New Models of the Cell Nucleus: Crowding, Entropic Forces, Phase Separation, and Fractals

Contributors

Preface

Chapter One. The Nuclear Physique

Abstract

1 Introduction: A Brief History of Biophysics

2 The Biophysical Nucleus

Acknowledgments

References

Chapter Two. The Crowded Nucleus

Abstract

1 Introduction

2 Macromolecular Crowding in the Nucleus

3 Entropic (Depletion) Forces in the Nucleus

4 Compartmentalization in the Nucleus

5 Phase Separation in the Nucleus

6 Concluding Remarks

References

Further-Reading

Chapter Three. Crowding in Polymer–Nanoparticle Mixtures

Abstract

1 Introduction

2 Models of Macromolecules: Polymers and Nanoparticles

3 Theoretical and Computational Methods

4 Response of Polymer Conformations to Nanoparticle Crowding

5 Concluding Remarks

Acknowledgments

References

Chapter Four. Crowding-Induced Formation and Structural Alteration of Nuclear Compartments: Insights from Computer Simulations

Abstract

1 Introduction

2 Structural Properties of Nuclear Compartments

3 Crowded Nature of Cell Nucleus

4 Structural Alterations of Chromosome Subcompartments by Macromolecular Crowding

5 Formation and Maintenance of NBs Influenced by Macromolecular Crowding

6 Concluding Remarks

Acknowledgments

References

Chapter Five. Phase Separation as a Possible Means of Nuclear Compartmentalization

Abstract

1 Introduction

2 Macromolecule Solution Chemistry

3 Aqueous Phase Separation

4 Nuclear Compartments as Crowded and Dynamic Structures

5 Potential Functional Significance of Phase Separation for Nuclear Compartmentalization

6 Experimental Model Systems for Crowded, Phase-Separated Microcompartments

7 Looking Forward

Acknowledgment

References

Chapter Six. Formation of Multiprotein Assemblies in the Nucleus: The Spindle Assembly Checkpoint

Abstract

1 Introduction

2 SAC Signaling

3 Disorder-to-Order Transitions

4 Macromolecular Crowding of Nuclear Proteins

5 Cooperative Interactions of Nuclear Multiprotein Complexes

6 Concluding Remarks

References

Chapter Seven. Characteristic Behavior of Crowding Macromolecules Confined in Cell-Sized Droplets

Abstract

1 Introduction

2 Confinement of Long DNA Molecules in Droplets

3 Cross-Talk of DNA with Other Semiflexible Polymers

4 Gene Expression in Cell-Sized Droplets

5 From Cell-Sized Droplet in Oil Phase to Liposome in Aqueous Phase

6 Concluding Remarks

References

Chapter Eight. Noncanonical Structures and Their Thermodynamics of DNA and RNA Under Molecular Crowding: Beyond the Watson–Crick Double Helix

Abstract

1 Introduction

2 Thermodynamic Studies on Nucleic Acids

3 Molecular Crowding Effects on the Canonical Structures of Nucleic Acids

4 Molecular Crowding Effects on Noncanonical Structures of Nucleic Acids

5 Molecular Crowding Effects on Functional RNAs

6 Molecular Crowding Effects Under Extreme Environments

7 Molecular Crowding Effects on Transcription and Translation

8 Perspectives

Acknowledgments

References

Chapter Nine. Computational Models of Large-Scale Genome Architecture

Abstract

1 Introduction

2 Direct Models of Genome Architecture

3 Inverse Models of Genome Architecture

4 Concluding Remarks

Acknowledgments

References

Chapter Ten. How Chromatin Looping and Nuclear Envelope Attachment Affect Genome Organization in Eukaryotic Cell Nuclei

Abstract

1 Introduction

2 The Model

3 Results

4 Perspectives

Acknowledgments

References

Chapter Eleven. Crowding, Diffusion, and Biochemical Reactions

Abstract

1 Introduction

2 Diffusion and Random Walks

3 Quantifying Diffusion in Living Cells

4 Diffusion as a Driving Force for Biochemical Reactions

5 Concluding Remarks

References

Chapter Twelve. Importance of Crowding in Signaling, Genetic, and Metabolic Networks

Abstract

1 Introduction

2 Diffusion of Transcription Factors Can Increase Noise in Gene Expression

3 Diffusion Between Compartments Can Reduce Protein Concentration Fluctuations

4 Crowding Can Enhance Information Transmission by Removing Correlations

5 Crowding Can Promote Membrane Rebinding, Which Can Enhance Downstream Signal Propagation

6 Crowding Can Qualitatively Change the Response of Biochemical Networks

7 Diffusion Can Affect Metabolic Flux

8 How to Model Biochemical Networks in the Presence of Crowding

9 Effect of Crowding: Diffusion or Entropy?

10 Perspectives

Acknowledgments

References

Further Reading

Chapter Thirteen. Relevance and Limitations of Crowding, Fractal, and Polymer Models to Describe Nuclear Architecture

Abstract

1 Introduction

2 First Glance at Methods to Investigate Nuclear Organization

3 Molecular Crowding

4 Fractal Models

5 Polymer Models for Chromosomes

6 Evaluating Chromosome Structural Properties with Combined Techniques

7 Uniformity of Chromatin Mechanical Parameters

8 Concluding Remarks

Acknowledgments

References

Index