New Models of the Cell Nucleus: Crowding, Entropic Forces, Phase Separation, and Fractals, Volume 307

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

International Review of Cell and Molecular Biology presents current advances and comprehensive reviews in cell biology--both plant and animal. Articles address structure and control of gene expression, nucleocytoplasmic interactions, control of cell development and differentiation, and cell transformation and growth. Impact factor for 2012: 4.973.

Ideas from the fields of biophysics, physical chemistry, of polymer and colloid, and soft matter science have helped clarify the structure and functions of the cell nucleus. The development of powerful methods for modeling conformations and interactions of macromolecules has also contributed. The book aims to encourage cell and molecular biologists to become more familiar with and understand these new concepts and methods, and the crucial contributions they are making to our perception of the nucleus.

• This is the first volume to present a comprehensive review of New Models of the Cell Nucleus

Cell biologists, molecular biologists, developmental biologists, physiologists (organ level), biomedical scientists, biochemists studying cell-cell interactions, cell variation and evolution