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Biomedical applications of biophysics / Thomas Jue, editor. — New York : Humana, c2010. – (58.171/B615a) |
Contents
Contents
1 Protein Structure Prediction
1.1. Introduction 1
1.2. Basic Principles of Protein Structure 3
1.3. The Energetics of Protein Structure 8
1.4. Homology Modeling 10
1.5. Ab-Initio Protein Structure Prediction 20
1.6. The CASP Experiment 25
1.7. Conclusions 26
2 Molecular Modeling of Biomembranes: A How-to Approach
2.1. Introduction to Molecular Dynamics
2.2. Specifics of the Molecular Modeling of Biomembranes
2.3. Force Fields: Simulation Models
2.4. Degree of Detail: Atomistic versus Coarse-Grained
2.5. Visualizations
2.6. Area per Molecule and Thickness， Comparison to X-Ray Data
2.7. Order Parameters and Other Single-Lipid Properties
2.8. Radial Distribution Functions
2.9. Hydrogen Bonding and Advanced Static Analysis
2.10. Pressure and Pressure Profiles
2.11. Two-Dimensional Diffusion
2.12. Reorientations and NMR
2.13. Dynamics of Individual Molecules: Correlations of Distribution Functions
2.14. Interactions with Small Molecules
2.15. Summary
3 Introduction to Electron Paramagnetic Resonance Spectroscopy
3.1. Introduction 59
3.2. Historical Background 60
3.3. Basic Equations 61
3.4. Spin Hamiltonian 63
3.5. Continuous Wave (CW) versus Pulsed EPR Techniques 70
3.6. EPR Instrumentation 75
3.7. EPR Measurements in Solution and Solid State 79
3.8. Time-Resolved EPR 82
3.9. Dynamic Processes Observed by EPR 83
3.10. Multifrequency Experiments 85
3.11. Quantum Chemistry Calculations 88
3.12. EPR in Biology and in Bioinorganic Chemistry 9!
4 Theory and Applications of Biomolecular NMR Spectroscopy
4.1. Introduction 99
4.2. Nuclear and Electronic Spin 100
4.3. Quantum Description of Nuclear Spin 100
4.4. Spin-State Populations in Ensembles 101
4.5. Nuclear Shielding and Chemical Shift 103
4.6. NMR Scalar Coupling 103
4.7. Dipolar Coupling 104
4.8. NMR Relaxation and Dynamics 105
4.9. Neuronal Calcium Sensor Proteins 108
4.10. NMR Structural Analysis of Ca2+-Myristoyl Switch Proteins 110
4.1l. Summary 114
5 FRET and Its Biological Application as a Molecular Ruler
5.1. Introduction 119
5.2. Distance Dependence of FRET Efficiency 121
5.3. Spectra Overlap between FRET Pairs
5.4. Orientation Factor
5.5. Advantages of FRET for Biological Applications
5.6. Donor Dequenching
5.7. Enhanced Acceptor Emission
5.8. Three-Cube FRET
5.9. Spectra FRET
5.10. Fluorescence Intensity Ratio between Donor and Acceptor
5.11. Lifetime Measurements
5.12. FRET Quantification through Photobleaching Rate Measurements
5.13. Protein Complex Formation
5.14. Subunit Stoichiometry of Protein Complex
5.15. Binding of Ligands or Modulatory Molecules
5.16. Conformational Rearrangements
5.17. Intracellular Event Indicators
6 Introduction to Modern Techniques in Mass Spectrometry
6.1. Introduction
6.2. Ionization Techniques (Ion Sources)
6.3. Electron Impact
6.4. Chemical Ionization
6.5. Electrospray Ionization
6.6. Matrix-Assisted Laser Desorption/Ionization
6.7. Fourier Transform Ion Cyclotron Resonance
6.8. Time of Flight
6.9. Tandem Mass Spectrometry
6.10. Collision-Induced Dissociation
6.11. Infrared Multiphoton Dissociation
6.12. Electron Capture Dissociation
6.13. Electron Transfer Dissociation
6.14. Summary
7 Transmission Electron Microscopy and Computer-Aided Image Processing for 3D Structural Analysis of Macromolecules
7.1. The Transmission Electron Microscope 155
7.2. Phase-Contrast Imaging 160
7.3. The Contrast Transfer Function 161
7.4. The Projection Theorem and Single-Particle Reconstruction 164
7.5. Advantages of SPR over X-Ray Crystallography 166
7.6. Sample Preparation 167
7.7. Imaging Conditions 168
7.8. Data Validation 168
7.9. Data Selection and Preparation 169
7.10. Multivariate Statistical Analysis 169
7.11. Classification 172
7.12. Angular Reconstitution 174
7.13. Reference-Based Refinement 174
7.14. Initial Model Generation 176
7.15. Reconstruction Techniques 179
7.16. Reliability Assessment 179
7.17. Analysis of Heterogeneity 180
7.18. Summary 181
8 Raman Spectroscopy of Living Cells
8.1. Introduction 185
8.2. Raman Scattering: Inelastic Light Scattering by Molecular Bonds 186
8.3. Summary 207
Problem Solutions 211
Index 231
