Jue Biomedical Applications of Biophysics

1. Auflage 2010
ISBN: 978-1-60327-233-9
Verlag: Humana Press
Format: PDF
Kopierschutz: 1 - PDF Watermark

E-Book, Englisch, Band 3, 237 Seiten

Reihe: Handbook of Modern Biophysics

In keeping with goal and style of the Handbook in Modern Biophysics series, the proposed book will maintain a chapter structure that contains two parts: concepts and biological application. The book also integrates all the chapters into a smooth, continuous discourse. The first and second chapters establish the mathematical methods and theoretical framework underpinning the different topics in the rest if the book. Other chapters will use the theoretical framework as a basis to discuss optical and NMR approaches. Each chapter will contain innovative didactic elements that facilitate teaching, self-study, and research preparation (key points, summary, exercise, references).

Thomas Jue is a Professor in the Department of Biochemistry and Molecular Medicine at the University of California Davis. He is an internationally recognized expert in develop-ing and applying magnetic resonance techniques to study animal as well as human physi-ology in vivo and has published extensively in the field of magnetic resonance spectroscopy and imaging, near-infrared spectroscopy, bioenergetics, cardiovascular regu-lation, exercise, and marine biology. As the Chair of the Biophysics Graduate Group Program at University of California Davis, he launched an initiative to establish a biophysics book series that will balance the physical-science/mathematics formalism with the biomedical perspective in order to develop an attractive education curriculum at the interface of physical science, engineering, mathematics, biology, and medicine. The Handbook of Modern Biophysics represents part of that curriculum development effort.

Autoren/Hrsg.

Jue, Thomas

Inhaltsverzeichnis

1;PREFACE;6
2;CONTENTS;8
3;CONTRIBUTORS;12
4;1 PROTEIN STRUCTURE PREDICTION;14
4.1;1.1. INTRODUCTION;14
4.1.1;1.1.1. The Importance of Shape;15
4.1.2;1.1.2. The Data Revolution;15
4.2;1.2. BASIC PRINCIPLES OF PROTEIN STRUCTURE;16
4.2.1;1.2.1. Protein Building Blocks;17
4.2.2;1.2.2. Protein Structure Hierarchy;18
4.2.3;1.2.3. Three Main Types of Proteins;18
4.2.4;1.2.4. Geometry of Globular Proteins;19
4.3;1.3. THE ENERGETICS OF PROTEIN STRUCTURE;21
4.3.1;1.3.1. Stability of Protein Structures;21
4.3.2;1.3.2. Internal Energy;21
4.3.2.1;1.3.2.1. Bonded Interactions;22
4.3.2.2;1.3.2.2. Non-Bonded Interactions;22
4.3.3;1.3.3. The Entropy of a Protein Structure;23
4.3.4;1.3.4. The Denatured State;23
4.4;1.4. HOMOLOGY MODELING;23
4.4.1;1.4.1. Finding a template;25
4.4.2;1.4.2. Aligning the Target and Template Sequences;26
4.4.3;1.4.3. Generating a Model;27
4.4.3.1;1.4.3.1. Loop Building;27
4.4.3.2;1.4.3.2 Sidechain Modeling;29
4.4.3.3;1.4.3.3. Model Refinement;31
4.4.4;1.4.4. Evaluation of Models;31
4.4.5;1.4.5. Applications of Homology Modeling;32
4.5;1.5. AB-INITIO PROTEIN STRUCTURE PREDICTION;33
4.5.1;1.5.1. Simple Models: Lattice Studies;33
4.5.2;1.5.2. Protein Structure Prediction Based on First Principles;35
4.5.3;1.5.3. Bioinformatics Approaches to ab-initio Structure Prediction;35
4.5.3.1;1.5.3.1. Secondary Structure Prediction;35
4.5.3.2;1.5.3.2. Conformational Sampling for ab-initio Structure Prediction;37
4.5.3.3;1.5.3.3. Scoring Protein Decoys;38
4.6;1.6. THE CASP EXPERIMENT;38
4.7;1.7. CONCLUSIONS;39
4.8;ACKNOWLEDGMENTS;40
4.9;PROBLEMS;40
4.10;FURTHER READING;41
4.11;REFERENCES;42
5;2 MOLECULARMODELING OF BIOMEMBRANES: A HOW-TO APPROACH;48
5.1;2.1. INTRODUCTION TO MOLECULAR DYNAMICS;48
5.2;2.2. SPECIFICS OF THE MOLECULAR MODELING OF BIOMEMBRANES;50
5.3;2.3. FORCE FIELDS: SIMULATION MODELS;51
5.4;2.4. DEGREE OF DETAIL: ATOMISTIC VERSUS COARSE-GRAINED;52
5.5;2.5. VISUALIZATIONS;54
5.6;2.6. AREA PER MOLECULE AND THICKNESS, COMPARISON TO X-RAY DATA;54
5.7;2.7. ORDER PARAMETERS AND OTHER SINGLE-LIPID PROPERTIES;55
5.8;2.8. RADIAL DISTRIBUTION FUNCTIONS;57
5.9;2.9. HYDROGEN BONDING AND ADVANCED STATIC ANALYSIS;57
5.10;2.10. PRESSURE AND PRESSURE PROFILES;59
5.11;2.11. TWO-DIMENSIONAL DIFFUSION;59
5.12;2.12. REORIENTATIONS AND NMR;61
5.13;2.13. DYNAMICS OF INDIVIDUAL MOLECULES: CORRELATIONS OF DISTRIBUTION FUNCTIONS;62
5.14;2.14. INTERACTIONS WITH SMALL MOLECULES;62
5.15;2.15. SUMMARY;64
5.16;ACKNOWLEDGMENTS;65
5.17;PROBLEMS;65
5.17.1;Preparing the Simulation Program;65
5.17.2;Water Box;66
5.17.3;Exercise 2.1;66
5.18;FURTHER STUDY;67
5.18.1;Molecular Dynamics and Other Modeling Techniques in General;67
5.18.2;Specific Software Packages and Force Fields;67
5.19;REFERENCES;67
6;3 INTRODUCTION TO ELECTRON PARAMAGNETIC RESONANCE SPECTROSCOPY;72
6.1;3.1. INTRODUCTION;72
6.2;3.2. HISTORICAL BACKGROUND;73
6.3;3.3. BASIC EQUATIONS;74
6.4;3.4. SPIN HAMILTONIAN;76
6.5;3.5. CONTINUOUS WAVE (CW) VERSUS PULSED EPR TECHNIQUES;83
6.5.1;3.5.1. Electron Spin Echo Envelope Modulation (ESEEM);86
6.5.2;3.5.2. Electron Nuclear Double Resonance (ENDOR);86
6.5.3;3.5.3. 2D Techniques;88
6.6;3.6. EPR INSTRUMENTATION;88
6.7;3.7. EPR MEASUREMENTS IN SOLUTION AND SOLID STATE;92
6.8;3.8. TIME-RESOLVED EPR;95
6.9;3.9. DYNAMIC PROCESSES OBSERVED BY EPR;96
6.10;3.10. MULTIFREQUENCY EXPERIMENTS;98
6.11;3.11. QUANTUM CHEMISTRY CALCULATIONS;101
6.12;3.12. EPR IN BIOLOGY AND IN BIOINORGANIC CHEMISTRY;104
6.12.1;3.12.1. Copper;105
6.12.2;3.12.2. Iron;105
6.12.3;3.12.3. Manganese;106
6.13;ACKNOWLEDGMENTS;109
6.14;NOTE;109
6.15;PROBLEMS;109
6.16;FURTHER STUDY;110
6.16.1;Monographs;110
6.17;REFERENCES;110
7;4 THEORY AND APPLICATIONS OF BIOMOLECULAR NMR SPECTROSCOPY;112
7.1;4.1. INTRODUCTION;112
7.2;4.2. NUCLEAR AND ELECTRONIC SPIN;113
7.3;4.3. QUANTUM DESCRIPTION OF NUCLEAR SPIN;113
7.4;4.4. SPIN-STATE POPULATIONS IN ENSEMBLES;114
7.5;4.5. NUCLEAR SHIELDING AND CHEMICAL SHIFT;116
7.6;4.6. NMR SCALAR COUPLING;116
7.7;4.7. DIPOLAR COUPLING;117
7.8;4.8. NMR RELAXATION AND DYNAMICS;118
7.9;4.9. NEURONAL CALCIUM SENSOR PROTEINS;121
7.10;4.10. NMR STRUCTURAL ANALYSIS OF CA2+-MYRISTOYL SWITCH PROTEINS;123
7.10.1;4.10.1. Nuclear Magnetic Resonance Spectroscopy;123
7.10.2;4.10.2. Calcium-Induced Conformational Changes;124
7.10.3;4.10.3. Structural Basis of Target Recognition;125
7.11;4.11. SUMMARY;127
7.12;PROBLEMS;127
7.13;FURTHER STUDY;128
7.14;REFERENCES;128
8;5 FRET AND ITS BIOLOGICAL APPLICATION AS A MOLECULAR RULER;132
8.1;5.1. INTRODUCTION;132
8.2;5.2. DISTANCE DEPENDENCE OF FRET EFFICIENCY;134
8.3;5.3. SPECTRA OVERLAP BETWEEN FRET PAIRS;135
8.4;5.4. ORIENTATION FACTOR;135
8.5;5.5. ADVANTAGES OF FRET FOR BIOLOGICAL APPLICATIONS;136
8.6;5.6. DONOR DEQUENCHING;138
8.7;5.7. ENHANCED ACCEPTOR EMISSION;138
8.8;5.8. THREE-CUBE FRET;139
8.9;5.9. SPECTRA FRET;139
8.10;5.10. FLUORESCENCE INTENSITY RATIO BETWEEN DONOR AND ACCEPTOR;139
8.11;5.11. LIFETIME MEASUREMENTS;140
8.12;5.12. FRET QUANTIFICATION THROUGH PHOTOBLEACHING RATE MEASUREMENTS;140
8.13;5.13. PROTEIN COMPLEX FORMATION;141
8.14;5.14. SUBUNIT STOICHIOMETRY OF PROTEIN COMPLEX;142
8.15;5.15. BINDING OF LIGANDS OR MODULATORY MOLECULES;142
8.16;5.16. CONFORMATIONAL REARRANGEMENTS;143
8.17;5.17. INTRACELLULAR EVENT INDICATORS;144
8.18;ACKNOWLEDGMENTS;145
8.19;PROBLEMS;145
8.20;FURTHER STUDY;145
8.21;REFERENCES;146
9;6 INTRODUCTION TO MODERN TECHNIQUES IN MASS SPECTROMETRY;150
9.1;6.1. INTRODUCTION;150
9.2;6.2. IONIZATION TECHNIQUES (ION SOURCES);151
9.3;6.3. ELECTRON IMPACT;151
9.4;6.4. CHEMICAL IONIZATION;152
9.5;6.5. ELECTROSPRAY IONIZATION;152
9.6;6.6. MATRIX-ASSISTED LASER DESORPTION/IONIZATION;154
9.7;6.7. FOURIER TRANSFORM ION CYCLOTRON RESONANCE;156
9.8;6.8. TIME OF FLIGHT;159
9.9;6.9. TANDEM MASS SPECTROMETRY;161
9.10;6.10. COLLISION-INDUCED DISSOCIATION;161
9.11;6.11. INFRARED MULTIPHOTON DISSOCIATION;162
9.12;6.12. ELECTRON CAPTURE DISSOCIATION;163
9.13;6.13. ELECTRON TRANSFER DISSOCIATION;163
9.14;6.14. SUMMARY;163
9.15;ACKNOWLEDGMENTS;164
9.16;PROBLEMS;164
9.17;FURTHER STUDY;164
9.18;REFERENCES;164
10;7 TRANSMISSION ELECTRONMICROSCOPY AND COMPUTER-AIDED IMAGE PROCESSING FOR 3D STRUCTURAL ANALYSIS OF MACROMOLECULES;168
10.1;7.1. THE TRANSMISSION ELECTRON MICROSCOPE;168
10.2;7.2. PHASE-CONTRAST IMAGING;173
10.3;7.3. THE CONTRAST TRANSFER FUNCTION;174
10.4;7.4. THE PROJECTION THEOREM AND SINGLE-PARTICLE RECONSTRUCTION;177
10.5;7.5. ADVANTAGES OF SPR OVER X-RAY CRYSTALLOGRAPHY;179
10.6;7.6. SAMPLE PREPARATION;180
10.7;7.7. IMAGING CONDITIONS;181
10.8;7.8. DATA VALIDATION;181
10.9;7.9. DATA SELECTION & PREPARATION;182
10.10;7.10. MULTIVARIATE STATISTICAL ANALYSIS;182
10.11;7.11. CLASSIFICATION;185
10.12;7.12. ANGULAR RECONSTITUTION;187
10.13;7.13. REFERENCE-BASED REFINEMENT;187
10.14;7.14. INITIAL MODEL GENERATION;189
10.15;7.15. RECONSTRUCTION TECHNIQUES;192
10.16;7.16. RELIABILITY ASSESSMENT;192
10.17;7.17. ANALYSIS OF HETEROGENEITY;193
10.18;7.18. SUMMARY;194
10.19;ACKNOWLEDGMENTS;194
10.20;PROBLEMS;194
10.21;FURTHER READING;195
10.22;REFERENCES;195
11;8 RAMAN SPECTROSCOPY OF LIVING CELLS;198
11.1;8.1. INTRODUCTION;198
11.2;8.2. RAMAN SCATTERING: INELASTIC LIGHT SCATTERING BY MOLECULAR BONDS;199
11.2.1;8.2.1. The Induced Dipole Moment;201
11.2.2;8.2.2. Polarizability and Raman Scattering;202
11.2.3;8.2.3. Spectroscopy;205
11.2.4;8.2.4. Experimental Implementation of Micro-Raman Spectroscopy;209
11.2.5;8.2.5. Signal Calibration;213
11.2.6;8.2.6. Sample Preparation;214
11.2.7;8.2.7. Advanced Forms of Raman Spectroscopy;215
11.2.7.1;8.2.7.1. Surface-Enhanced Raman Scattering (SERS);216
11.2.7.2;8.2.7.2. Coherent Anti-Stokes Raman Scattering (CARS) Microscopy;217
11.3;8.3. SUMMARY;220
11.4;PROBLEMS;221
11.5;FURTHER READING;221
11.6;REFERENCES;221
12;PROBLEM SOLUTIONS;224
12.1;CHAPTER 1;224
12.2;CHAPTER 3;229
12.3;CHAPTER 4;233
12.4;CHAPTER 5;236
12.5;CHAPTER 6;237
12.6;CHAPTER 7;238
12.7;CHAPTER 8;239
13;INDEX;244