Protein NMR Spectroscopy -  John Cavanagh,  Wayne J. Fairbrother,  Arthur G. Palmer III,  Mark Rance,  Nicholas J. Skelton

Protein NMR Spectroscopy (eBook)

Principles and Practice
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2010 | 2. Auflage
912 Seiten
Elsevier Science (Verlag)
978-0-08-047103-7 (ISBN)
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Protein NMR Spectroscopy 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, Protein NMR Spectroscopy 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. The second edition 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.

Protein NMR Spectroscopy is written as a graduate-level textbook and will be of interest to biochemists, chemists, biophysicists, and structural biologists who utilize NMR spectroscopy or who 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
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

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

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 ħ is Planck’s constant divided by 2π. Due to the restrictions of quantum mechanics, only one of the three Cartesian components of I can be specified simultaneously with I2 ≡ II. 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, γ, 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 γ, 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, mħγB0/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...

Erscheint lt. Verlag 21.7.2010
Sprache englisch
Themenwelt Naturwissenschaften Biologie Biochemie
Naturwissenschaften Biologie Zellbiologie
Naturwissenschaften Chemie Analytische Chemie
Naturwissenschaften Physik / Astronomie Elektrodynamik
Technik
ISBN-10 0-08-047103-X / 008047103X
ISBN-13 978-0-08-047103-7 / 9780080471037
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