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ОбложкаNew 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
 

Место хранения: 02 | Отделение ГПНТБ СО РАН | Новосибирск

Оглавление / Contents
 
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

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