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Electron Paramagnetic Resonance Investigations of Biological Systems by Using Spin Labels, Spin Probes, and Intrinsic Metal Ions Part A

1st Edition - October 5, 2015

Editors: Peter Z Qin, Kurt Warncke

Hardback ISBN:

9 7 8 - 0 - 1 2 - 8 0 2 8 3 4 - 6

eBook ISBN:

9 7 8 - 0 - 1 2 - 8 0 2 8 4 6 - 9

Electron Paramagnetic Resonance Investigations of Biological Systems by Using Spin Labels, Spin Probes, and Intrinsic Metal Ions Part A & B, are the latest volumes in the… Read more

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Electron Paramagnetic Resonance Investigations of Biological Systems by Using Spin Labels, Spin Probes, and Intrinsic Metal Ions Part A & B, are the latest volumes in the Methods in Enzymology series, continuing the legacy of this premier serial with quality chapters authored by leaders in the field. This volume covers research methods centered on the use of Electron Paramagnetic Resonance (EPR) techniques to study biological structure and function.

Preface
Section I: EPR Methodology and Instrumentation
- Chapter One: Rapid-Scan EPR of Nitroxide Spin Labels and Semiquinones
  - Abstract
  - 1 Introduction
  - 2 Rapid-Scan Method
  - 3 Why Rapid Scan Improves S/N
  - 4 Other Advantages of Rapid Scan
  - 5 Hardware Requirements
  - 6 Parameter Selection
  - 7 Examples
  - 8 Wider Scans
  - 9 Future Applications
  - Acknowledgments
- Chapter Two: Fourier Deconvolution Methods for Resolution Enhancement in Continuous-Wave EPR Spectroscopy
  - Abstract
  - 1 Introduction
  - 2 Historical Perspective
  - 3 Overlapping Signals
  - 4 Fourier Filtering
  - 5 Overview of Method
  - 6 Practical Examples
  - 7 Limitations of the Method
  - 8 Summary
  - Acknowledgment
  - Supplementary materials
- Chapter Three: Multifrequency Pulsed EPR and the Characterization of Molecular Dynamics
  - Abstract
  - 1 Introduction
  - 2 Contributions to Electron Spin-Lattice Relaxation and Dependence of Relaxation on Motions in Fluid Solution
  - 3 Measurement of Spin-Lattice Relaxation, T₁
  - 4 Examples of Motions Elucidated by Measuring T₁ as a Function of Frequency
  - 5 Conclusion
  - Acknowledgments
- Chapter Four: Resolution and Characterization of Chemical Steps in Enzyme Catalytic Sequences by Using Low-Temperature and Time-Resolved, Full-Spectrum EPR Spectroscopy in Fluid Cryosolvent and Frozen Solution Systems
  - Abstract
  - 1 Introduction
  - 2 Low-Temperature Fluid Cryosolvent System
  - 3 Low-Temperature Frozen Solution System
  - 4 Analysis and Interpretations: General Cases and Guidelines
  - 5 Conclusions
  - Acknowledgments
- Chapter Five: 230/115 GHz Electron Paramagnetic Resonance/Double Electron–Electron Resonance Spectroscopy
  - Abstract
  - 1 Introduction
  - 2 HF EPR/DEER Spectrometer
  - 3 Examples of HF EPR: Paramagnetic Impurities in Diamonds Studied by 230 GHz EPR/DEER Spectroscopy
  - 4 Summary
  - Acknowledgments
  - Appendix
Section II: EPR Spectral Simulation and Software
- Chapter Six: CW-EPR Spectral Simulations: Solid State
  - Abstract
  - 1 Introduction
  - 2 Spins and SH
  - 3 Dynamic Regime
  - 4 Levels of Theory
  - 5 Orientational Order and Disorder
  - 6 Structural Order and Disorder
  - 7 Other Line Broadenings
  - 8 Experimental Effects
  - 9 Fitting
  - 10 Conclusions
- Chapter Seven: CW-EPR Spectral Simulations: Slow-Motion Regime
  - Abstract
  - 1 Introduction
  - 2 Magnetic Parameters
  - 3 Methods of Modeling Slow Motion
  - 4 Outlook
  - Acknowledgment
- Chapter Eight: Quantitative Interpretation of Multifrequency Multimode EPR Spectra of Metal Containing Proteins, Enzymes, and Biomimetic Complexes
  - Abstract
  - 1 Introduction
  - 2 Basic EPR Theory
  - 3 g-Factor Anisotropy
  - 4 Hyperfine Structure
  - 5 Spin Hamiltonian
  - 6 Basic EPR Instrumentation
  - 7 Simulation of Powder Spectra
  - 8 Quantitative Aspects
  - 9 Applications
  - 10 Conclusion
  - Acknowledgments
Section III: EPR Studies of Metal-Containing Proteinsand Metal Cofactors
- Chapter Nine: Pulse Double-Resonance EPR Techniques for the Study of Metallobiomolecules
  - Abstract
  - 1 Introduction
  - 2 Pulse EPR
  - 3 Pulse ENDOR
  - 4 ELDOR-Detected NMR (EDNMR)
  - 5 ESEEM
  - 6 Conclusions and Outlook
  - Acknowledgments
- Chapter Ten: Mapping the Structure of Metalloproteins with RIDME
  - Abstract
  - 1 Introduction
  - 2 Basic Principles
  - 3 Spin B Flip Probability
  - 4 Detrimental Effects
  - 5 Experimental Strategy
  - 6 Pulse Sequences
  - 7 Comparison with DEER
  - 8 Experimental Examples
  - 9 Conclusion
  - Acknowledgments
- Chapter Eleven: Structural Characterization of the Catalytic Sites of Mononuclear Nonheme Fe Hydroxylases Using ²H-ESEEM
  - Abstract
  - 1 Introduction
  - 2 Cw-EPR of the Ternary Complex TyrH/NO/tyr
  - 3 ²H-ESEEM Spectroscopy
  - 4 Summary
  - Acknowledgments
- Chapter Twelve: Pulsed EPR in the Study of Drug Binding in Cytochrome P450 and NOS
  - Abstract
  - 1 Introduction
  - 2 Background
  - 3 Spectroscopy
  - 4 The Water-Bridged Complex
  - 5 Experimental Considerations
  - Acknowledgments
- Chapter Thirteen: EPR Methods for Biological Cu(II): L-Band CW and NARS
  - Abstract
  - 1 Background and Introduction
  - 2 Information from EPR of Cu(II)
  - 3 Strain Broadening, Isotope Broadening, and the Overshoot Line
  - 4 Low-Frequency EPR of Cu(II)
  - 5 Nonadiabatic Rapid Sweep (NARS) EPR Spectroscopy
Section IV: Advances in Spin Label Incorporation
- Chapter Fourteen: Development and Application of Spin Traps, Spin Probes, and Spin Labels
  - Abstract
  - 1 Introduction
  - 2 Spin Trapping
  - 3 Spin Labeling
  - 4 Conclusions
  - Acknowledgment
- Chapter Fifteen: Site-Directed Spin Labeling of RNA by Postsynthetic Modification of 2′-Amino Groups
  - Abstract
  - 1 Introduction
  - 2 2′-Amino Spin-Labeling with Aliphatic Isocyanates and Aromatic Isothiocyanates
  - 3 Summary and Conclusions
  - Acknowledgments
- Chapter Sixteen: Gd^3 + Spin Labeling for Measuring Distances in Biomacromolecules: Why and How?
  - Abstract
  - 1 Introduction
  - 2 Gd^3 + Tags
  - 3 Theoretical Background and the Effect of the High Spin
  - 4 Relaxation
  - 5 Experimental Set Up and Data Analysis
  - 6 Multispin Effects
  - 7 The SL Does Matter
  - 8 In-Cell DEER
  - 9 Outlook
  - Acknowledgments
- Chapter Seventeen: Cu^2 + as an ESR Probe of Protein Structure and Function
  - Abstract
  - 1 Introduction
  - 2 Cu^2 + as a Probe to Measure Interspin Distances
  - 3 Examples of Applications and Other Developments
  - Acknowledgment
- Chapter Eighteen: Genetically Encoded Spin Labels for In Vitro and In-Cell EPR Studies of Native Proteins
  - Abstract
  - 1 Introduction
  - 2 Experimental Guidelines
  - Acknowledgments
- Chapter Nineteen: Genetic Incorporation of the Unnatural Amino Acid p-Acetyl Phenylalanine into Proteins for Site-Directed Spin Labeling
  - Abstract
  - 1 Introduction
  - 2 Site-Specific Incorporation of pAcPhe
  - 3 Spin Labeling of Proteins Containing Site-Specific pAcPhe
  - 4 Inter-Nitroxide Distance Measurement in Doubly K1-Labeled PrP by DEER EPR
  - 5 Concluding Remarks
  - Acknowledgments
Section V: Inter-Spin Label Distance Measurements: Analysis Considerations and Approaches
- Chapter Twenty: A Straightforward Approach to the Analysis of Double Electron–Electron Resonance Data
  - Abstract
  - 1 Introduction
  - 2 Double Electron–Electron Resonance
  - 3 Theory
  - 4 Using DD
  - 5 Error Analysis
  - 6 The Background Signal
  - 7 Global Analysis
  - 8 Conclusions
  - Acknowledgments
- Chapter Twenty-One: Computer Modeling of Spin Labels: NASNOX, PRONOX, and ALLNOX
  - Abstract
  - 1 Introduction
  - 2 NASNOX
  - 3 PRONOX
  - 4 ALLNOX
- Chapter Twenty-Two: mtsslSuite: Probing Biomolecular Conformation by Spin-Labeling Studies
  - Abstract
  - 1 Introduction
  - 2 Planning the Project
  - 3 Where to Put the Spin Label?
  - 4 Selecting Optimal Labeling Sites
  - 5 Which Spin Label Should Be Used?
  - 6 Preparation of Spin-Labeled Samples and the PELDOR Experiment
  - 7 Translating Distance Data into Structural Information
  - 8 Caveats of In Silico Spin Labeling
  - 9 Docking with mtsslDock
  - 10 Trilateration with mtsslTrilaterate
  - 11 Conclusion
  - Acknowledgments
- Chapter Twenty-Three: Full Atom Simulations of Spin Label Conformations
  - Abstract
  - 1 Introduction
  - 2 Molecular Modeling
  - 3 Simulation Strategy
  - 4 Alternative Solution—Bifunctional Spin Labels
Author Index
Subject Index