Fundamentals of Protein NMR Spectroscopy

ISBN-10: 1402034997

ISBN-13: 9781402034992

Edition: 2006

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Description: NMR spectroscopy has proven to be a powerful technique to study the structure and dynamics of biological macromolecules. Fundamentals of Protein NMR Spectroscopy is a comprehensive textbook that guides the reader from a basic understanding of the phenomenological properties of magnetic resonance to the application and interpretation of modern multi-dimensional NMR experiments on 15 N/ 13 C-labeled proteins. Beginning with elementary quantum mechanics, a set of practical rules is presented and used to describe many commonly employed multi-dimensional, multi-nuclear NMR pulse sequences. A modular analysis of NMR pulse sequence building blocks also provides a basis for understanding and developing novel pulse programs. This text not only covers topics from chemical shift assignment to protein structure refinement, as well as the analysis of protein dynamics and chemical kinetics, but also provides a practical guide to many aspects of modern spectrometer hardware, sample preparation, experimental set-up, and data processing. End of chapter exercises are included to emphasize important concepts. Fundamentals of Protein NMR Spectroscopy not only offer students a systematic, in-depth, understanding of modern NMR spectroscopy and its application to biomolecular systems, but will also be a useful reference for the experienced investigator.

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Book details

List price: $149.00
Copyright year: 2006
Publisher: Springer
Publication date: 10/28/2005
Binding: Hardcover
Pages: 532
Size: 6.25" wide x 9.25" long x 1.00" tall
Weight: 2.442
Language: English

Professor of Biological Sciences at Carnegie Mellon University. Professor Rule's research is directed at understanding inter-molecular interactions in biological systems. An understanding of these interactions is required if biological systems are to be comprehended at the molecular level. The combined tools of molecular biology, NMR spectroscopy and x-ray crystallography are used to provide important information to aid in our understanding of these interactions. Our research efforts have been directed at enzyme-substrate interactions, protein-lipid interactions, antibody-antigen interactions, and protein-nucleic acid interactions

List of Figures
List of Tables
NMR Spectroscopy
Introduction to NMR Spectroscopy
One Dimensional NMR Spectroscopy
Classical Description of NMR Spectroscopy
Nuclear Spin Transitions
Detection of Nuclear Spin Transitions
Continuous Wave NMR
Pulsed NMR
Summary of the Process of Acquiring a One Dimensional Spectrum
Phenomenological Description of Relaxation
Relaxation and the Evolution of Magnetization
Chemical Shielding
Characteristic [superscript 1]H, [superscript 13]C and [superscript 15]N Chemical Shifts
Effect of Electronic Structure on Chemical Shifts
Ring Current Effects
Effects of Local Environment on Chemical Shifts
Use of Chemical Shifts in Resonance Assignments
Chemical Shift Dispersion & Multi-dimensional NMR
Exercises
Solutions
Practical Aspects of Acquiring NMR Spectra
Components of an NMR Spectrometer
Magnet
Computer
Probe
Pre-amplifier Module
The Field-frequency Lock
Shim System
Transmitter & Pulse Generation
Receiver
Acquiring a Spectrum
Sample Preparation
Beginning the Experiment
Temperature Measurement
Shimming
Tuning and Matching the Probe
Adjusting the Transmitter
Calibration of the 90[degree] Pulse Length
Setting the Sweepwidth: Dwell Times and Filters
Setting the Receiver Gain
Spectral Resolution and Acquisition Time of the FID
Experimental 1D-pulse Sequence: Pulse and Receiver Phase
Phase Cycle
Phase Cycle and Artifact Suppression
Exercises
Solutions
Introduction to Signal Processing
Removal of DC Offset
Increasing Resolution by Extending the FID
Increasing Resolution by Zero-filling
Increasing Resolution by Linear Prediction (LP)
Removal of Truncation Artifacts: Apodization
Effect of Apodization on Resolution and Noise
Using LP & Apodization to Increase Resolution
Solvent Suppression
Spectral Artifacts Due to Intensity Errors
Errors from the Digital Fourier Transform
Effect of Distorted and Missing Points
Delayed Acquisition
Phasing of the Spectrum
Origin of Phase Shifts
Applying Phase Corrections
Chemical Shift Referencing
Exercises
Solutions
Quantum Mechanical Description of NMR
Schrodinger Equation
Vector Spaces and Properties of Wavefunctions
Particle in a Box
Expectation Values
Dirac Notation
Wavefunctions in Dirac Notation
Scalar Product in Dirac Notation
Operators in Dirac Notation
Expectation Values in Dirac Notation
Hermitian Operators
Determining Eigenvalues
Additional Properties of Operators
Commuting Observables
Time Evolution of Observables
Trace of an Operator
Exponential Operator
Unitary Operators
Exponential Hermitian Operators
Hamiltonian and Angular Momentum Operators for a Spin-1/2 Particle
Rotations
Rotation Groups
Rotation Operators
Rotations of Wave Functions and Operators
Exercises
Solutions
Quantum Mechanical Description of a One Pulse Experiment
Preparation: Evolution of the System Under B[subscript o]
Excitation: Effect of Application of B[subscript 1]
The Resonance Condition
Detection: Evolution of the System Under B[subscript o]
The Density Matrix & Product Operators
Introduction to the Density Matrix
Calculation of Expectation Values From [rho]
Density Matrix for a Statistical Mixture
One-pulse Experiment: Density Matrix Description
Effect of Pulses on the Density matrix
Product Operators
Transformation Properties of Product Operators
Description of the One-pulse Experiment
Evaluation of Composite Pulses
Exercises
Solutions
Scalar Coupling
Introduction to Scalar Coupling
Basis of Scalar Coupling
Coupling to Multiple Spins
Quantum Mechanical Description
Analysis of an AX System
Analysis of an AB System
Decoupling
Experimental Implementation of Decoupling
Decoupling Methods
Performance of Decoupling Schemes
Exercises
Solutions
Coupled Spins: Density Matrix and Product Operator Formalism
Density Matrix for Two Coupled Spins
Product Operator Representation of the Density Matrix
Detectable Elements of [rho]
Density Matrix Treatment of a One-pulse Experiment
Manipulation of Two-spin Product Operators
Transformations of Two-spin Product Operators
Product Operator Treatment of a One-pulse Experiment
Two Dimensional Homonuclear J-Correlated Spectroscopy
Multi-dimensional Experiments
Elements of Multi-dimensional NMR Experiments
Generation of Multi-dimensional NMR Spectra
Homonuclear J-correlated Spectra
COSY Experiment
Double Quantum Filtered COSY (DQF-COSY)
Product Operator Treatment of the DQF-COSY Experiment
Effect of Passive Coupling on COSY Crosspeaks
Scalar Correlation by Isotropic Mixing: TOCSY
Analysis of TOCSY Pulse Sequence
Isotropic Mixing Schemes
Time Dependence of Magnetization Transfer by Isotropic Mixing
Exercises
Solutions
Two Dimensional Heteronuclear J-Correlated Spectroscopy
Introduction
Two Dimensional Heteronuclear NMR Experiments
HMQC Experiment
HSQC Experiment
Refocused-HSQC Experiment
Comparison of HMQC, HSQC, and Refocused-HSQC Experiments
Sensitivity in 2D-Heteronuclear Experiments
Behavior of XH[subscript 2] Systems in HSQC-type Experiments
Coherence Editing: Pulsed-Field Gradients and Phase Cycling
Principals of Coherence Selection
Spherical Basis Set
Coherence Changes in NMR Experiments
Coherence Pathways
Phase Encoding With Pulsed-Field Gradients
Gradient Coils
Effect of Coherence Levels on Gradient Induced Phase Changes
Coherence Selection by Gradients in Heteronuclear NMR Experiments
Coherence Selection Using Phase Cycling
Coherence Changes Induced by RF-Pulses
Selection of Coherence Pathways
Phase Cycling in the HMQC Pulse Sequence
Exercises
Solutions
Quadrature Detection in Multi-Dimensional NMR Spectroscopy
Quadrature Detection Using TPPI
Hypercomplex Method of Quadrature Detection
States-TPPI - Removal of Axial Peaks
Sensitivity Enhancement
Echo-AntiEcho Quadrature Detection: N-P Selection
Absorption Mode Lineshapes with N-P Selection
Resonance Assignments: Homonuclear Methods
Overview of the Assignment Process
Homonuclear Methods of Assignment
[superscript 15]N Separated Homonuclear Techniques
2D [superscript 15]N HSQC Experiment
3D [superscript 15]N Separated TOCSY Experiment
The HNHA Experiment - Identifying H[subscript alpha] Protons
The HNHB Experiment- Identifying H[subscript beta] Protons
Establishing Spin-system Connectivities with Dipolar Coupling
Exercises
Solutions
Resonance Assignments: Heteronuclear Methods
Mainchain Assignments
Strategy
Methods for Mainchain Assignments
Description of Triple-resonance Experiments
HNCO Experiment
HNCA Experiment
Selective Excitation and Decoupling of [superscript 13]C
Selective 90[degree] Pulses
Selective 180[degree] Pulses
Selective Decoupling: SEDUCE
Frequency Shifted Pulses
Sidechain Assignments
Triple-resonance Methods for Sidechain Assignments
The HCCH Experiment
Exercises
Solutions
Practical Aspects of N-Dimensional Data Acquisition and Processing
Sample Preparation
NMR Sample Tubes
Sample Requirements
Solvent Considerations - Water Suppression
Amide Exchange Rates
Solvent Suppression
Instrument Configuration
Probe Tuning
Calibration of Pulses
Proton Pulses
Heteronuclear Pulses
T[subscript 1], T[subscript 2] and Experimental Parameters
Fundamentals of Nuclear Spin Relaxation
Effect of Molecular Weight and Magnetic Field Strength on T[subscript 1] and T[subscript 2]
Effect of Temperature on T[subscript 2]
Relaxation Interference: TROSY
Determination of T[subscript 1] and T[subscript 2]
Acquisition of Multi-Dimensional Spectra
Setting Polarization Transfer Delays
Defining the Directly Detected Dimension: t[subscript 3]
Defining Indirectly Detected Dimensions
Processing 3-Dimensional Data
Data Structure
Defining the Spectral Matrix
Data Processing
Processing the Directly Detected Domain
Variation in Processing
Useful Manipulations of the Free Induction Decay
Dipolar Coupling
Introduction
Energy of Interaction
Effect of Isotropic Tumbling on Dipolar Coupling
Effect of Anisotropic Tumbling
Measurement of Inter-proton Distances
NOESY Experiment
Crosspeak Intensity in the NOESY Experiment
Effect of Molecular Weight on the Intensity of NOESY Crosspeaks
Experimental Determination of Inter-proton Distances
Residual Dipolar Coupling (RDC)
Generating Partial Alignment of Macromolecules
Theory of Dipolar Coupling
Measurement of Residual Dipolar Couplings
Estimation of the Alignment Tensor
Protein Structure Determination
Energy Functions
Experimental Data
Covalent and Non-covalent Interactions
Energy Minimization and Simulated Annealing
Energy Minimization
Simulated Annealing
Generation of Starting Structures
Random Coordinates
Distance Geometry
Refinement
Illustrative Example of Protein Structure Determination
Exchange Processes
Introduction
Chemical Exchange
General Theory of Chemical Exchange
Fast Exchange Limit
Slow Exchange Limit
Intermediate Time Scales
Measurement of Chemical Exchange
Very Slow Exchange: k[subscript ex] << [Delta nu]
Slow Exchange: k[subscript ex] < [Delta nu]
Slow to Intermediate Exchange: k[subscript ex approximate Delta nu]
Fast Exchange: k[subscript ex] > [Delta nu]
Measurement of Exchange Using CPMG Methods
Distinguishing Fast from Slow Exchange
Effect of Temperature
Magnetic Field Dependence
Ligand Binding Kinetics
Slow Exchange
Intermediate Exchange
Fast Exchange
Exercises
Solutions
Nuclear Spin Relaxation and Molecular Dynamics
Introduction
Relaxation of Excited States
Time Dependent Field Fluctuations
Chemical Shift Anisotropy
Dipolar Coupling
Frequency Components from Molecular Rotation
Spin-lattice (T[subscript 1]) and Spin-spin (T[subscript 2]) Relaxation
Spin-lattice Relaxation
Spin-lattice Relaxation of Like Spins
Spin-lattice Relaxation of Unlike Spins
Spin-spin Relaxation
Heteronuclear NOE
Motion and the Spectral Density Function
Random Isotropic Motion
Anisotropic Motion - Non-spherical Protein
Constrained Internal Motion
Combining Internal and External Motion
Effect of Internal Motion on Relaxation
Anisotropic Rotational Diffusion
Measurement and Analysis of Relaxation Data
Pulse Sequences
Measuring Heteronuclear T[subscript 1]
Measuring Heteronuclear T[subscript 2]
Data Analysis and Model Fitting
Defining Rotational Diffusion
Determining Internal Rotation
Systematic Errors in Model Fitting
Statistical Tests
X[superscript 2] Test for Goodness-of-fit
Test for Inclusion of Additional Parameters
Alternative Methods of Model Selection
Error Propagation
Exercises
Solutions
Appendices
Fourier Transforms
Fourier Series
Non-periodic Functions - The Fourier Transform
Complex Variables, Scalars, Vectors, and Tensors
Complex Numbers
Representation of Signals with Complex Numbers
Scalars, Vectors, and Tensors
Solving Simultaneous Differential Equations: Laplace Transforms
Laplace Transforms
Building Blocks of Pulse Sequences
Product operators
Common Elements of Pulse Sequences
References
Index
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