title: Multiscale coarse-grained modelling of chromatin components: DNA and the nucleosome.
abstract: To model large biomolecular systems, such as cell and organelles an atomistic description is not currently achievable and is not generally practical. Therefore, simplified coarse-grained (CG) modelling becomes a necessity. One of the most important cellular components is chromatin, a large DNA-protein complex where DNA is highly compacted. Recent progress in coarse graining modelling of the major chromatin components, double helical DNA and the nucleosome core particle (NCP) is presented. First, general principles and approaches allowing rigorous bottom-to-top generation of interaction potentials in the CG models are presented. Then, recent CG models of DNA are reviewed and their adequacy is benchmarked against experimental data on the salt dependence of DNA flexibility (persistence length). Furthermore, a few recent CG models of the NCP are described and their application for studying salt-dependent NCP-NCP interaction is discussed. An example of a multiscale approach to CG modelling of chromatin is presented where interactions and self-assembly of thousands of NCPs in solution are observed.
authors.affiliation: School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore.
authors.forename: Nikolay
authors.initials: N
authors.lastname: Korolev
authors.affiliation: School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore. Electronic address: larsnor@ntu.edu.sg.
authors.forename: Lars
authors.initials: L
authors.lastname: Nordenskiöld
authors.affiliation: Division of Physical Chemistry, Department of Materials and Environmental Chemistry, Arrhenius Laboratory, Stockholm University, 106 91 Stockholm, Sweden. Electronic address: alexander.luybartsev@mmk.su.se.
authors.forename: Alexander P
authors.initials: AP
authors.lastname: Lyubartsev
mesh_terms: D000818:Animals; D002843:Chromatin; D004247:DNA; D006801:Humans; D008954:Models, Biological; D009707:Nucleosomes
chemical_list: D002843:Chromatin; D009707:Nucleosomes; D004247:DNA
keywords: Computer simulations; DNA condensation; Inverse Monte Carlo; Macromolecular assembly; Polyelectrolytes