Vibrational Spectroscopy in Life Science / Edition 1

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Overview

The authors describe basic theoretical concepts of vibrational spectroscopy, address instrumental aspects and experimental procedures, and discuss experimental and theoretical methods for interpreting vibrational spectra. It is shown how vibrational spectroscopy provides information on general aspects of proteins, such as structure, dynamics, and protein folding. In addition, the authors use selected examples to demonstrate the application of Raman and IR spectroscopy to specific biological systems, such as metalloproteins, and photoreceptors. Throughout, references to extensive mathematical and physical aspects, involved biochemical features, and aspects of molecular biology are set in boxes for easier reading.
Ideal for undergraduate as well as graduate students of biology, biochemistry, chemistry, and physics looking for a compact introduction to this field.

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Editorial Reviews

From the Publisher
"This work offers not only a detailed introduction to theory andinstrumentation, but also an in-depth discussion of thesetechniques in protein-related studies, which will benefit studentsand researchers wishing to include them in their research …Highly recommended." (CHOICE, March 2009)

"The book is a successful effort to bridge the gap betweenphysical and life sciences…" (Colloid Plymer Science,February 2008)

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Product Details

  • ISBN-13: 9783527405060
  • Publisher: Wiley
  • Publication date: 12/21/2007
  • Series: Tutorials in Biophysics Series
  • Edition number: 1
  • Pages: 320
  • Product dimensions: 6.97 (w) x 9.69 (h) x 0.80 (d)

Meet the Author

Friedrich Siebert is Professor for Biophysics at theUniversity of Freiburg. He studied physics in Freiburg and Hamburg,receiving his PhD in solid-state physics. Since his diploma thesishe is working with different methods of vibrational spectroscopy.In 1972 he changed to biophysics, establishing the method of staticand time-resolved infrared difference spectroscopy. Currentresearch interests are photo-biological systems, membrane proteinsand receptors, surface-enhanced techniques, time-resolved IRtechniques.

Peter Hildebrandt received his PhD in chemistry from theUniversität Göttingen in 1985. After a post-doc stay inPrinceton, he worked in research institutes in Göttingen,Mülheim, and Lisboa. Since 2003 he is Professor for PhysicalChemistry and Biophysical Chemistry at the TechnischeUniversität Berlin. His research is dedicated to vibrationalspectroscopy of biological systems, focussing on Ramanspectroscopic techniques applied to redox proteins andphotoreceptors.

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Table of Contents

Preface IX

1 Introduction 1

1.1 Aims of Vibrational Spectroscopy in Life Sciences 2

1.2 Vibrational Spectroscopy - An Atomic-scale Analytical Tool3

1.3 Biological Systems 4

1.4 Scope of the Book 7

1.5 Further Reading 9

2 Theory of Infrared Absorption and Raman Spectroscopy11

2.1 Molecular Vibrations 12

2.1.1 Normal Modes 15

2.1.2 Internal Coordinates 18

2.1.3 The FG-Matrix 19

2.1.4 Quantum Chemical Calculations of the FG-Matrix 23

2.2 Intensities of Vibrational Bands 25

2.2.1 Infrared Absorption 25

2.2.2 Raman Scattering 28

2.2.3 Resonance Raman Effect 32

2.3 Surface Enhanced Vibrational Spectroscopy 38

2.3.1 Surface Enhanced Raman Effect 39

2.3.2 Surface Enhanced Infrared Absorption 43

3 Instrumentation 63

3.1 Infrared Spectroscopy 63

3.1.1 Fourier Transform Spectroscopy 64

3.1.1.1 Interferometer 67

3.1.1.2 Infrared Detectors 69

3.1.2 Advantages of Fourier Transform Infrared Spectroscopy70

3.1.3 Optical Devices: Mirrors or Lenses? 71

3.1.4 Instrumentation for Time-resolved Infrared Studies 72

3.1.4.1 Time-resolved Rapid-scan Fourier Transform InfraredSpectroscopy 72

3.1.4.2 Time-resolved Studies Using Tunable MonochromaticInfrared Sources 74

3.1.4.3 Time-resolved Fourier Transform Infrared SpectroscopyUsing the Step-scan Method 74

3.1.5 Time-resolved Pump-probe Studies with Sub-nanosecondTime-resolution 76

3.2 Raman Spectroscopy 79

3.2.1 Laser 80

3.2.1.1 Laser Beam Properties 81

3.2.1.2 Optical Set-up 83

3.2.2 Spectrometer and Detection Systems 84

3.2.2.1 Monochromators 84

3.2.2.2 Spectrographs 86

3.2.2.3 Confocal Spectrometers 87

3.2.2.4 Fourier Transform Raman Interferometers 89

4 Experimental Techniques 99

4.1 Inherent Problems of Infrared and Raman Spectroscopy in LifeSciences 99

4.1.1 The ‘‘Water’’ Problem in InfraredSpectroscopy 99

4.1.2 Unwanted Photophysical and Photochemical Processes inRaman Spectroscopy 101

4.1.2.1 Fluorescence and Raman Scattering 102

4.1.2.2 Photoinduced Processes 104

4.2 Sample Arrangements 105

4.2.1 Infrared Spectroscopy 106

4.2.1.1 Sandwich Cuvettes for Solution Studies 106

4.2.1.2 The Attenuated Total Reflection (ATR) Method 108

4.2.1.3 Electrochemical Cell for Infrared Spectroscopy 113

4.2.2 Raman and Resonance Raman Spectroscopy 116

4.2.2.1 Measurements in Solutions 116

4.2.2.2 Solid State and Low-temperature Measurements 117

4.3 Surface Enhanced Vibrational Spectroscopy 118

4.3.1 Colloidal Suspensions 119

4.3.2 Massive Electrodes in Electrochemical Cells 120

4.3.3 Metal Films Deposited on ATR Elements 122

4.3.4 Metal/Electrolyte Interfaces 123

4.3.5 Adsorption-induced Structural Changes of Biopolymers127

4.3.6 Biocompatible Surface Coatings 128

4.3.7 Tip-enhanced Raman Scattering 130

4.4 Time-resolved Vibrational Spectroscopic Techniques 131

4.4.1 Pump–Probe Resonance Raman Experiments 132

4.4.1.1 Continuous-wave Excitation 133

4.4.1.2 Pulsed-laser Excitation 138

4.4.1.3 Photoinduced Processes with Caged Compounds 141

4.4.2 Rapid Mixing Techniques 141

4.4.2.1 Rapid Flow 144

4.4.2.2 Rapid Freeze–Quench 145

4.4.3 Relaxation Methods 146

4.4.4 Spatially Resolved Vibrational Spectroscopy 148

4.5 Analysis of Spectra 149

5 Structural Studies 155

5.1 Basic Considerations 155

5.2 Practical Approaches 158

5.3 Studies on the Origin of the Sensitivity of Amide I Bands toSecondary Structure 161

5.4 Direct Measurement of the Interaction of the Amide IOscillators 167

5.5 UV-resonance Raman Studies Using the Amide III Mode 169

5.6 Protein Folding and Unfolding Studies Using VibrationalSpectroscopy 171

6 Retinal Proteins and Photoinduced Processes 181

6.1 Rhodopsin 183

6.1.1 Resonance Raman Studies of Rhodopsin 185

6.1.2 Resonance Raman Spectra of Bathorhodopsin 188

6.1.3 Fourier Transform Infrared Studies of the ActivationMechanism of Rhodopsin 195

6.1.3.1 Low-temperature Photoproducts 197

6.1.3.2 The Active State Metarhodopsin II (MII) 201

6.2 Infrared Studies of the Light-driven Proton PumpBacteriorhodopsin 206

6.3 Study of the Anion Uptake by the Retinal ProteinHalorhodopsin Using ATR Infrared Spectroscopy 214

6.4 Infrared Studies Using Caged Compounds as the Trigger Source217

7 Heme Proteins 227

7.1 Vibrational Spectroscopy of Metalloporphyrins 228

7.1.1 Metalloporphyrins Under D4h Symmetry 228

7.1.2 Symmetry Lowering 231

7.1.3 Axial Ligation 232

7.1.4 Normal Mode Analyses 233

7.1.5 Empirical Structure-Spectra Relationships 234

7.2 Hemoglobin and Myoglobin 236

7.2.1 Vibrational Analysis of the Heme Cofactor 237

7.2.2 Iron-Ligand and Internal Ligand Modes 239

7.2.3 Probing Quaternary Structure Changes 240

7.3 Cytochrome c - a Soluble Electron-transferring Protein244

7.3.1 Vibrational Assignments 245

7.3.2 Redox Equilibria in Solution 246

7.3.3 Conformational Equilibria and Dynamics 248

7.3.4 Redox and Conformational Equilibria in the ImmobilisedState 253

7.3.5 Electron Transfer Dynamics and Mechanism 260

7.3.6 The Relevance of Surface-enhanced VibrationalSpectroscopic Studies for Elucidating Biological Functions 267

7.4 Cytochrome c Oxidase 268

7.4.1 Resonance Raman Spectroscopy 268

7.4.2 Redox Transitions 271

7.4.3 Catalytic Cycle 274

7.4.4 Oxidases from Extremophiles and Archaea 277

8 Non-heme Metalloproteins 283

8.1 Copper Proteins 284

8.2 Iron-Sulfur Proteins 290

8.3 Di-iron Proteins 296

8.4 Hydrogenases 300

References 302

Index 305

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