Kosarim_et_al_2024

Supplementary data

Molecular dynamics simulations of the nucleosome containing histone variant H2A.J

Nikita A.Kosarim, Anastasiia S.Fedulova, Aleksandra S.Shariafetdinova, Grigoriy A.Armeev and Alexey K.Shaytan

GitHub repository

https://github.com/intbio/Kosarim_et_al_2024

Interactive preview of MD trajectories

• N_cH2A^run_1 - Canonical nucleosome with full tails (PDB ID 5AV9), run_1
• N_cH2A^run_2 - Canonical nucleosome with full tails (PDB ID 5AV9), run_2
• N_H2A.J^run_1 - Nucleosome with H2A.J with full tails (PDB ID 5AV9), run_1
• N_H2A.J^run_2 - Nucleosome with H2A.J with full tails (PDB ID 5AV9), run_2
• N_H2A.J,PSER^run_1 - Nucleosome with H2A.J with H2AS122ph with full tails (PDB ID 5AV9), run_1
• N_H2A.J,PSER^run_2 - Nucleosome with H2A.J with H2AS122ph with full tails (PDB ID 5AV9), run_2
• D_cH2A - H2A-H2B dimer
• D_H2A.J - H2A.J-H2B dimer

Trajectory files

• N_cH2A^run_1 - Canonical nucleosome with full tails (PDB ID 5AV9), run_1: pdb, xtc
• N_cH2A^run_2 - Canonical nucleosome with full tails (PDB ID 5AV9), run_2: pdb, xtc
• N_H2A.J^run_1 - Nucleosome with H2A.J with full tails (PDB ID 5AV9), run_1: pdb, xtc
• N_H2A.J^run_2 - Nucleosome with H2A.J with full tails (PDB ID 5AV9), run_2: pdb, xtc
• N_H2A.J,PSER^run_1 - Nucleosome with H2A.J with H2AS122ph with full tails (PDB ID 5AV9), run_1: pdb, xtc
• N_H2A.J,PSER^run_2 - Nucleosome with H2A.J with H2AS122ph with full tails (PDB ID 5AV9), run_2: pdb, xtc
• D_cH2A - H2A-H2B dimer: pdb, xtc
• D_H2A.J - H2A.J-H2B dimer: pdb, xtc

Force field for phosphoserine (PSER)

https://github.com/intbio/gromacs_ff/amber14sb_parmbsc1_cufix_PTM.ff