Raw nuclear magnetic resonance data of human linker histone H1x lacking the C-terminal domain (NGH1x) and trajectory data of nanosecond molecular dynamics simulations of GH1x- and NGH1x-chromatosomes (MD data).

Published: 14 May 2020| Version 3 | DOI: 10.17632/3kvcfkzpth.3
Contributors:
Herna de Wit,
Louis Lategan Du Preez,
Gerrit Koorsen

Description

GH1x (PDB: 2LSO) or NGH1x (residues 1 – 120 of human H1x; UniProtKB: Q92522(H1X_HUMAN) were docked to the nucleosome structure (PDB: 4QLC) as described (De Wit, H., Koorsen, G. Docking data of selected human linker histone variants to the nucleosome. Data in Brief (2020) 30: 105580 https://doi.org/10.1016/j.dib.2020.105580) and superimposed on complete nucleosome structures (L.L. Du Preez, The structure and position of the histone terminal domains as a function of linker histone variants and post-translational modifications - A molecular dynamics study, Unpublished doctoral dissertation (2019) University of the Free State, South Africa.). MD simulations were performed at the University of the Free State (UFS) High-Performance Computing (HPC) Cluster using GROMACS v 4.6.7. The AMBER03 all-atom force field and TIP3P water model were used. Periodic boundary conditions were applied, and long-range electrostatics were treated with the PME method (grid spacing: 0.16 nm and 0.8 nm cut-off). The data provided gives the trajectory files of GH1x- and NGH1x-chromatosomes the in TPR, GRO and XTC formats. Starting structures are provided in PDB format: GH1x-chromatosome_frame1.pdb and NGH1x-chromatosome_frame1.pdb. Quality control of each trajectory was conducted after the 600 ns simulation run was complete (Quality_control_analyses.pdf).

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Institutions

University of Johannesburg, University of the Free State

Categories

Histone, Chromatin, Nucleosome, Molecular Dynamics, Molecular Dynamics Study, Epigenetics, Histone Code, Human, Histone Modification

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