectra of ubiquitin provides a reference for validation of experimental methods

Dr. Cavanagh is the William Neal Reynolds Distinguished Professor of Biochemistry at North Carolina State University. He is an expert in protein structural biology, particularly in how bacteria are able to protect themselves. Dr. Cavanagh received his Ph.D. in Chemistry/NMR spectroscopy from the University of Cambridge in 1988. He has held positions as a Senior Research Associate at The Scripps Research Institute, Director of Structural Biology at the Wadsworth Center (New York State Department of Health), Associate Professor of Biomedical Sciences (SUNY) and Professor of Chemistry (Purdue). Since 2000 he has been Professor of Biochemistry in the Department of Molecular & Structural Biochemistry at North Carolina State University. Dr. Cavanagh has served on numerous NIH and NSF grant review panels and is currently a permanent member of the MSFB Study Section at NIH . He has authored over 100 peer-reviewed research publications and has been awarded the Foulerton Gift & Binmore Kenner Fellowship of the Royal Society (1990), the Fullsome Award (1996), the NC State University Alumni Associations Outstanding Research Award (2005) and Entrepreneur of the Year- NC State University (2012). He runs the Jimmy V-NCSU Cancer Therapeutics Training Program, was Assistant Vice Chancellor for Research at NC State from 2012-2014 and is the co-founder and Chief Scientific Officer of Agile Sciences Inc., a Raleigh based biotechnology company focusing on antibiotic resistance.

Zielgruppe

Academic/professional/technical: Research and professional

Autoren/Hrsg.

Cavanagh, John

Skelton, Nicholas J.

Fairbrother, Wayne J.

Rance, Mark

Palmer III, Arthur G.

Inhaltsverzeichnis

1;Front cover;1
2;Title page;4
3;Copyright page;5
4;Preface;6
5;Preface to the First Edition;8
6;Acknowledgements;12
7;Table of Contents;14
8;1 Classical NMR Spectroscopy;28
8.1;1.1 Nuclear Magnetism;29
8.2;1.2 The Bloch Equations;34
8.3;1.3 The One-Pulse NMR Experiment;43
8.4;1.4 Linewidth;45
8.5;1.5 Chemical Shift;48
8.6;1.6 Scalar Coupling and Limitations of the Bloch Equations;50
8.7;References;54
9;2 Theoretical Description of NMR Spectroscopy;56
9.1;2.1 Postulates of Quantum Mechanics;56
9.2;2.2 The Density Matrix;64
9.3;2.3 Pulses and Rotation Operators;77
9.4;2.4 Quantum Mechanical NMR Spectroscopy;81
9.5;2.5 Quantum Mechanics of Multispin Systems;85
9.6;2.6 Coherence;97
9.7;2.7 Product Operator Formalism;104
9.8;2.8 Averaging of the Spin Hamiltonians and Residual Interactions;129
9.9;References;139
10;3 Experimental Aspects of NMR Spectroscopy;141
10.1;3.1 NMR Instrumentation;141
10.2;3.2 Data Acquisition;151
10.3;3.3 Data Processing;163
10.4;3.4 Pulse Techniques;192
10.5;3.5 Spin Decoupling;228
10.6;3.6 B0 Field Gradients;244
10.7;3.7 Water Suppression Techniques;248
10.8;3.8 One-Dimensional 1H NMR Spectroscopy;261
10.9;References;294
11;4 Multidimensional NMR Spectroscopy;298
11.1;4.1 Two-Dimensional NMR Spectroscopy;300
11.2;4.2 Coherence Transfer and Mixing;307
11.3;4.3 Coherence Selection, Phase Cycling, and Field Gradients;319
11.4;4.4 Resolution and Sensitivity;353
11.5;4.5 Three- and Four-Dimensional NMR Spectroscopy;354
11.6;References;358
12;5 Relaxation and Dynamic Processes;360
12.1;5.1 Introduction and Survey of Theoretical Approaches;361
12.2;5.2 The Master Equation;378
12.3;5.3 Spectral Density Functions;392
12.4;5.4 Relaxation Mechanisms;397
12.5;5.5 Nuclear Overhauser Effect;415
12.6;5.6 Chemical Exchange Effects in NMR Spectroscopy;418
12.7;References;429
13;6 Experimental 1H NMR Methods;432
13.1;6.1 Assessment of the 1D 1H Spectrum;433
13.2;6.2 COSY-Type Experiments;436
13.3;6.3 Multiple-Quantum Filtered COSY;464
13.4;6.4 Multiple-Quantum Spectroscopy;490
13.5;6.5 TOCSY;513
13.6;6.6 Cross-Relaxation NMR Experiments;529
13.7;6.7 1H 3D Experiments;552
13.8;References;556
14;7 Heteronuclear NMR Experiments;560
14.1;7.1 Heteronuclear Correlation NMR Spectroscopy;562
14.2;7.2 Heteronuclear-Edited NMR Spectroscopy;608
14.3;7.3 13C-13C Correlations: The HCCH-COSY and HCCH-TOCSY Experiments;628
14.4;7.4 3D Triple-Resonance Experiments;640
14.5;7.5 Measurement of Scalar Coupling Constants;683
14.6;7.6 Measurement of Residual Dipolar Coupling Constants;692
14.7;References;700
15;8 Experimental NMR Relaxation Methods;706
15.1;8.1 Pulse Sequences and Experimental Methods;707
15.2;8.2 Picosecond-Nanosecond Dynamics;712
15.3;8.3 Microsecond-Second Dynamics;729
15.4;References;748
16;9 Larger Proteins and Molecular Interactions;752
16.1;9.1 Larger Proteins;752
16.2;9.2 Intermolecular Interactions;780
16.3;9.3 Methods for Rapid Data Acquisition;796
16.4;References;802
17;10 Sequential Assignment, Structure Determination, and Other Applications;808
17.1;10.1 Resonance Assignment Strategies;809
17.2;10.2 Three-Dimensional Solution Structures;823
17.3;10.3 Conclusion;840
17.4;References;841
18;Table of Symbols;846
19;List of Figures;852
20;List of Tables;864
21;Suggested Reading;866
21.1;Biomolecular NMR Spectroscopy;866
21.2;NMR Spectroscopy;867
21.3;Quantum Mechanics;867
22;Index;868
23;Spin-1/2 Product Operator Equations;914
24;Table of Constants;915

Leseproben

CHAPTER 1 CLASSICAL NMR SPECTROSCOPY The explosive growth in the field of nuclear magnetic resonance (NMR) spectroscopy that continues today originated with the development of pulsed Fourier transform NMR spectroscopy by Ernst and Anderson (1) and the conception of multidimensional NMR spectroscopy by Jeener (2, 3). Currently, NMR spectroscopy and x-ray crystallography are the only techniques capable of determining the three-dimensional structures of macromolecules at atomic resolution. In addition, NMR spectroscopy is a powerful technique for investigating time-dependent chemical phenomena, including reaction kinetics and intramolecular dynamics. Historically, NMR spectroscopy of biological macromolecules was limited by the low inherent sensitivity of the technique and by the complexity of the resultant NMR spectra. The former limitation has been alleviated partially by the development of more powerful magnets and more sensitive NMR spectrometers and by advances in techniques for sample preparation (both synthetic and biochemical). The latter limitation has been transmuted into a significant advantage by the phenomenal advances in the theoretical and experimental capabilities of NMR spectroscopy (and spectroscopists). The history of these developments has been reviewed by Ernst and by Wüthrich in their 1991 and 2002 Nobel Laureate lectures, respectively (4, 5). In light of subsequent developments, the conclusion of Bloch’s initial report of the observation of nuclear magnetic resonance in water proved prescient: “We have thought of various investigations in which this effect can be used fruitfully” (6). 1.1 Nuclear Magnetism
Nuclear magnetic resonances in bulk condensed phase were reported for the first time in 1946 by Bloch et al. (6) and by Purcell et al. (7). Nuclear magnetism and NMR spectroscopy are manifestations of nuclear spin angular momentum. Consequently, the theory of NMR spectroscopy is largely the quantum mechanics of nuclear spin angular momentum, an intrinsically quantum mechanical property that does not have a classical analog. The physical origins of the nuclear spin angular momentum are complex, but have been discussed in review articles (8, 9). The spin angular momentum is characterized by the nuclear spin quantum number, I. Although NMR spectroscopy takes the nuclear spin as a given quantity, certain systematic features can be noted: (i) nuclei with odd mass numbers have half-integral spin quantum numbers, (ii) nuclei with an even mass number and an even atomic number have spin quantum numbers equal to zero, and (iii) nuclei with an even mass number and an odd atomic number have integral spin quantum numbers. Because the NMR phenomenon relies on the existence of nuclear spin, nuclei belonging to category (ii) are NMR inactive. Nuclei with spin quantum numbers greater than 1/2 also possess electric quadrupole moments arising from nonspherical nuclear charge distributions. The lifetimes of the magnetic states for quadrupolar nuclei in solution normally are much shorter than are the lifetimes for nuclei with I = 1/2. NMR resonance lines for quadrupolar nuclei are correspondingly broad and can be more difficult to study. Relevant properties of nuclei commonly found in biomolecules are summarized in Table 1.1. For NMR spectroscopy of biomolecules, the most important nuclei with I = 1/2 are 1H, 13C, 15N, 19F, and 31P; the most important nucleus with I = 1 is the deuteron (2H). TABLE 1.1 Properties of selected nucleia The nuclear spin angular momentum, I, is a vector quantity with magnitude given by
[1.1]
in which I is the nuclear spin angular momentum quantum number and h is Planck’s constant divided by 2p. Due to the restrictions of quantum mechanics, only one of the three Cartesian components of I can be specified simultaneously with I2 = I • I. By convention, the value of the z-component of I is specified by the following equation:
[1.2]
in which the magnetic quantum number m = (-I, -I + 1, …, I -1, I). Thus, Iz has 2I + 1 possible values. The orientation of the spin angular momentum vector in space is quantized, because the magnitude of the vector is constant and the z-component has a set of discrete possible values. In the absence of external fields, the quantum states corresponding to the 2I + 1 values of m have the same energy, and the spin angular momentum vector does not have a preferred orientation. Nuclei that have nonzero spin angular momentum also possess nuclear magnetic moments. As a consequence of the Wigner—Eckart theorem (10), the nuclear magnetic moment, µ, is collinear with the vector representing the nuclear spin angular momentum vector and is defined by
[1.3]
in which the magnetogyric ratio, ?, is a characteristic constant for a given nucleus (Table 1.1). Because angular momentum is a quantized property, so is the nuclear magnetic moment. The magnitude of ?, in part, determines the receptivity of a nucleus in NMR spectroscopy. In the presence of an external magnetic field, the spin states of the nucleus have energies given by
[1.4]
in which B is the magnetic field vector. The minimum energy is obtained when the projection of µ onto B is maximized. Because |I| > Iz, µ cannot be collinear with B and the m spin states become quantized with energies proportional to their projection onto B. In an NMR spectrometer, the static external magnetic field is directed by convention along the z-axis of the laboratory coordinate system. For this geometry, [1.4] reduces to
[1.5]
in which B0 is the static magnetic field strength. In the presence of a static magnetic field, the projections of the angular momentum of the nuclei onto the z-axis of the laboratory frame results in 2I + 1 equally spaced energy levels, which are known as the Zeeman levels. The quantization of Iz is illustrated by Fig. 1.1. FIGURE 1.1 Angular momentum. Shown are the angular momentum vectors, I, and the allowed z-components, Iz, for (a) a spin-1/2 particle and (b) a spin-1 particle. The location of I on the surface of the cone cannot be specified because of quantum mechanical uncertainties in the Ix and Iy components. At equilibrium, the different energy states are unequally populated because lower energy orientations of the magnetic dipole vector are more probable. The relative population of a state is given by the Boltzmann distribution,
[1.6]
in which Nm is the number of nuclei in the mth state and N is the total number of spins, T is the absolute temperature, and kB is the Boltzmann constant. The last two lines of [1.6] are obtained by expanding the exponential functions to first order using Taylor series, because at temperatures relevant for solution NMR spectroscopy, mh?B0/kBT « 1. The populations of the states depend both on the nucleus type and on the applied field strength. As the external field strength increases, the energy differences between the nuclear spin energy levels become larger and the population differences between the states increase. Of course, polarization of the spin system to generate a population difference between spin states does not occur instantaneously upon application of the magnetic field; instead, the polarization, or magnetization, develops with a characteristic rate constant, called the spin-lattice relaxation rate constant (see Chapter 5). The bulk magnetic moment, M, and the bulk angular momentum, J, of a macroscopic sample are given by the vector sum of the corresponding quantities for individual nuclei, µ and I. At thermal equilibrium, the transverse components (e.g., the x- or y-components) of µ and I for different nuclei in the sample are uncorrelated and sum to zero. The small population differences between energy levels give rise to a bulk magnetization of the sample parallel (longitudinal) to the static magnetic field, M = M0k, in which k is the unit vector in the z-direction. Using [1.2], [1.3], and [1.6], M0 is given by
[1.7]
By analogy with other areas of spectroscopy, transitions between Zeeman levels can be stimulated by applied electromagnetic radiation. The selection rule governing magnetic dipole...