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Title: Multiscale modelling of nucleosome core particle aggregation
Authors: Fan, Yanping
Nordenskiöld, Lars
Lyubartsev, Alexander P
Korolev, Nikolay
Keywords: Nucleosome core particles
Chromatin compaction
Multivalent ions
Coarse-grained models
Multiscale simulations
Inverse Monte Carlo
Issue Date: 2015
Source: Lyubartsev, A. P., Korolev, N., Fan, Y., & Nordenskiöld, L. (2015). Multiscale modelling of nucleosome core particle aggregation. Journal of Physics: Condensed Matter, 27(6), 064111-.
Series/Report no.: Journal of Physics: Condensed Matter
Abstract: The nucleosome core particle (NCP) is the basic building block of chromatin. Under the influence of multivalent cations, isolated mononucleosomes exhibit a rich phase behaviour forming various columnar phases with characteristic NCP–NCP stacking. NCP stacking is also a regular element of chromatin structure in vivo. Understanding the mechanism of nucleosome stacking and the conditions leading to self-assembly of NCPs is still incomplete. Due to the complexity of the system and the need to describe electrostatics properly by including the explicit mobile ions, novel modelling approaches based on coarse-grained (CG) methods at the multiscale level becomes a necessity. In this work we present a multiscale CG computer simulation approach to modelling interactions and self-assembly of solutions of NCPs induced by the presence of multivalent cations. Starting from continuum simulations including explicit three-valent cobalt(III)hexammine (CoHex3+) counterions and 20 NCPs, based on a previously developed advanced CG NCP model with one bead per amino acid and five beads per two DNA base pair unit (Fan et al 2013 PLoS One 8 e54228), we use the inverse Monte Carlo method to calculate effective interaction potentials for a 'super-CG' NCP model consisting of seven beads for each NCP. These interaction potentials are used in large-scale simulations of up to 5000 NCPs, modelling self-assembly induced by CoHex3+. The systems of 'super-CG' NCPs form a single large cluster of stacked NCPs without long-range order in agreement with experimental data for NCPs precipitated by the three-valent polyamine, spermidine3+.
ISSN: 0953-8984
DOI: 10.1088/0953-8984/27/6/064111
Schools: School of Biological Sciences 
Rights: © 2015 IOP Publishing Ltd. Content from this work may be used under the terms of the Creative Commons Attribution 3.0 licence. Any further distribution of this work must maintain attribution to the author(s) and the title of the work, journal citation and DOI.
Fulltext Permission: open
Fulltext Availability: With Fulltext
Appears in Collections:SBS Journal Articles

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