Both gH5A and gH5B were docked using rigid body BD based docking simulations to eight nucleosome structures with different L-DNA1 conformations and L-DNA2 fixed in a specific, highly-populated conformation. These were selected from the CMD simulation without LH based on the γ1 and γ2 angles (Figure 7C and D ). In addition, we docked gH5B in the nucleosome structure taken from the recent chromatosome structure by Zhou et al. (pdb ID 4qlc, 3.5 Å resolution) (36 (link)) using the protocol of Pachov et al. (32 (link)). In short, NMA was applied using the NOMAD-Ref web-server (62 (link)) to generate nucleosome conformations with different degrees of L-DNA opening. The original structure (conformation 0), as well as two conformations with RMSD of 1 and 2 Å, respectively (all non-hydrogen atoms superimposed) along the first mode (‘conformation 1’ and ‘conformation 2’), were selected. The RMSD of the L-DNAs in these two structures from the original structure was 4.7 and 9.2 Å (the non-hydrogen atoms of the core histones superimposed), respectively.
First, polar hydrogen atoms were added to the structures by using PDB2PQR 1.8 (63 (link)) and partial atomic charges and atomic radii were assigned from the AMBER99 force field. The electrostatic potential was calculated for all structures by solving the non-linear Poisson–Boltzmann equation on a grid with a 1 Å spacing and dimension of 1933 in APBS 1.4 (64 ) at temperature 298.15 K. The solvent and solute dielectric constants were 78.54 and 2, respectively and the ionic strength was 100 mM. Higher solute dielectric constants of 4, 6 and 8 were also tested for docking gH5 to the highly populated conformation of the nucleosome from snapshot 5 (Figure7C and D ). The results were insensitive to varying the solute dielectric constant in this range. To define dielectric boundary conditions, the van der Waals surface was used.
The BD simulations were performed with SDA7 (Simulation of Diffusional Association) (65 (link)) using electrostatic interaction forces. Short-range interactions were neglected, and a 0.5 Å excluded volume criterion to prevent overlap was applied. Effective charges were assigned to charged residues on the protein and to P atoms on the DNA using the ECM program (66 ). The trajectories were started randomly on a sphere at a center-to-center distance of b = 280 Å and stopped at a center-to-center distance of c = 500 Å. The time step was set to 1 ps for center-to-center distances up to 160 Å and increased linearly up to 100 ps at a distance of 260 Å. A total of 20 000 trajectories were generated for each pair of LH-nucleosome conformations simulated. The diffusional encounter complex was considered formed when the following two geometric conditions were satisfied: (i) the center-to-center distance of gH5 and the nucleosome <73 Å, and (ii) the nucleosome dyad point and gH5 separation <40 Å. The interaction energies and the coordinates of a complex were recorded if the RMSD to previously recorded complexes was >1 Å and the interaction energy was within the 5000 lowest (most favorable) energy complexes recorded. A complex with RMSD < 1 Å to a previously recorded complex but lower energy was recorded as a substitute of that complex. The 5000 recorded complexes were clustered into 10 groups according to the backbone RMSD values between them. Upon ranking the clusters by their population during the BD simulations, representative structures of the clusters were generated.
First, polar hydrogen atoms were added to the structures by using PDB2PQR 1.8 (63 (link)) and partial atomic charges and atomic radii were assigned from the AMBER99 force field. The electrostatic potential was calculated for all structures by solving the non-linear Poisson–Boltzmann equation on a grid with a 1 Å spacing and dimension of 1933 in APBS 1.4 (64 ) at temperature 298.15 K. The solvent and solute dielectric constants were 78.54 and 2, respectively and the ionic strength was 100 mM. Higher solute dielectric constants of 4, 6 and 8 were also tested for docking gH5 to the highly populated conformation of the nucleosome from snapshot 5 (Figure
The BD simulations were performed with SDA7 (Simulation of Diffusional Association) (65 (link)) using electrostatic interaction forces. Short-range interactions were neglected, and a 0.5 Å excluded volume criterion to prevent overlap was applied. Effective charges were assigned to charged residues on the protein and to P atoms on the DNA using the ECM program (66 ). The trajectories were started randomly on a sphere at a center-to-center distance of b = 280 Å and stopped at a center-to-center distance of c = 500 Å. The time step was set to 1 ps for center-to-center distances up to 160 Å and increased linearly up to 100 ps at a distance of 260 Å. A total of 20 000 trajectories were generated for each pair of LH-nucleosome conformations simulated. The diffusional encounter complex was considered formed when the following two geometric conditions were satisfied: (i) the center-to-center distance of gH5 and the nucleosome <73 Å, and (ii) the nucleosome dyad point and gH5 separation <40 Å. The interaction energies and the coordinates of a complex were recorded if the RMSD to previously recorded complexes was >1 Å and the interaction energy was within the 5000 lowest (most favorable) energy complexes recorded. A complex with RMSD < 1 Å to a previously recorded complex but lower energy was recorded as a substitute of that complex. The 5000 recorded complexes were clustered into 10 groups according to the backbone RMSD values between them. Upon ranking the clusters by their population during the BD simulations, representative structures of the clusters were generated.
