Structural Biology

PREFACE.- CHAPTER 1 BASIC PRINCIPLES OF NMR: Introduction.- Nuclear Spin in a Static Magnetic Field.- Rotating Frame.- Bloch Equations.- Fourier Transformation and its Applications in NMR.- Nyquist Theorem and Digital Filters.- Chemical Shift.- Nuclear Coupling.- Nuclear Overhauser Effect.- Relaxation.- Selection of Coherence Transfer Pathways.- Approaches to Understanding NMR Experiments.- Questions.- Appendix A: Product Operators.- Uncoupled Spins.- A2. Two Coupled Spins.- References.- CHAPTER 2 INSTRUMENTATION: System Overview.- Magnet.- Transmitter.- Receiver.- Probe.- Quarter-wavelength Cable.- Analog/Digital Converters.- Instrument specifications.- Test or Measurement Equipment.- Spectrum Analyzer.- System Noise Measurement.- Questions.- References.- CHAPTER 3 NMR SAMPLE PREPARATION: Introduction.- Expression Systems.- Overexpression of Isotope-Labeled Proteins.- Purification of Isotope-Labeled Proteins.- NMR Sample Preparation.- Examples of Protocols for Preparing 15N/13C Labeled Proteins.- Questions.- References.- CHAPTER 4 PRACTICAL ASPECTS: Tuning the Probe.- Shimming and Locking.- Instrument Calibrations.- Selective Excitation with Narrow Band and Off-Resonance Shape Pulses.- Composite Pulses.- Adiabatic Pulses.- Pulsed Field Gradients.- Solvent Suppression.- NMR Data Processing.- Two-Dimensional Experiments.- Questions.- References.- CHAPTER 5 MULTIDIMENSIONAL HETERONUCLEAR NMR EXPERIMENTS: Two-dimensional heteronuclear experiments.- Overview of Triple-Resonance Experiments.- General Procedure of Setup and Data Processing for 3D Experiments.- Experiments for Backbone Assignments.- Experiments for Side-Chain Assignment.- 3D Isotope-Edited Experiments.- Sequence-Specific Resonance Assignments of Proteins.- Assignment of NOE Cross-Peaks.- Questions.- References.- CHAPTER 6 STUDIES OF SMALL BIOLOGICAL MOLECULES: Ligand-protein Complexes.- Study of Metabolic Pathways by NMR.- Questions.- References.- CHAPTER 7 PROTEIN STRUCTURE DETERMINATION FROM NMR DATA: Introduction and Historical Overview.- NMR Structure Calculation Methods.- NMR Parameters for Structure Calculation.- Preliminary Secondary Structural Analysis.- Tertiary Structure Determination.- Protein Complexes.- Questions.- Appendix B1. Sa.inp-XPLOR Protocol for Protein Structure Calculation.- Appendix B2. Example of NOE Table.- Appendix B3. Example of Dihedral Angle Restraint Table.- Appendix B4. Example of Chemical Shift Table for TALOS.- Appendix B5. Example of Hydrogen Bond Table.- Appendix B6. Example of Input File to Generate a Random-Coil Coordinates.- Appendix B7. Example of Input File to Generate a Geometric PSF File.- References.- CHAPTER 8 PROTEIN DYNAMICS: Theory of Spin Relaxation in Proteins.- Experiments for Measurements of Relaxation Parameters.- Relaxation Data Analysis.- Questions.- References.- MULTIPLE-CHOICE QUESTIONS.- ANSWERS TO MULTIPLE CHOICE QUESTIONS.- NOMENCLATURE AND SYMBOLS.- INDEX.