Modeling and simulation of nucleosomes

• Main Author: Yang, Ye
• Other Authors: Lars Nordenskiold
• Format: Theses and Dissertations
• Language: English
• Published: 2012
• Subjects: DRNTU::Science::Biological sciences::Biophysics; DRNTU::Engineering::Computer science and engineering::Computer applications::Physical sciences and engineering; DRNTU::Science::Chemistry::Physical chemistry
• Online Access: https://hdl.handle.net/10356/50806
• Institution: Nanyang Technological University

Nucleosome is composed of highly charged DNA and histones with unstructured termini exposed to the outside. In nucleus, huge number of them are aggregated and highly compacted. In order to elucidate the roles of tails and cations of various valances in NCP aggregation and single nucleosome array folding, we model NCP as a coarse-grained model of a spherical core with flexible tails, surrounded by explicit mobile ions. By inclusion of such details, we extend the conventional polyelectrolyte model of NCP based on mean-field Debye-Hückel approximation. Exhaustive simulations under various conditions have been able to reproduce experiment results quantitatively and qualitatively, especially in the effects of multivalent cations and tails modification. We are also able to understand the mechanisms of NCP aggregation in relation to cations and tails more clearly. Our models could be improved with inclusion of more details to describe other inter-nucleosome interactions.