Chemical Biology: Techniques and Applications

List of Contributors.

1. Introduction.

1.1 Chemical biology - the present.

1.2 Chemical biology - the past.

1.3 Chemical biology - the future.

1.4 Chemical biology - mind the interdisciplinary gap.

1.5 An introduction to the following chapters.

2. Cryomicroscopy.

2.1 The need for (electron) microscopy.

2.2 Development of cryomicroscopy.

2.3 Sample-electron interaction.

2.4 Contrast in negatively stained and cryo preparations.

2.5 Image formation.

2.6 Image analysis.

2.7 Software used in the analysis of electron micrographs.

2.8 Examples.

2.9 Conclusions.

3. Atomic force microscopy: applications in biology.

3.1 A brief history of microscopy.

3.2 The scanning pribe microscope revolution.

3.3 The workings of an AFM instrument.

3.4 Imaging biological molecules with force.

3.5 Factors influencing image quality.

3.6 Biological applications of AFM and recent developments.

3.7 Conclusions and future directions.

4. Differential scanning calorimetry in the study of lipid structures.

4.1 Introduction.

4.2 Membranes, lipids and lipid phases.

4.3 Heat exchanges and calorimetry.

4.4 Phase transitions in pure lipid-water systems.

4.5 Selected examples of transitions in lipid mixtures.

4.6 Complex systems: lipid-protein mixtures and cell membranes.

4.7 Conclusion.

5. Membrane potentials and membrane probes.

5.1 Introduction: biological membranes; structure and electrical properties.

5.2 Phospholipid membranes as molecular environments.

5.3 The physical origins of the transmembrane (ΔΨ), surface (φS) and dipolar (φD) membrane potentials.

5.4 Measurement of membrane potentials.

5.5 Problems with Spectroscopic Measurements of Membrane Potentials.

5.6 Spatial Imaging of membrane potentials.

6. Identification and quantification of lipids using mass spectrometry.

6.1 Introduction.

6.2 Lipid analysis by mass spectrometry.

6.3 Conclusion.

7. Liquid-state NMR.

7.1 Introduction.

7.2 How NMR works: the basics.

7.3 Some NMR applications in biology.

7.4 Conclusion.

8. Solid-state NMR in biomembranes.

8.1 Introduction.

8.2 NMR basics for membrane systems.

8.3 Applications of wide-line NMR to membrane systems.

8.4 Applications of MAS to biomembranes and natural colloids.

8.5 Conclusion.

9. Molecular dynamics.

9.1 Introduction.

9.2 The basis of molecular mechanics.

9.3 The basis of molecular dynamics.

9.4 Factors affecting the length of simulations.

9.5 Problems caused by solvents.

9.6 How to build a lipid bilayer for simulation purposes.

9.7 Special cases of membrane proteins.

9.8 Summary.

10. Two-dimensional infrared studies of biomolecules.

10.1 Introduction.

10.2 Description of the technique.

10.3 Spectral simulations.

10.4 Two-dimensional studies of human lipoproteins.

10.5 Summary.

11. Biological applications of single- and two-photon fluorescence.

11.1 Introduction.

11.2 Basic principles of fluorescence.

11.3 Main principles of RET via single-photon excitation.

11.4 Detection of RET.

11.5 Biological examples of RET monitored by frequency-domain FLIM.

11.6 Two-photon fluorescence.

11.7 Applications of two-photon fluorescence.

11.8 Photoselection and fluorescence anisotropy.

11.9 Fluorescence anisotropy and isotropic rotational diffusion.

11.10 Fluorescent probes in proteins and membranes.

11.11 Future developments.

11.12 Conclusions.

12. Optical tweezers.

12.1 Introduction.

12.2 Theoretical background.

12.3 Apparatus.

12.4 Data collection and analysis.

12.5 A biological application.

12.6 Other biological examples.

12.7 Summary.

13. PET imaging in chemical biology.

13.1 Introduction.

13.2 Positron emission tomography: principles and instrumentation.

13.3 Applications of PET imaging in the biomedical sciences.

13.4 Conclusions and outlook.

14. Chemical genetics.

14.1 Introduction.

14.2 Why chemicals?.

14.3 Chemical genetics - why now?.

14.4 The relationship between classical genetics and chemical genetics.

14.5 Forward chemical genetics.

14.6 Reverse chemical genetics.

14.7 Closing remarks.

Index.