Orientation Dependence of Inter-NCP Interaction: Insights into the Behavior of Liquid Crystal Phase and Chromatin Fiber Organization

Saurabh, S and Jang, YH and Lansac, Y and Maiti, PK (2020) Orientation Dependence of Inter-NCP Interaction: Insights into the Behavior of Liquid Crystal Phase and Chromatin Fiber Organization. In: Journal of Physical Chemistry B, 124 (2). pp. 314-323.

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Abstract

We report equilibrium and nonequilibrium molecular dynamics (MD) simulations of two nucleosome core particles (NCPs) stacked with their dyad axes oriented in parallel or antiparallel fashion. From the equilibrium trajectories, we determine the bridging behavior of different histone tails and observe that different sets of histone tails play important roles in the two orientations in stabilizing the NCP stack. While the H4 and H2A tails play important intermediary roles in the parallel stack, the H3 and H2B tails are important in the antiparallel stack. We use steered MD simulations to unstack the two NCPs and find a stark difference in their unstacking pathways. While the average rupture force was found to be higher for the parallel stack, the work done for complete unstacking was similar for both orientations. We use Jarzynski equality to determine the PMF profiles along the unstacking pathway, relate our findings to the behavior of NCP mesophases, and derive insights into the enigmatic nucleosomal organization in the chromatin fiber.

Item Type:	Journal Article
Publication:	Journal of Physical Chemistry B
Publisher:	American Chemical Society
Additional Information:	The copyright for this article belongs to American Chemical Society
Keywords:	Chromosomes; Liquid crystals; Molecular dynamics, Chromatin fibers; Jarzynski equality; Liquid crystal phase; MD simulation; Non equilibrium molecular dynamic (NEMD); Nucleosome core particles; Orientation dependence; Rupture forces, Crystal orientation, DNA; histone; Xenopus protein, animal; chemistry; conformation; human; liquid crystal; molecular dynamics; nucleosome; protein conformation; Xenopus laevis, Animals; DNA; Histones; Humans; Liquid Crystals; Molecular Dynamics Simulation; Nucleic Acid Conformation; Nucleosomes; Protein Conformation; Xenopus laevis; Xenopus Proteins
Department/Centre:	Division of Physical & Mathematical Sciences > Physics
Date Deposited:	06 Feb 2023 09:54
Last Modified:	06 Feb 2023 09:54
URI:	https://eprints.iisc.ac.in/id/eprint/79929

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