A Bottom-Up Coarse-Grained Model for Nucleosome-Nucleosome Interactions with Explicit Ions

Overview

Journal J Chem Theory Comput

Publisher American Chemical Society

Specialties Biochemistry
Chemistry

Date 2022 May 17

PMID 35580041

Authors

Tiedong Sun

Vishal Minhas

Alexander Mirzoev

Nikolay Korolev

Alexander P Lyubartsev

Lars Nordenskiold

Affiliations

Soon will be listed here.

Abstract

The nucleosome core particle (NCP) is a large complex of 145-147 base pairs of DNA and eight histone proteins and is the basic building block of chromatin that forms the chromosomes. Here, we develop a coarse-grained (CG) model of the NCP derived through a systematic bottom-up approach based on underlying all-atom MD simulations to compute the necessary CG interactions. The model produces excellent agreement with known structural features of the NCP and gives a realistic description of the nucleosome-nucleosome attraction in the presence of multivalent cations (Mg(HO) or Co(NH)) for systems comprising 20 NCPs. The results of the simulations reveal structural details of the NCP-NCP interactions unavailable from experimental approaches, and this model opens the prospect for the rigorous modeling of chromatin fibers.

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