 | New models of the cell nucleus: crowding, entropic forces, phase separation, and fractals / ed. by R.Hancock, K.W.Jeon. - Amsterdam [et al.]: Elsevier/AP, 2014. - xiii, 96 p.: ill. - (International review of cell and molecular biology; vol.307). - Incl. bibl. ref. - Ind.: p.481-496. - ISBN 978-0-12-800046-5; ISSN 1937-6448
Шифр: (И/Е0-N52) 02
|
Contributors ................................................... xi
Preface ................................................... xiii
1 The Nuclear Physique ......................................... 1
Thoru Pederson
1 Introduction: A Brief History of Biophysics ............... 1
2 Biophysical Nucleus ....................................... 5
Acknowledgments 1 ........................................... 1
References .................................................. 11
2 The Crowded Nucleus ......................................... 15
Ronald Hancock
1 Introduction ............................................. 15
2 Macromolecular Crowding in the Nucleus ................... 16
3 Entropie (Depletion) Forces in the Nucleus ............... 16
4 Compartmentalization in the Nucleus ...................... 18
5 Phase Separation in the Nucleus .......................... 20
6 Concluding Remarks ....................................... 20
References .................................................. 22
3 Crowding in Polymer-Nanoparticle Mixtures ................... 27
Alan R. Denton
1 Introduction ............................................. 28
2 Models of Macromolecules: Polymers and Nanoparticles ..... 32
3 Theoretical and Computational Methods .................... 46
4 Response of Polymer Conformations to Nanoparticle
Crowding ................................................. 54
5 Concluding Remarks ....................................... 65
Acknowledgments ............................................. 66
References .................................................. 66
4 Crowding-Induced Formation and Structural Alteration
of Nuclear Compartments: Insights from Computer
Simulations ................................................. 73
Jun Soo Kim and Igal Szleifer
1 " Introduction ........................................... 74
2 Structural Properties of Nuclear Compartments ............ 74
3 Crowded Nature of Cell Nucleus ........................... 77
4 Structural Alterations of Chromosome Subcompartments by
Macromolecular Crowding .................................. 85
5 Formation and Maintenance of NBs Influenced by
Macromolecular Crowding .................................. 93
6 Concluding Remarks ...................................... 104
Acknowledgments ............................................ 105
References ................................................. 105
5 Phase Separation as a Possible Means of Nuclear
Compartmentalization ....................................... 109
William M. Aumiller Jr., Bradley W. Davis, and Christine
D. Keating
1 Introduction ............................................ 110
2 Macromolecule Solution Chemistry ........................ 113
3 Aqueous Phase Separation ................................ 118
4 Nuclear Compartments as Crowded and Dynamic Structures .. 122
5 Potential Functional Significance of Phase Separation
for Nuclear Compartmentalization ........................ 126
6 Experimental Model Systems for Crowded, Phase-Separated
Microcompartments ....................................... 129
7 Looking Forward ......................................... 142
Acknowledgment ............................................. 143
References ................................................. 143
6 Formation of Multiprotein Assemblies in the Nucleus:
The Spindle Assembly Checkpoint ............................ 151
Victor M. Bolanos-Garcia
1 Introduction ............................................ 152
2 SAC Signaling ........................................... 153
3 Disorder-to-Order Transitions ........................... 158
4 Macromolecular Crowding of Nuclear Proteins ............. 161
5 Cooperative Interactions of Nuclear Multiprotein
Complexes ............................................... 165
6 Concluding Remarks ...................................... 167
References ................................................. 167
7 Characteristic Behavior of Crowding Macromolecules
Confined in Cell-Sized Droplets ............................ 175
Miho Yanagisawa, Takahiro Sakaue, and Kenichi Yoshikawa
1 Introduction ............................................ 176
2 Confinement of Long DNA Molecules in Droplets ........... 179
3 Cross-Talk of DNA with Other Semiflexible Polymers ...... 185
4 Gene Expression in Cell-Sized Droplets .................. 193
5 From Cell-Sized Droplet in Oil Phase to Liposome in
Aqueous Phase ........................................... 198
6 Concluding Remarks ...................................... 200
References ................................................. 201
8 Noncanonical Structures and Their Thermodynamics
of DNA and RNA Under Molecular Crowding: Beyond
the Watson-Crick Double Helix .............................. 205
Naoki Sugimoto
1 Introduction ............................................ 206
2 Thermodynamic Studies on Nucleic Acids .................. 209
3 Molecular Crowding Effects on the Canonical Structures
of Nucleic Acids ........................................ 212
4 Molecular Crowding Effects on Noncanonical Structures
of Nucleic Acids ........................................ 216
5 Molecular Crowding Effects on Functional RNAs ........... 226
6 Molecular Crowding Effects Under Extreme Environments ... 232
7 Molecular Crowding Effects on Transcription and
Translation ............................................. 242
8 Perspectives ............................................ 257
Acknowledgments ............................................ 258
References ................................................. 258
9 Computational Models of Large-Scale Genome Architecture .... 275
Angelo Rosa and Christophe Zimmer
1 Introduction ............................................ 276
2 Direct Models of Genome Architecture .................... 279
3 Inverse Models of Genome Architecture ................... 311
4 Concluding Remarks ...................................... 330
Acknowledgments ............................................ 344
References ................................................. 344
10 How Chromatin Looping and Nuclear Envelope Attachment
Affect Genome Organization in Eukaryotic Cell Nuclei ....... 351
Hansjoerg Jerabek and Dieter W. Heermann
1 Introduction ............................................ 352
2 The Model ............................................... 359
3 Results ................................................. 364
4 Perspectives ............................................ 378
Acknowledgments ............................................ 379
References ................................................. 379
|
|
