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Multiscale coarse-grained modelling of chromatin components: DNA and the nucleosome
Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).
Number of Authors: 3
2016 (English)In: Advances in Colloid and Interface Science, ISSN 0001-8686, E-ISSN 1873-3727, Vol. 232, 36-48 p.Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
2016. Vol. 232, 36-48 p.
Keyword [en]
Macromolecular assembly, DNA condensation, Polyelectrolytes, Computer simulations, Inverse Monte Carlo
National Category
Chemical Sciences
Identifiers
URN: urn:nbn:se:su:diva-132411DOI: 10.1016/j.cis.2016.02.002ISI: 000379563300005PubMedID: 26956528OAI: oai:DiVA.org:su-132411DiVA: diva2:952286
Conference
International Workshop on Polyelectrolytes in Chemistry, Biology and Technology, Nanyang Technological University, Singapore, January 26-28, 2015
Available from: 2016-08-12 Created: 2016-08-11 Last updated: 2016-08-12Bibliographically approved

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Lyubartsev, Alexander P.
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