Chemical Biology Techniques and Applications

, by Larijani, Banafshe; Rosser, Colin A.; Woscholski, Rudiger

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ISBN: 9780470090657 | 0470090650
Cover: Paperback
Copyright: 8/25/2006

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This book provides an up-to-date guide to chemical biology. It is a modular textbook that brings together the tools and techniques used by physical scientists and makes them available to biological and biomedical scientists. Tools and techniques are explained at a suitable level and the book addresses topical chemical biology questions within each chapter.

Preface

List of Contributors

xiii

1 Introduction

(150)

Banafshé Larijani, Colin. A. Rosser and Rudiger Woscholski

1.1 Chemical biology – the present

(1)

1.2 Chemical biology – the past

(1)

1.3 Chemical biology – the future

(1)

1.4 Chemical biology – mind the interdisciplinary gap

(1)

1.5 An introduction to the following chapters

(6)

1.5.1 Cryo-electron microscopy

(1)

1.5.2 Atomic force microscopy

(1)

1.5.3 Differential scanning calorimetry in the study of lipid structures

(1)

1.5.4 Membrane potentials and membrane probes

(1)

1.5.5 Identification and quantification of lipids using mass spectroscopy

(1)

1.5.6 Liquid-state NMR

(1)

1.5.7 Solid-state NMR in biomembranes

(1)

1.5.8 Molecular dynamics

(1)

1.5.9 Two-dimensional infrared studies of biomolecules

(1)

1.5.10 Biological applications of single and two-photon fluorescence

(1)

1.5.11 Optical tweezers

(1)

1.5.12 PET imaging in chemical biology

(1)

1.5.13 Chemical genetics

(2)

2 Cryomicroscopy

(18)

Frank Booy and Elena Orlova

2.1 The need for (electron) microscopy

(1)

2.2 Development of cryomicroscopy

(2)

2.3 Sample–electron interaction

(1)

2.4 Contrast in negatively stained and cryo preparations

(2)

2.5 Image formation

(1)

2.6 Image analysis

(3)

2.7 Software used in the analysis of electron micrographs

(2)

2.8 Examples

(6)

2.8.1 Two-dimensional crystals

(1)

2.8.2 Helical structures

(3)

2.8.3 Single particles with low symmetry

(1)

2.8.4 Cellular tomography

(3)

2.9 Conclusions

(2)

3 Atomic force microscopy: applications in biology

(18)

James Moody and Stephanie Allen

3.1 A brief history of microscopy

(1)

3.2 The scanning probe microscope revolution

(1)

3.2.1 The stylus profiler

(1)

3.2.2 The scanning tunnelling microscope

(1)

3.2.3 The atomic force microscope

(1)

3.3 The workings of an AFM instrument

(3)

3.3.1 The imaging probe

(1)

3.3.2 The piezoelectric scanner

(1)

3.3.3 The deflection detection system

(1)

3.3.4 The electronic feedback system

(1)

3.4 Imaging biological molecules with force

(4)

3.4.1 Contact mode

(1)

3.4.2 Oscillating cantilever imaging modes

(2)

3.4.3 Imaging in liquid

(1)

3.5 Factors influencing image quality

(4)

3.5.1 Sample preparation and immobilization

(1)

3.5.2 Tip convolution/broadening

(1)

3.5.3 Double tipping

(1)

3.5.4 Sample roughness

(1)

3.5.5 Temperature variation and vibration isolation

(1)

3.6 Biological applications of AFM and recent developments

(3)

3.6.1 Imaging dynamic processes

(1)

3.6.2 Measuring Biomolecular forces

(2)

3.7 Conclusions and future directions

(2)

4 Differential scanning calorimetry in the study of lipid structures

(20)

Félix M. Goñi and Alicia Alonso

4.1 Introduction

(1)

4.2 Membranes, lipids and lipid phases

(3)

4.3 Heat exchanges and calorimetry

(3)

4.3.1 Heat and related entities

(1)

4.3.2 Differential scanning calorimetry

(1)

4.4 Phase transitions in pure lipid–water systems

(2)

4.4.1 Gel (Lβ) to rippled (Pβ) phase transition (the 'pre-transition')

(1)

4.4.2 Rippled (Pβ) to liquid-crystalline (Lα) phase transition

(1)

4.4.3 Gel (Lβ) to liquid-crystalline (Lα) phase transition

(1)

4.4.4 Lamellar (Lα) to inverted hexagonal (HII) phase transition

(1)

4.5 Selected examples of transitions in lipid mixtures

(7)

4.5.1 Phospholipid–cholesterol mixtures

(3)

4.5.2 Lamellar-to-inverted hexagonal transitions

(2)

4.6 Complex systems: lipid–protein mixtures and cell membranes

(3)

4.6.1 Lipid–protein systems

(2)

4.6.2 Cell membranes and cell walls

(1)

4.7 Conclusion

(2)

5 Membrane potentials and membrane probes

(18)

Paul O'Shea

5.1 Introduction: biological membranes; structure and electrical properties

(1)

5.2 Phospholipid membranes as molecular environments

(1)

5.3 The physical origins of the transmembrane (Vm or Δψ) surface (øs) and dipolar (øD) membrane potentials

(5)

5.3.1 The transmembrane potential difference (Vm or Δψ)

(2)

5.3.2 The membrane surface potential (øs)

(2)

5.3.3 The membrane dipole potential (ød)

(1)

5.4 Measurement of membrane potentials

(8)

5.4.1 Electrodes

(3)

5.4.2 Spectroscopic measurements of the transmembrane potential difference

(1)

5.4.3 Spectroscopic measurements of the membrane surface potential

(1)

5.4.4 Spectroscopic measurements of the membrane dipole potential

(3)

5.5 Problems with spectroscopic measurements of membrane potentials

(1)

5.6 Spatial imaging of membrane potentials

(3)

6 Identification and quantification of lipids using mass spectrometry

(10)

Trevor R. Pettitt and Michael J.O. Wakelam

6.1 Introduction

(1)

6.2 Lipid analysis by mass spectrometry

(7)

6.2.1 HPLC-ESI-MS

(3)

6.2.2 Tandem mass spectrometry

(2)

6.3 Conclusion

(2)

7 Liquid-state NMR

(18)

Charlie Dickinson

7.1 Introduction

(1)

7.2 How NMR works: the basics

(4)

7.3 Some NMR applications in biology

100

(11)

7.3.1 In vivo cell metabolism made 'visible' by NMR

100

(1)

7.3.2 In vivo phosphorus and nitrogen metabolism

101

(3)

7.3.3 Identification and quantification of small quantities in a complex mixture by 2D¹H-³¹ P-HMQC-TOCSY NMR

104

(2)

7.3.4 Simultaneous separation and identification of very complex mixtures: LC-NMR

106

(2)

7.3.5 Three-dimensional molecular structures in solution

108

(3)

7.4 Conclusion

111

(2)

8 Solid-state NMR in biomembranes

113

(20)

Erick J. Dufourc

8.1 Introduction

113

(1)

8.2 NMR basics for membrane systems

114

(5)

8.2.1 Anisotropy of NMR interactions in membranes

114

(2)

8.2.2 Spectra and the effect of motional averages

116

(2)

8.2.3 A special case of motional averaging: magic angle sample spinning

118

(1)

8.2.4 Relaxations times: measuring dynamics

118

(1)

8.3 Applications of wide-line NMR to membrane systems

119

(7)

8.3.1 Lipid phases: diagrams, peptide-induced fusion–fragmentation

120

(1)

8.3.2 Bilayer internal dynamics: order parameters, membrane thickness, sterols

121

(3)

8.3.3 Orientation of molecules (sterols, helical peptides) in membranes

124

(1)

8.3.4 Membrane dynamics from picoseconds to milliseconds

124

(2)

8.4 Applications of MAS to biomembranes and natural colloids

126

(2)

8.4.1 Three-dimensional structure of peptides in membranes

126

(2)

8.4.2 Three-dimensional structure of wine tannin–salivary protein colloidal complexes

128

(1)

8.4.3 Distance determination using MAS recoupling techniques

128

(1)

8.5 Conclusion

128

(5)

9 Molecular dynamics

133

(18)

Michel Laguerre

9.1 Introduction

133

(1)

9.2 The basis of molecular mechanics

133

(4)

9.2.1 Force fields

134

(1)

9.2.2 The energy problem

135

(2)

9.3 The basis of molecular dynamics

137

(2)

9.3.1 Influence of temperature

138

(1)

9.4 Factors affecting the length of simulations

139

(1)

9.5 Problems caused by solvents

140

(2)

9.6 How to build a lipid bilayer for simulation purposes

142

(4)

9.7 Special case of membrane proteins

146

(3)

9.8 Summary

149

(2)

10 Two-dimensional infrared studies of biomolecules

151

(12)

Xabier Coto, Ibón Iloro and José Luis R. Arrondo

10.1 Introduction

151

(1)

10.2 Description of the technique

152

(1)

10.3 Spectral simulations

152

(6)

10.3.1 Intensity changes

154

(2)

10.3.2 Band shifting

156

(1)

10.3.3 Bandwidth

157

(1)

10.4 Two-dimensional studies of human lipoproteins

158

(3)

10.5 Summary

161

(2)

11 Biological applications of single- and two-photon fluorescence

163

(36)

Banafshe Larijani and Angus Bain

11.1 Introduction

163

(1)

11.2 Basic principles of fluorescence

163

(1)

11.3 Main principles of RET via single-photon excitation

164

(1)

11.4 Detection of RET

165

(3)

11.4.1 Steady-state method

165

(1)

11.4.2 Time-resolved method

166

(2)

11.5 Biological examples of RET monitored by frequency-domain FLIM

168

(3)

11.6 Two-photon fluorescence

171

(7)

11.6.1 Basic concepts

171

(3)

11.6.2 Two-photon fluorescence

174

(4)

11.7 Applications of two-photon fluorescence

178

(7)

11.7.1 Two-photon fluorescence imaging

178

(6)

11.7.2 Biological example – two-photon time-domain FLIM

184

(1)

11.8 Photoselection and fluorescence anisotropy

185

(1)

11.9 Fluorescence anisotropy and isotropic rotational diffusion

185

(3)

11.10 Fluorescent probes in proteins and membranes

188

(5)

11.10.1 Ordered molecular systems

190

(3)

11.11 Future developments

193

(3)

11.11.1 New chromophores for two-photon fluorescence

193

(1)

11.11.2 Stimulated emission depletion in two-photon excited states

193

(3)

11.12 Conclusions

196

(3)

12 Optical tweezers

199

(18)

Christopher Batters and Justin E. Molloy

12.1 Introduction

199

(2)

12.1.1 History of optical tweezers

199

(1)

12.1.2 Single-molecule studies

200

(1)

12.2 Theoretical background

201

(2)

12.3 Apparatus

203

(4)

12.3.1 Building an optical tweezers transducer

203

(1)

12.3.2 Creating multiple laser traps: acousto-optical deflectors

204

(2)

12.3.3 Camera and light path

206

(1)

12.4 Data collection and analysis

207

(2)

12.4.1 Collecting data with an optical tweezer

207

(1)

12.4.2 Calibration of the detectors and of the optical tweezer stiffness

208

(1)

12.4.3 Stokes calibration

208

(1)

12.4.4 Equipartition principle

208

(1)

12.5 A biological application

209

(5)

12.5.1 Studying acto-myosin interactions

209

(2)

12.5.2 Identification of events and data analysis

211

(1)

12.5.3 Measuring the powerstroke

211

(2)

12.5.4 Lifetime analysis

213

(1)

12.6 Other biological examples

214

(2)

12.7 Summary

216

(1)

13 PET imaging in chemical biology

217

(14)

Ramón Vilar

13.1 Introduction

217

(1)

13.2 Positron emission tomography: principles and instrumentation

218

(2)

13.3 Applications of PET imaging in the biomedical sciences

220

(8)

13.3.1 A labelled glucose analogue: an indirect probe to measure energy metabolism

221

(1)

13.3.2 Imaging dopamine metabolism with PET

222

(2)

13.3.3 PET imaging in gene expression

224

(2)

13.3.4 Molecular imaging in drug discovery and development

226

(2)

13.4 Conclusions and outlook

228

(3)

14 Chemical genetics

231

(18)

Piers Gaffney

14.1 Introduction

231

(1)

14.2 Why chemicals?

232

(1)

14.3 Chemical genetics — why now?

233

(1)

14.4 The relationship between classical genetics and chemical genetics

234

(1)

14.5 Forward chemical genetics

235

(10)

14.5.1 Obtain a compound library

236

(6)

14.5.2 Screening

242

(2)

14.5.3 Target identification

244

(1)

14.6 Reverse chemical genetics

245

(2)

14.7 Closing remarks

247

(2)

Index

249

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Chemical Biology Techniques and Applications

Summary

Author Biography

Table of Contents

Supplemental Materials