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

Title
Orientation Dependence of Inter-NCP Interaction: Insights into the Behavior of Liquid Crystal Phase and Chromatin Fiber Organization
Authors
Saurabh, SumanJang, Yun HeeLansac, YvesMaiti, Prabal K.
DGIST Authors
Jang, Yun Hee
Issue Date
2020-01
Citation
Journal of Physical Chemistry B, 124(2), 314-323
Type
Article
Article Type
Article
Keywords
STEERED MOLECULAR-DYNAMICSNUCLEOSOME CORE PARTICLEHIGHER-ORDER STRUCTURECOARSE-GRAINED MODELHISTONE TAILSFORCE-FIELDH4 TAILDNAACETYLATIONPROTEIN
ISSN
1520-6106
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. Copyright © 2019 American Chemical Society.
URI
http://hdl.handle.net/20.500.11750/11516
DOI
10.1021/acs.jpcb.9b07898
Publisher
American Chemical Society
Related Researcher
  • Author Jang, Yun Hee CMMM Lab(Curious Minds Molecular Modeling Laboratory)
  • Research Interests Multiscale molecular modeling (quantum mechanics calculation; molecular dynamics simulation) : Supercomputer-assisted molecular-level understanding of materials and their chemistry; which leads to rational design of high-performance organic-inorganic-hybrid materials for clean and renewable energy as well as low-energy-consumption electronic devices
Files:
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Collection:
Department of Energy Science and EngineeringCMMM Lab(Curious Minds Molecular Modeling Laboratory)1. Journal Articles


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