Biophysics of Molecular Chaperones : Function, Mechanisms and Client Protein Interactions / edited by Sebastian Hiller, Maili Liu, and Lichun He.

Format:

Book

Contributor:

Hiller, J. Sabastian (John Sabastian), editor.

Liu, Maili, editor.

He, Lichun, editor.

Series:

New developments in NMR ; Number 29.

New Developments in NMR ; Number 29

Language:

English

Subjects (All):

Biophysics.

Molecular chaperones.

Physical Description:

1 online resource (413 pages)

Edition:

First edition.

Place of Publication:

Piccadilly, England : The Royal Society of Chemistry, [2024]

Summary:

Providing a comprehensive overview of advanced biophysical methods for the characterization of molecular chaperones, most of the contributions are NMR methodology targeted at both current practitioners of structural biology and scientists who are interested in entering the field.

Contents:

Cover

Preface

Acknowledgement

Contents

Chapter 1 Introduction: Molecular Chaperones and Protein Quality Control

1.1 Lifecycle of a Protein

1.1.1 De Novo Folding and Assembly

1.1.2 Conformational Maintenance

1.1.3 Degradation

1.2 Protein Aggregation

1.2.1 Biophysical Perspective

1.2.2 Physiological Roles of Protein Aggregation In Vivo

1.3 Major Molecular Chaperone Families

1.3.1 Generic Ribosome-associated Chaperones

1.3.2 Hsp70

1.3.3 Hsp90

1.3.4 Hsp60

1.3.5 Small HSPs (sHSPs)

1.3.6 AAAþ Family Chaperones

1.4 Protein Quality Control

1.4.1 Folding vs. Degradation

1.4.2 Spatial Sequestration

1.5 Chaperone Dysfunction in Diseases

1.6 Outstanding Questions and Future Directions

Acknowledgements

References

Chapter 2 Structural Disorder in Chaperone Functions Probed by NMR

2.1 Introduction

2.2 NMR Methods for Studying Dynamic Protein Interactions

2.2.1 2D HSQC Spectra

2.2.2 Relaxation Measurements

2.2.3 Chemical Exchange Saturation Transfer (CEST)

2.2.4 19F NMR Spectroscopy

2.3 Structural Disorder in Chaperone Functions

2.3.1 Redox- regulated Heat Shock Protein Hsp33

2.3.2 pH-regulated Bacterial Periplasmic Chaperone HdeA

2.3.3 Small Heat Shock Proteins

2.3.4 Tight Complex Between the Linker Histone H1 and Prothymosin- a (ProTa)

2.4 Conclusions and Perspectives

Chapter 3 Solution NMR Approaches for Studying Molecular Chaperones

3.1 Introduction

3.2 Key Principles of Solution-based NMR Spectroscopy

3.2.1 NMR Observables

3.2.2 Mechanisms of Magnetization Decay

3.2.3 Interactions Between Nuclear Spins and Higher Dimensional NMR Spectroscopy

3.3 NMR as a Tool for Structural Elucidation

3.3.1 NMR Experiments Used to Assign the Spectra and Elucidate the Structure

3.3.2 Hydrogen-Deuterium Exchange.

3.3.3 Complimentary NMR Experiments for Structural Elucidation of Large Proteins

3.4 Exchange-based NMR Experiments for Elucidatingthe Structures and Interactions and Detecting NMR-invisible States

3.4.1 Nuclear Spin Relaxation and Heteronuclear NOEs

3.4.2 T1 Relaxation in the Rotating Frame

3.4.3 Paramagnetic Relaxation Enhancement

3.4.4 CPMG Relaxation- dispersion Spectroscopy

3.4.5 Saturation-transfer Spectroscopy: CEST and DEST

3.4.6 Cross-saturation Transfer

3.4.7 Combining Multiple Experiments toElucidate Structures, Interactions and Thermodynamics

3.5 Future Directions and Perspectives

Abbreviations

Chapter 4 Solution NMR Studies of Chaperone-Client Systems

4.1 Introduction

4.2 Solution NMR - A Powerful Tool for Chaperone-Client Systems

4.3 Isotope Labelling Strategies for Large Chaperone-Client Systems in Solution NMR

4.3.1 Uniform Isotopic Labelling

4.3.2 Selective Isotopic Labelling

4.3.3 Segmental Isotopic Labelling and LEGO

4.3.4 Spin Labelling

4.4 Advancement of NMR Techniques

4.4.1 TROSY and CRINEPT

4.4.2 PRE and PCS

4.4.3 CPMG

4.4.4 Saturation Transfer (CEST and DEST)

4.5 NMR Applications in Chaperone-Client Systems

4.5.1 The Dynamic Skp-OMP System

4.5.2 The Dynamic Hsp70-Client Interaction and the Hsp70 Machinery

4.5.3 The Complicated Hsp90-Client System

4.5.4 ClpB Works on the Protein Disaggregation and Reactivation

4.5.5 The Trigger Factor (TF) Chaperone-PhoA Complex

4.5.6 The SecB-PhoA Complex

4.5.7 Hsp40 Recognizes the Non-native Protein PhoA and the Diverse Hsp40 Family

4.5.8 Small Heat-shock Protein Hsp27 Modulates FUS Phase Separation

4.5.9 The Dynamic Chaperonin and Its Co-chaperonin

4.5.10 The Dynamic Mitochondrial TIM Chaperone Systems

4.6 Conclusion and Outlook

Acknowledgements.

References

Chapter 5 Preparing Chaperone-Client Protein Complexes for Biophysical and Structural Studies

5.1 Introduction

5.2 Client-Chaperone Complex Formation

5.2.1 General Considerations

5.2.2 Overview of the Possibilities toPrepare Chaperone-Client Complexes

5.3 Different Complex-formation Approaches in Practice

5.3.1 Forming Complexes in Solution by MixingChaperones and Their Soluble Client Proteins

5.3.2 Making a Client Protein Bind by Adjusting the Sample Conditions

5.3.3 Mutating Client Proteins to Make ThemChaperone- binding Prone (or Reduce Their Aggregation Propensity)

5.3.4 Complex Formation upon Removal of a Denaturant

5.3.5 Hampering Aggregation by ClientImmobilization: Complex Formation with a Pull-down Approach

5.3.6 Purifying P-C Complexes from the Cell

5.3.7 Capturing Emerging Client Proteins in a Cell-free System

5.3.8 Fusing Chaperone and Client into a Single Polypeptide Chain

5.3.9 Chaperones Bound to Protein Aggregates

5.4 Concluding Remarks

Chapter 6 NMR Study of the Structure and Dynamics of Chaperone-Client Complexes

6.1 Introduction

6.2 Technical Developments in the Structural Study of Chaperone-Client Complexes

6.2.1 NMR as a Tool for Structure Determination of Chaperone-Client Complexes

6.2.2 Preparation of Unfolded Proteins for Structural Studies

6.3 Structural Features of Chaperone-Client Complexes

6.3.1 Hydrophobic Stretches of Unfolded Proteins are Recognized by Molecular Chaperones

6.3.2 Dynamic Features of Chaperone-Client Complexes

6.3.3 Activity-Kinetics Relationship

6.3.4 Catalytic Domains of Molecular Chaperones

6.4 Perspective/Conclusion

Chapter 7 Single Molecule Fluorescence Methods for Molecular Chaperones and Their Client Interactions

7.1 Introduction.

7.1.1 Single Molecule Fluorescence for Biomolecular Machines

7.1.2 Single Molecule Fluorescence to Study Chaperone Machineries

7.2 Investigation of Chaperone Dynamics Across Timescales

7.2.1 Dynamics on the Millisecond to Minutes Timescale

7.2.2 Dynamics on the Microsecond to Millisecond Timescale

7.2.3 Dynamics on the Nanosecond Timescale

7.2.4 The Dynamic Picture of Hsp90 Across Timescales

7.3 Chaperone-Cochaperone-Client Interactions

7.4 Summary and Outlook

Chapter 8 Visualization of Chaperone Mediated Protein Folding Using X-ray Crystallography

8.1 Introduction

8.2 Hsp70

8.3 Chaperonins

8.4 Trigger Factor

8.5 Spy

8.6 Conclusions

Chapter 9 Studying Molecular Chaperones and Their ClientInteractions by Nanometer Distance Restraints from Electron Paramagnetic Resonance Spectroscopy

9.1 Introduction

9.2 Site-directed Spin-labeling

9.2.1 Spin Labels Reactive to Cysteine Residues

9.3 Distance Restraints from Continuous Wave and Pulsed EPR Spectroscopy

9.3.1 Distances from Continuous Wave EPR Experiments

9.3.2 Distances from Pulsed EPR Experiments

9.4 Molecular Chaperones Studied by EPR Spectroscopy

9.4.1 The Ribosome-associated Complex RAC

9.4.2 The Heat Shock Protein Hsp70

9.4.3 The Heat Shock Protein Hsp90

9.4.4 The SecB Chaperone

9.4.5 Other Types of Chaperones

9.5 Outlook

Chapter 10 EPR Studies of Chaperone Interactions and Dynamics

10.1 Introduction

10.2 Overview of Continuous-wave EPR: Theory and Experimental Considerations

10.2.1 Theory of CW-EPR

10.2.2 EPR as a Site- specific Probe for Protein Structure and Interaction

10.3 SDSL- EPR Studies of Molecular Chaperones: Structure, Dynamics, and Interactions.

10.3.1 Defining Chaperone- Client Interactions

10.3.2 Client Conformational Remodeling

10.3.3 Conformational Changes of the Chaperone

10.3.4 Molecular Architecture of Protein Aggregates

10.4 Conclusions

Chapter 11 Probing Single Chaperone Substrates

11.1 Introduction

11.2 The Optical Tweezers Approach

11.3 Co-translational Folding

11.3.1 Nascent Chains at the Ribosome

11.3.2 Trigger Factor

11.4 Post-translational Folding

11.4.1 The Hsp70 System

11.4.2 GroEL-GroES

11.4.3 Hsp90

11.5 Controlling Protein Aggregation

11.5.1 Small Heat Shock Proteins

11.5.2 The ClpB Disaggregase

11.6 Outlook

Chapter 12 Integrative Methods to Investigate Chaperones in Regulating Protein Phase Separation and Aggregation

12.1 Emerging Roles of Chaperones in Protein Phase Separation and Aggregation

12.1.1 Chaperones in Regulation of Protein Phase Separation

12.1.2 Chaperones in Modulating Protein Aggregation

12.2 Methods to Investigate Chaperones Interacting with Client Proteins in Different States

12.2.1 Methods for Exploring the Interaction ofChaperones with Client Proteins in the Diluted State

12.2.2 Methods to Study the Interaction ofChaperones with Client Proteins in Dynamic Phase Separated State

12.2.3 Methods to Explore the Interaction ofChaperones with Client Proteins in the Aggregated Fibrillar State

12.2.4 Summary

Chapter 13 Structural Biology in Cells by In-cell NMR

13.1 Introduction

13.2 Historical Aspects of In-cell NMR

13.3 In-cell NMR Methods Using Overexpression

13.4 Transexpression in Mammalian Cells

13.5 Transexpression Methods for In-cell NMR

13.5.1 Plasma Membrane Cell-penetrating Peptides or CPP

13.5.2 Plasma Membrane Permeabilization by Bacterial Toxins.

13.5.3 Plasma Membrane Permeabilization by Electroporation.

Notes:

Includes bibliographical references.

Description based on publisher supplied metadata and other sources.

Description based on print version record.

ISBN:

1-83916-598-7

1-83916-599-5