Brownian dynamics simulation of nucleosome formation and disruption under stretching

DOI10.1016/J.JTBI.2004.03.028MaRDI QIDQ2186502zbMATH OpenOpenAlexWikidataFDO

Authors Yanyan Li

Publication date 9 June 2020

Published in Journal of Theoretical Biology (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/q-bio/0312036

zbMATH Keywords

DNAhistoneinteractionnucleosome disruptionnucleosome formation

Mathematics Subject Classification ID

Applications of Brownian motions and diffusion theory (population genetics, absorption problems, etc.) (60J70) Biochemistry, molecular biology (92C40)

Abstract: Using a Brownian dynamics simulation, we numerically studied the interaction of DNA with histone and proposed an octamer-rotation model to describe the process of nucleosome formation. Nucleosome disruption under stretching was also simulated. The theoretical curves of extension versus time as well as of force versus extension are consistent with previous experimental results.

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(3)

• The histone octamer influences the wrapping direction of DNA on it: Brownian dynamics simulation of the nucleosome chirality
• A Markov model for the dynamics of the nucleosome
• Chromatin remodelers as active Brownian dimers

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