Biological NMR. Part B / edited by A. Joshua Wand.

Format:

Book

Contributor:

Wand, A. Joshua, editor.

Series:

Methods in enzymology ; Volume 615.

Methods in enzymology ; Volume 615

Language:

English

Subjects (All):

Nuclear magnetic resonance.

Physical Description:

1 online resource (xvii, 526 pages) : illustrations.

Place of Publication:

Cambridge, Massachusetts : Academic Press, 2019.

Summary:

Biological NMR, Part B, the latest release in the Methods of Enzymology series, highlights new advances in the field, with this new volume presenting interesting chapters on a variety of topics, including Protein methyl labeling, Membrane protein expression - yeast, Protein aromatic labeling, His-tag/Metal contamination, Bicelles, nanodiscs & micelles MP host, PTM - phosphorylation, PTM - lipidation, Screening platform for receptor-ligand discovery, Solution Spectroscopy, Large protein strategies, NUS data collection/analysis, F19 incl. hydration, ODNP - hydration, Reverse micelle - Hydration, Solid State Spectroscopy, SS NMR membrane proteins, SS NMR soluble/aggregate proteins, SS DNP - general, SS NMR nucleic acids, and much more.- Authoritative contributors- Protocols for state-of-the-art advances- Timeliness

Contents:

Front Cover

Biological NMR Part B

Copyright

Contents

Contributors

Preface

Chapter One: Companion Simulations and Modeling to NMR-Based Dynamical Studies of Proteins

1. Introduction

2. The Generalized NMR Order Parameter

2.1. Definition

2.2. Simulation of Order Parameters

2.3. Interpretation of Experimental and Simulated Order Parameters: The Role of Simple Models

2.4. Molecular Dynamics Simulation of Methyl Order Parameters

2.5. Simulation of Aromatic Group Order Parameters

3. Conformational Entropy and Protein Dynamics

3.1. Definition and Properties of Entropy

3.2. Extraction of Conformational Entropy of Proteins

4. J-couplings

5. Residual Dipolar Couplings

6. Protein Compressibility

7. Molecular Tumbling

8. Water Dynamics

Acknowledgment

References

Chapter Two: Reverse Micelle Encapsulation of Proteins for NMR Spectroscopy

2. Sample Composition Considerations

2.1. Aqueous Phase: Protein and Buffer

2.2. Surfactants

2.3. Bulk Alkane

3. Spectroscopic Considerations

4. Method for Screening RM Conditions

4.1. Preparing 10MAG/LDAO Samples

4.1.1. Adjusting the pH of LDAO

4.1.2. Completing 10MAG/LDAO Samples

4.2. Preparing CTAB/Hexanol Samples

4.3. Preparing AOT Samples

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

5.1. Safety Considerations

5.2. Preparing Sample Components

5.3. Procedure for Elevated-Pressure RM Encapsulation

6. Benchmarking Encapsulation

7. Conclusions and Outlook

Acknowledgments

Chapter Three: Characterizing Protein Hydration Dynamics Using Solution NMR Spectroscopy

2. Theoretical and Practical Considerations

2.1. Foundation Theory

2.2. Overcoming Artifacts and Limitations

3. Preparation of Protein Encapsulated RM Samples.

3.1. Protein Labeling and Purification

3.2. RM Encapsulation and Considerations

4. NMR Spectroscopy and Experimental Setup

4.1. NOESY and ROESY Experiments

4.2. Two-Dimensional vs Three-Dimensional Experiments

4.3. Nonuniform Sampling

4.4. Identification of Hydrogen Exchange

4.5. Quantification of Hydrogen Exchange-Relayed Magnetization

5. Data Collection and Analysis

5.1. Data Collection

5.2. General Fitting Strategy

5.3. Simplified Analysis in the Absence of Hydrogen Exchange

6. Conclusions

Chapter Four: Understanding Protein Function Through an Ensemble Description: Characterization of Functional States by F 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

6.1. Pseudocontact Shift Reagents

6.2. Multiple Quantum Spectroscopy

7. Validating F NMR Spectroscopy by Computational Methods

8. Overview

Chapter Five: Overhauser Dynamic Nuclear Polarization for the Study of Hydration Dynamics, Explained

2. Motivation for Studying Hydration Water Dynamics

3. Experimental Techniques for Studying Hydration Water Dynamics

3.1. Access to Spatially Heterogeneous Hydration Layers

3.2. Magnetic Resonance Offers Unique Capabilities

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

7.1. The ODNP Instrument

7.2. Data Acquisition Protocol

7.3. Data-Processing Protocol

7.4. Protocol for Interpolation of T1(p)

8. Common Questions for ODNP Hydration Studies

9. Development of the ODNP Technique

10. Concluding Remarks

Chapter Six: Chemical Exchange

2. Theory

2.1. Free Precession

2.2. Carr-Purcell-Meiboom-Gill Relaxation

2.3. Rotating-Frame Relaxation

3. Experimental Techniques and Examples

3.1. ZZ-Exchange

3.2. Hahn-Echo, CPMG, and R1ρ Experiments

3.3. CEST and DEST

3.4. Determination of Rex from Relaxation Dispersion Experiments

3.5. Choosing Appropriate Relaxation Dispersion Experiments

4. Conclusion

Appendix A

A.1. Cayley-Hamilton Theorem

A.2. Effective Relaxation Rate Constant in CPMG Experiments

Chapter Seven: Characterization of Internal Protein Dynamics and Conformational Entropy by NMR Relaxation

2. NMR Spin Relaxation Methods

2.1. The Relationship Between Relaxation and Fast Timescale Dynamics

2.2. Measuring N Relaxation of Amide Groups

2.2.1. Overview

2.2.2. Sample Preparation

2.2.3. Pulse Sequences

2.2.4. Systematic Errors

2.2.5. R2 vs R1ρ

2.3. Measuring H Relaxation of Methyl Groups

2.3.1. Overview

2.3.2. Sample Preparation

2.3.3. Pulse Sequences

2.4. Measuring C Relaxation of Methyl Groups

2.4.1. Overview

2.4.2. Sample Preparation

2.4.3. Pulse Sequences

2.5. Measuring H Dipolar Cross-Correlated Relaxation of Methyl Groups

2.5.1. Overview

2.5.2. Sample Preparation

2.5.3. Pulse Sequences

2.6. Ancillary Methods for Difficult Systems

2.6.1. Unstable and/or Dilute Samples

2.6.2. Highly Overlapped Spectra.

3. Practical Aspects of Data Collection and Analysis

3.1. Guidelines for Setting Up Experiments

3.1.1. Sample Concentration

3.1.2. High Salt Samples

3.1.3. Sample Lifetime

3.1.4. Temperature Calibration

3.1.5. Sampling Relaxation Decays

3.2. Data Fitting and Error Analysis

3.2.1. Curve Fitting

3.2.2. Determining Uncertainties in Peak Height

3.2.3. Determining Uncertainties in Fitted Parameters

3.3. Model-Free Formalism

3.3.1. The Spectral Density

3.3.2. Relating the Spectral Density to Relaxation Parameters

3.4. Characterization of Macromolecular Tumbling

3.4.1. Anisotropic Tumbling

3.4.2. T1/T2 Ratio

3.4.3. TRACT

3.5. Data Reproducibility

3.5.1. H2O vs D2O Solvent

3.5.2. Intralab Reproducibility

3.5.3. Interlab Reproducibility

4. The Entropy Meter

5. Concluding Remarks

Chapter Eight: NMR Methods for Characterizing the Basic Side Chains of Proteins: Electrostatic Interactions, Hydrogen Bond ...

2. NMR of Lys and Arg Side Chains

2.1. N Resonances of Lys/Arg Side Chains

2.1.1. Chemical Shifts and Protonation States

2.1.2. Degenerate H Resonances of Lys NH3+

2.1.3. Hindered 180° Rotations of Arg Guanidinium Cζ-N Bonds

2.2. Impact of Hydrogen Exchange on Lys/Arg Side-Chain NMR

2.2.1. Direct Influence of Hydrogen Exchange on 1H Line Shapes

2.2.2. Indirect Influence of Hydrogen Exchange on 15N Line Shapes

2.2.3. Self-decoupling Due to Hydrogen Exchange

2.3. Importance of Maintaining In-Phase Single-Quantum 15N Coherence

2.3.1. HISQC Drastically Improves Lys NH3+ 15N Line Shapes

2.3.2. HISQC Can Also Improve Arg 15Nε Line Shapes

2.4. Resonance Assignment for Lys/Arg Side Chains

2.4.1. Resonance Assignment for Lys Side-Chain NH3+ Groups

2.4.2. Resonance Assignment for Arg Guanidinium Moieties.

2.4.3. Selective 15N Pulses for Lys and Arg Side Chains

2.4.4. Chemical Approach

2.5. Sample Conditions for NMR Studies of Lys/Arg Cations

2.5.1. Two Critical Factors: pH and Temperature

2.5.2. Coaxial NMR Tubes to Avoid Partial Deuteration by D2O

2.5.3. Dealkalization of NMR Tubes

3. Conformational Dynamics of Lys/Arg Side Chains

3.1. 15N Relaxation Analysis for Lys NH3 + Groups

3.1.1. Removal of Adverse Effects of Multispin Terms

3.1.2. 15N R1 Relaxation Measurements for Lys NH3+ Groups

3.1.3. 15N R2 Relaxation Measurements for Lys NH3+ Groups

3.1.4. Heteronuclear 15N NOE for Lys NH3+ Groups

3.2. 15N Relaxation Analysis for Arg NεH Groups

3.2.1. NMR Relaxation Measurements for Arg 15Nε Nuclei

3.2.2. Impact of 15N-15N Couplings on Arg 15Nε R2 Measurements

3.2.3. 15Nε Relaxation Analysis Using Direct 13Cζ Detection

3.3. Determination of Lys/Arg Side-Chain Order Parameters

3.3.1. Overall Procedures

3.3.2. Determination of Molecular Rotational Correlation Time

3.3.3. Determination of Lys NH3+ Order Parameters

3.3.4. Determination of Arg NεH Order Parameters

3.3.5. Different Dynamic Properties of Lys and Arg Side Chains

3.4. 3JCN Measurements to Analyze Side-Chain Dynamics

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

4.1. Hydrogen-Bond Scalar Couplings

4.1.1. Heteronuclear Correlation via Hydrogen-Bond Scalar Couplings

4.1.2. Determination of Hydrogen-Bond Scalar Coupling Constants

4.2. Dynamic Ion Pairs and Hydrogen Bonds

4.2.1. Dynamic Hydrogen Bonding and Ion Pairing

4.2.2. Self-decoupling Due to Molecular Dissociation

5. Data Interpretation Facilitated by Molecular Dynamics Simulations

5.1. NMR vs MD for Dynamics of Basic Side Chains

5.1.1. Lys/Arg Side-Chain Order Parameters From MD Trajectories.

5.1.2. Three-Bond Scalar Couplings From MD Trajectories.

Notes:

Description based on print version record.

ISBN:

0-12-816763-7

0-12-816762-9