Kniazeva_et_al_2022

Supplementary data

“H2A-H2B histone dimer plasticity and its functional implications”

GitHub repository

https://github.com/intbio/Kniazeva_et_al_2022

Interactive preview of MD trajectories

Dimer systems:

• H2A-H2B^tt_1KX5 - H2A-H2B dimer, truncated histone tails, based on PDB ID 1KX5 starting position
• H2A-H2B^tt_3LZ0 - H2A-H2B dimer, truncated histone tails, based on PDB ID 3LZ0 starting position
• H2A-H2B/DNA^tt_1KX5 - H2A-H2B dimer with 30 bp DNA segment, truncated histone tails (PDB ID 1KX5)
• H2A.Z-H2B^tt_1F66 - H2A.Z-H2B dimer, truncated histone tails (PDB ID 1F66)

Nucleosome systems:

• NCP^tt_H2A.Z - Nucleosome core particle with H2A.Z histones, truncated histone tails (PDB ID 3LZ0/1F66)
• NCP^tt_{25 unwrapped} - Nucleosome core particle with canonical histones, truncated histone tails, 25 bp DNA segment is unwrapped in initial state (PDB ID 3LZ0)
• NCP^tt_{50 unwrapped} - Nucleosome core particle with canonical histones, truncated histone tails, 50 bp DNA segment is unwrapped in initial state (PDB ID 3LZ0)
• Previously published NCP trajectories were published previously, see Armeev et al., 2021 materials.
• Collective motions of the H2A-H2B histones α2-helixes in previously publushed trajectories

Trajectory files

Dimer systems:

• Dimer^tt_1KX5 - H2A-H2B dimer, truncated histone tails, based on PDB ID 1KX5 starting position: pdb, xtc
• Dimer^tt_3LZ0 - H2A-H2B dimer, truncated histone tails, based on PDB ID 3LZ0 starting position: pdb, xtc
• Dimer^tt_DNA - H2A-H2B dimer with 30 bp DNA fragment, truncated histone tails (PDB ID 1KX5): pdb, xtc
• Dimer^tt_H2A.Z - H2A.Z-H2B dimer, truncated histone tails (PDB ID 3LZ0/1F66): pdb, xtc

Nucleosome systems:

• NCP^tt_H2A.Z - Nucleosome core particle with H2A.Z histones, truncated histone tails (PDB ID 3LZ0/1F66): pdb, xtc
• NCP^tt_{25 unwrapped} - Nucleosome core particle with canonical histones, truncated histone tails, 25 bp DNA segment is unwrapped in initial state (PDB ID 3LZ0): pdb, xtc
• NCP^tt_{50 unwrapped} - Nucleosome core particle with canonical histones, truncated histone tails, 50 bp DNA segment is unwrapped in initial state (PDB ID 3LZ0): pdb, xtc

Protocols

• Production run MDP-file for Gromacs