Biomedical Applications of Biophysics (eBook)

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.

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