Armeev_et_al_2021

Supplementary data

“Histone dynamics mediate DNA unwrapping and sliding in nucleosomes”

G.A. Armeev, A.S. Kniazeva, G.A. Komarova, M.P. Kirpichnikov, A.K. Shaytan. Nature Communications, 2021.

GitHub repository

https://github.com/intbio/Armeev_et_al_2021

Interactive preview of MD trajectories

• NCP₁₄₇ - 147 bp pseudosymmetric α-satellite DNA, full length histone tails in symmetric starting positions (PDB ID 1KX5)
• NCP^tt₁₄₇ - same as NCP₁₄₇, but with truncated histone tails (PDB ID 1KX5)
• NCP^tt₁₄₆ - 146 bp α-satellite DNA sequence, truncated histone tails (PDB ID 1AOI)
• NCP^tt₁₄₅ - 145 bp Widom 601 DNA sequence, truncated histone tails (PDB ID 3LZ0)
• NCP^fixed₁₄₇ - same as NCP₁₄₇, but Cα-atoms of histone folds were restrained in motion (PDB ID 1KX5)

Trajectory files

• NCP₁₄₇ - 147 bp pseudosymmetricα-satellite DNA, full length histone tails in symmetric starting positions (PDB ID 1KX5): pdb, xtc
• NCP^tt₁₄₇ - same as NCP₁₄₇, but with truncated histone tails (PDB ID 1KX5): pdb, xtc
• NCP^tt₁₄₆ - 146 bp α-satellite DNA sequence, truncated histone tails (PDB ID 1AOI): pdb, xtc
• NCP^tt₁₄₅ - 145 bp Widom 601 DNA sequence, truncated histone tails (PDB ID 3LZ0): pdb, xtc
• NCP^fixed₁₄₇ - same as NCP₁₄₇, but Cα-atoms of histone folds were restrained in motion (PDB ID 1KX5)s: pdb, xtc

Protocols

• Production run MDP-file for Gromacs

Analysis scripts and algorithms

This site is open source. Improve this page.