Foreword ...................................................... vii
Preface ........................................................ ix
Chapter I
Introduction and Future of Site-Directed Spin Labeling of
Membrane Proteins
Marcus A. Hemminga
1. Structural Biology and Proteomics ........................ 1
2. Membrane Proteins: Production and Reconstitution
Challenges ............................................... 2
3. SDSL-ESR ................................................. 2
4. Cysteine Modification .................................... 3
5. Structure and Dynamics Information from SDSL-ESR ......... 4
6. Pulsed ESR Spectroscopy .................................. 6
7. High-Field ESR Spectroscopy .............................. 8
8. Molecular Dynamics Simulations ........................... 9
9. Spectral Simulation and Analysis ........................ 11
10. Comparison with Site-Directed Fluorescence Labeling ..... 11
11. Future .................................................. 13
Chapter 2
Instrumentation and Experimental Setup
Gunnar Jeschke
1. Continuous-Wave ESR ..................................... 18
2. Basics of Pulsed ESR .................................... 25
3. Pulsed ENDOR ............................................ 31
4. Pulsed ELDOR (DEER) ..................................... 39
5. Acknowledgments ......................................... 43
6. Problems ................................................ 44
7. Answers ................................................. 44
Chapter 3
Advanced ESR Spectroscopy in Membrane Biophysics
Janez Štrancar
1. Introduction ............................................ 49
2. Motional Averaging in a Spin-Labeled Biomembrane ........ 55
3. Strategies for Calculating Powder Spectra ............... 66
4. Solving an Inverse Problem and Condensation
of Results .............................................. 77
5. Appendix ................................................ 89
Chapter 4
Practical Pulsed Dipolar ESR (DEER)
Piotr G. Fajer, Louise Brown, and Likai Song
1. DEER Signal ............................................. 95
2. Practical DEER ......................................... 104
3. Applications ........................................... 113
Chapter 5
Membrane Protein Structure and Dynamics Studied by
Site-Directed Spin-Labeling ESR
Enrica Bordignon and Heinz-Jürgen Steinhoff
1. Introduction ........................................... 129
2. Spin Labeling .......................................... 130
3. Structural Information Derived from ESR Spectra
Analysis ............................................... 133
4. Detection of Conformational Changes .................... 155
Chapter 6
High-Field ESR Spectroscopy in Membrane and Protein
Biophysics
Tatyana I. Smirnova and Alex I. Smirnov
1. Introduction ........................................... 165
2. Analysis of High-Field ESR Spectra of Spin Labels ...... 166
3. High-Field ESR of Spin-Labeled Aqueous Samples:
Experimental Considerations ............................ 193
4. High-field ESR in Studies of Molecular Dynamics ........ 204
5. High-field ESR in Studies of Molecular Structure ....... 215
6. Characterization of the Nitroxide Microenvironment by
High-Field ESR ......................................... 223
7. Perspectives ........................................... 234
Appendices: Software Descriptions
Appendix 1
Molecular Modeling of Spin Labels
Mikolai I. Fajer, Kenneth L. Sale, and Piotr G. Fajer
1. System Requirements .................................... 254
2. Preparation of Structures .............................. 254
3. Simulations ............................................ 255
4. Analysis of Nitroxide Trajectories ..................... 256
5. Force Fields ........................................... 256
6. Spin Label Topologies .................................. 257
Appendix 2
SIMPOW6: A Software Package for the Simulation of ESR
Powder-Type Spectra
Mark J. Nilges, Karen Mattson, and R. Linn Belford
1. Introduction ........................................... 261
2. Spin Hamiltonian for SIMPOW6 ........................... 262
3. Calculation of Resonance Fields ........................ 263
4. Lineshapes ............................................. 264
5. Intensity (Transition Moment) .......................... 266
6. Generation (Integration) of a Powder Spectrum .......... 266
7. Spectral Optimization .................................. 267
8. Summary of Input Parameters ............................ 268
9. Running the Program .................................... 268
10. Examples ............................................... 270
11. Appendix A: Format of the Input Files: Spin
Hamiltonian Parameters ................................. 276
12. Appendix B: Format of the Input Files:
Optimization Parameters and Control .................... 279
13. Appendix C: Format of the Output Simulation Files ...... 280
Appendix 3
ACERT Software: Simulation and Analysis of ESR Spectra
Jack H. Freed
Appendix 4
Deer Analysis 2006: Distance Measurements on Nanoscopic
Length Scales by Pulse ESR
Gunnar Jeschke
Appendix 5
EWVoigt and EWVoigtn: Inhomogeneous Line Shape Simulation
and Fitting Programs
Alex I. Smirnov
1. Introduction ........................................... 289
2. Convolution-Based Fitting of Continuous Wave EPR
Spectra ................................................ 289
3. Brief Description of EWVOIGT Capabilities .............. 292
4. Convolution Algorithm with Levenberg-Marquardt
Optimization for Fitting Inhomogeneous EPR Spectra ..... 293
Appendix 6
EasySpin: Simulating cw ESR Spectra
Stefan Stoll and Arthur Schweiger
1. Introduction ........................................... 299
2. Four Dynamic Regimes in cw ESR ......................... 300
3. Simulation of cw ESR Spectra ........................... 302
4. Other EasySpin functions ............................... 316
Appendix 7
EPRSIM-C: A Spectral Analysis Package
Janez Štrancar
1. Introduction ........................................... 323
2. Main Characteristics ................................... 325
3. EPRSIM-C Library ....................................... 326
4. EPRSIM-C Programs ...................................... 338
Contents of Previous Volumes .................................. 343
Index ......................................................... 369
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