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.
Preface IX
1 Introduction 1
1.1 Aims of Vibrational Spectroscopy in Life Sciences 2
1.2 Vibrational Spectroscopy An Atomic-scale Analytical Tool 3
1.3 Biological Systems 4
1.4 Scope of the Book 7
1.5 Further Reading 9
References 10
2 Theory of Infrared Absorption and Raman Spectroscopy 11
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
References 60
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 Spectroscopy 70
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 Infrared Spectroscopy 72
3.1.4.2 Time-resolved Studies Using Tunable Monochromatic Infrared Sources 74
3.1.4.3 Time-resolved Fourier Transform Infrared Spectroscopy Using the Step-scan Method 74
3.1.5 Time-resolved Pump-probe Studies with Sub-nanosecond Time-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
References 97
4 Experimental Techniques 99
4.1 Inherent Problems of Infrared and Raman Spectroscopy in Life Sciences 99
4.1.1 The Water Problem in Infrared Spectroscopy 99
4.1.2 Unwanted Photophysical and Photochemical Processes in Raman 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 Biopolymers 127
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 PumpProbe 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 FreezeQuench 145
4.4.3 Relaxation Methods 146
4.4.4 Spatially Resolved Vibrational Spectroscopy 148
4.5 Analysis of Spectra 149
References 151
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 to Secondary Structure 161
5.4 Direct Measurement of the Interaction of the Amide I Oscillators 167
5.5 UV-resonance Raman Studies Using the Amide III Mode 169
5.6 Protein Folding and Unfolding Studies Using Vibrational Spectroscopy 171
References 178
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 Activation Mechanism 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 Pump Bacteriorhodopsin 206
6.3 Study of the Anion Uptake by the Retinal Protein Halorhodopsin Using ATR Infrared Spectroscopy 214
6.4 Infrared Studies Using Caged Compounds as the Trigger Source 217
References 222
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 StructureSpectra Relationships 234
7.2 Hemoglobin and Myoglobin 236
7.2.1 Vibrational Analysis of the Heme Cofactor 237
7.2.2 IronLigand and Internal Ligand Modes 239
7.2.3 Probing Quaternary Structure Changes 240
7.3 Cytochrome c a Soluble Electron-transferring Protein 244
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 Immobilised State 253
7.3.5 Electron Transfer Dynamics and Mechanism 260
7.3.6 The Relevance of Surface-enhanced Vibrational Spectroscopic 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
References 278
8 Non-heme Metalloproteins 283
8.1 Copper Proteins 284
8.2 IronSulfur Proteins 290
8.3 Di-iron Proteins 296
8.4 Hydrogenases 300
References 302
Index 305
