Biological NMR. Part B / edited by A. Joshua Wand. -- Cambridge, MA : Academic Press, 2019. – (58.17435/C719/v.615)

Contents

Contributors

Preface

 1. Companion Simulations and Modeling to NMR-Based Dynamical Studies of Proteins

    1. Introduction

    2. The Generalized NMR Order Parameter

    3. Conformational Entropy and Protein Dynamics

    4. J-couplings

    5. Residual Dipolar Couplings

    6. Protein Compressibility

    7. Molecular Tumbling

    8. Water Dynamics

    Acknowledgment

    References

 2. Reverse Micelle Encapsulation of Proteins for NMR Spectroscopy

    1. Introduction

    2. Sample Composition Considerations

    3. Spectroscopic Considerations

    4. Method for Screening RM Conditions

    5. Method for Preparation of RM Solutions in Propane or Ethane

    6. Benchmarking Encapsulation

    7. Conclusions and Outlook

    Acknowledgments

    References

 3. Characterizing Protein Hydration Dynamics Using Solution NMR Spectroscopy

    1. Introduction

    2. Theoretical and Practical Considerations

   3. Preparation of Protein Encapsulated RM Samples

    4. NMR Spectroscopy and Experimental Setup

    5. Data Collection and Analysis

    6. Conclusions

    Acknowledgments

    References

4. Understanding Protein Function Through an Ensemble Description: Characterization of Functional States by ¹⁹F NMR

    1. ¹⁹F-Reporters That Can Be Biosynthetically Incorporated Into Proteins

    2. Approaches to Chemical Tagging of Proteins by ¹⁹F Reporters

    3. Improving Delineation of States by ¹⁹F NMR

    4. Distinguishing States by Topology Measurements That Focus on Solvent Exposure and Hydrophobicity

    5. Relaxation Experiments and Simple Approaches to Delineating States in Fast and Slow Exchange

    6. Extending Resolution of States by 19F NMR

    7. Validating ¹⁹F NMR Spectroscopy by Computational Methods

    8. Overview

    Acknowledgments

    References

5. Overhauser Dynamic Nuclear Polarization for the Study of Hydration Dynamics, Explained

    1. Introduction

    2. Motivation for Studying Hydration Water Dynamics

    3. Experimental Techniques for Studying Hydration Water Dynamics

    4. Translational Diffusion Dynamics of Hydration Water Informs on Correlated Properties

    5. Principle and Benefits of ODNP Relaxometry

    6. Mechanism of ODNP Relaxometry

    7. Experimental Protocol for ODNP Measurements

    8. Common Questions for ODNP Hydration Studies

    9. Development of the ODNP Technique

    10. Concluding Remarks

    Acknowledgments

    References

6. Chemical Exchange

    1. Introduction

    2. Theory

    3. Experimental Techniques and Examples

    4. Conclusion

    Acknowledgments

    Appendix A

    References

7. Characterization of Internal Protein Dynamics and Conformational Entropy by NMR Relaxation

    1. Introduction

    2. NMR Spin Relaxation Methods

    3. Practical Aspects of Data Collection and Analysis

    4. The Entropy Meter

    5. Concluding Remarks

    Acknowledgments

    References

8. NMR Methods for Characterizing the Basic Side Chains of Proteins: Electrostatic Interactions, Hydrogen Bonds, and Conformational Dynamics

    1. Introduction

    2. NMR of Lys and Arg Side Chains

    3. Conformational Dynamics of Lys/Arg Side Chains

    4. Ion Pairs and Hydrogen Bonds Involving Lys/Arg Side Chains

    5. Data Interpretation Facilitated by Molecular Dynamics Simulations

    6. Concluding Remarks

    Acknowledgments

    References

9. Solid-State NMR Spectroscopy of RNA

    1. Introduction

    2. Sample Preparation

    3. Resonance Assignment

    4. Restraints and Structural Calculations

    5. Characterization of Protein-RNA Interfaces

    6. Outlook

    References

10. DNP-Assisted NMR Investigation of Proteins at Endogenous Levels in Cellular Milieu

    1. Introduction

    2. DNP Samples of Proteins at Endogenous Levels in Native Environments

    3. Purified Amyloid Samples

    4. Summary and Conclusions

    Acknowledgments

    References

11. Identification of Unknown Metabolomics Mixture Compounds by Combining NMR, MS, and Cheminformatics

    1. Introduction

    2. Sample Preparation

    3. NMR Experiments

    4. Analysis of NMR Spectra

    5. MS Experiments

    6. Analysis of MS Spectra

    7. NMR Chemical Shift Prediction of Library Compounds

    8. Spin System Scoring and Molecular Structural Motif Identification of Chemical Compounds

    9. Compound Verification: Spiking With Purchased or Synthesized Candidate Compounds

    10. Conclusions and Outlook

    Acknowledgments

    References

12. STD NMR as a Technique for Ligand Screening and Structural Studies

1. Introduction

    2. The STD NMR Experiment

    3. Ligand Screening

    4. Ligand Epitope Mapping

    5. Determination of the Dissociation Constant (Kd)

    6. DEEP-STD NMR

    7. Summary and Conclusions

    References

13. An ELISA-Based Screening Platform for Ligand-Receptor Discovery

    1. Introduction

    2. Overview of Workflow

    3. The High-Throughput Screen

    4. Data Analysis and Laboratory Information Management

    5. Validation of PPIs and Biophysical Characterization

    6. PPI ELISA Results

    7. Comparison With Affinity Chromatography Methods

    8. Future Prospects

    Acknowledgments

    References

14. Protein-Small Molecule Interactions by WaterLOGSY

    1. Introduction

    2. The Basis of WaterLOGSY

    3. Pulse Sequence of WaterLOGSY

    4. Basic Setup for Conventional WaterLOGSY Experiments

    5. Screening by WaterLOGSY

    6. Binding Constant (KD) Determination by WaterLOGSY

    7. The Use of WaterLOGSY to Measure Bound-Ligand Solvent Accessibility

    8. Conclusion

    Acknowledgments

    References

15. Applications of Dissolution-DNP for NMR Screening

    1. Introduction

    2. Methods

    3. Conclusions

    Acknowledgment

    References