ESR spectroscopy in membrane biophysics

Spectroscopic methods are not only important as an analytical tool, they also provide information about fundamental physical and chemical properties of molecules, the molecular and electronic structure, and the dynamic behaviour of molecules. Starting from a comprehensive quantum mechanical description, ESR Spectroscopy in Membrane Biophysics introduces the optical (IR, Raman, UV/Vis, CD, fluorescence and laser spectroscopy) and magnetic resonance (1D and 2D-NMR, ESR) techniques.

ESR Spectroscopy in Membrane Biophysics is a timely review of the increasing interest in using spin-label ESR as an alternative structural technique for NMR or X-ray diffraction. It is aimed at training an audience to learn ESR spectroscopy to determine membrane protein structures, conformational dynamics and protein-lipid interaction.

Author Notes

Dr. Marcus A. Hemminga is an Associate Professor in Molecular Biophysics at Wageningen University
Dr. Lawrence J. Berliner is currently Professor and Chair of the Department of Chemistry and Biochemistry at the University of Denver

Foreword	p. vii
Preface	p. ix
Chapter 1 Introduction and Future of Site-Directed Spin Labeling of Membrane ProteinsMarcus A. Hemminga
1 Structural Biology and Proteomics	p. 1
2 Membrane Proteins: Production and Reconstitution Challenges	p. 2
3 SDSL-ESR	p. 2
4 Cysteine Modification	p. 3
5 Structure and Dynamics Information from SDSL-ESR	p. 4
6 Pulsed ESR Spectroscopy	p. 6
7 High-Field ESR Spectroscopy	p. 8
8 Molecular Dynamics Simulations	p. 9
9 Spectral Simulation and Analysis	p. 11
10 Comparison with Site-Directed Fluorescence Labeling	p. 11
11 Future	p. 13
Chapter 2 Instrumentation and Experimental SetupGunnar Jeschke
1 Continuous-Wave ESR	p. 18
2 Basics of Pulsed ESR	p. 25
3 Pulsed ENDOR	p. 31
4 Pulsed ELDOR (DEER)	p. 39
5 Acknowledgments	p. 43
6 Problems	p. 44
7 Answers	p. 44
Chapter 3 Advanced ESR Spectroscopy in Membrane BiophysicsJanez Strancar
1 Introduction	p. 49
2 Motional Averaging in a Spin-Labeled Biomembrane	p. 55
3 Strategies for Calculating Powder Spectra	p. 66
4 Solving an Inverse Problem and Condensation of Results	p. 77
5 Appendix	p. 89
Chapter 4 Practical Pulsed Dipolar ESR (DEER)Piotr G. Fajer and Louise Brown and Likai Song
1 DEER Signal	p. 95
2 Practical DEER	p. 104
3 Applications	p. 113
Chapter 5 Membrane Protein Structure and Dynamics Studied by Site-Directed Spin-Labeling ESREnrica Bordignon and Heinz-Jurgen Steinhoff
1 Introduction	p. 129
2 Spin Labeling	p. 130
3 Structural Information Derived from ESR Spectra Analysis	p. 133
4 Detection of Conformational Changes	p. 155
Chapter 6 High-Field ESR Spectroscopy in Membrane and Protein BiophysicsTatyana I. Smirnova and Alex I. Smirnov
1 Introduction	p. 165
2 Analysis of High-Field ESR Spectra of Spin Labels	p. 166
3 High-Field ESR of Spin-Labeled Aqueous Samples: Experimental Considerations	p. 193
4 High-field ESR in Studies of Molecular Dynamics	p. 204
5 High-field ESR in Studies of Molecular Structure	p. 215
6 Characterization of the Nitroxide Microenvironment by High-Field ESR	p. 223
7 Perspectives	p. 234
Appendices: Software Descriptions
Appendix 1 Molecular Modeling of Spin LabelsMikolai I. Fajer and Kenneth L. Sale and Piotr G. Fajer
1 System Requirements	p. 254
2 Preparation of Structures	p. 254
3 Simulations	p. 255
4 Analysis of Nitroxide Trajectories	p. 256
5 Force Fields	p. 256
6 Spin Label Topologies	p. 257
Appendix 2 SIMPOW6: A Software Package for the Simulation of ESR Powder-Type SpectraMark J. Nilges and Karen Mattson and R. Linn Belford
1 Introduction	p. 261
2 Spin Hamiltonian for SIMP0W6	p. 262
3 Calculation of Resonance Fields	p. 263
4 Lineshapes	p. 264
5 Intensity (Transition Moment)	p. 266
6 Generation (Integration) of a Powder Spectrum	p. 266
7 Spectral Optimization	p. 267
8 Summary of Input Parameters	p. 268
9 Running the Program	p. 268
10 Examples	p. 270
11 Appendix A: Format of the Input Files: Spin Hamiltonian Parameters	p. 276
12 Appendix B: Format of the Input Files: Optimization Parameters and Control	p. 279
13 Appendix C: Format of the Output Simulation Files	p. 280
Appendix 3 ACERT Software: Simulation and Analysis of ESR SpectraJack H. Freed
Appendix 4 DeerAnalysis 2006: Distance Measurements on Nanoscopic Length Scales by Pulse ESRGunnar Jeschke
Appendix 5 EWVoigt and EWVoigtn: Inhomogeneous Line Shape Simulation and Fitting ProgramsAlex I. Smirnov
1 Introduction	p. 289
2 Convolution-Based Fitting of Continuous Wave EPR Spectra	p. 289
3 Brief Description of EWVOIGT Capabilities	p. 292
4 Convolution Algorithm with Levenberg-Marquardt Optimization for Fitting Inhomogeneous EPR Spectra	p. 293
Appendix 6 EasySpin: Simulating cw ESR SpectraStefan Stoll and Arthur Schweiger
1 Introduction	p. 299
2 Four Dynamic Regimes in cw ESR	p. 300
3 Simulation of cw ESR Spectra	p. 302
4 Other EasySpin functions	p. 316
Appendix 7 EPRSIM-C: A Spectral Analysis PackageJanez Strancar
1 Introduction	p. 323
2 Main Characteristics	p. 325
3 EPRSIM-C Library	p. 326
4 EPRSIM-C Programs	p. 338
Contents of Previous Volumes	p. 343
Index	p. 369

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