Exploring the conformational space of chromatin fibers and their stability by numerical dynamic phase diagrams

• Verfasst von: Stehr, René [VerfasserIn]
• Verfasst von: Schöpflin, Robert [VerfasserIn]
• Verfasst von: Ettig, Ramona [VerfasserIn]
• Verfasst von: Kepper, Frank Nikolaus [VerfasserIn]
• Verfasst von: Rippe, Karsten [VerfasserIn]
• Verfasst von: Wedemann, Gero [VerfasserIn]
• Titel: Exploring the conformational space of chromatin fibers and their stability by numerical dynamic phase diagrams
• Verf.angabe: René Stehr, Robert Schöpflin, Ramona Ettig, Nick Kepper, Karsten Rippe, and Gero Wedemann
• E-Jahr: 2010
• Jahr: March 2010
• Umfang: 10 S.
• Fussnoten: Gesehen am 08.11.2023
• Titel Quelle: Enthalten in: Biophysical journal
• Ort Quelle: Cambridge, Mass. : Cell Press, 1960
• Jahr Quelle: 2010
• Band/Heft Quelle: 98(2010), 6, Seite 1028-1037
• ISSN Quelle: 1542-0086
• DOI: doi:10.1016/j.bpj.2009.11.040
• Datenträger: Online-Ressource
• Sprache: eng
• Sach-SW: Algorithms
• Sach-SW: Chromatin
• Sach-SW: Computer Simulation
• Sach-SW: Models, Chemical
• Sach-SW: Models, Molecular
• Sach-SW: Phase Transition
• Sach-SW: Protein Conformation..
• K10plus-PPN: 1869686071

Abstract

The three-dimensional structure of chromatin affects DNA accessibility and is therefore a key regulator of gene expression. However, the path of the DNA between consecutive nucleosomes, and the resulting chromatin fiber organization remain controversial. The conformational space available for the folding of the nucleosome chain has been analytically described by phase diagrams with a two-angle model, which describes the chain trajectory by a DNA entry-exit angle at the nucleosome and a torsion angle between consecutive nucleosomes. Here, a novel type of numerical phase diagrams is introduced that relates the geometric phase space to the energy associated with a given chromatin conformation. The resulting phase diagrams revealed differences in the energy landscape that reflect the probability of a given conformation to form in thermal equilibrium. Furthermore, we investigated the effects of entropy and additional degrees of freedom in the dynamic phase diagrams by performing Monte Carlo simulations of the initial chain trajectories. Using our approach, we were able to demonstrate that conformations that initially were geometrically impossible could evolve into energetically favorable states in thermal equilibrium due to DNA bending and torsion. In addition, dynamic phase diagrams were applied to identify chromatin fibers that reflect certain experimentally determined features.