Gamma-hemolysin components: computational strategies for LukF-Hlg2 dimer reconstruction on a model membrane

Project files provided as supporting information to the manuscript “Gamma-Hemolysin Components: Computational Strategies for LukF-Hlg2 Dimer Reconstruction on a Model Membrane”. The data set contains the following folders:

• LukF_Hlg2_distance: files with the minimum distance between LukF and Hlg2 as a function of time for the simulated replica (Fig. S1); files with the minimum distance between each LukF residue and the Hlg2 monomer and vice versa, averaged over the last 600 ns of simulation in the replica where the spontaneous dimerization is observed (fig. S5).
• HADDOCK_dimer_crystal_pore_displacement: files with the displacement between Hlg2 residues in the HADDOCK model dimer and the same dimer in the crystal pore, after alignment on the LukF monomer (for both the HADDOCK model in presence and in absence of the LukF N-ter) (Fig. S13)
• interface_area: files with the interface area between the LukF and the Hlg2 monomers in the replica where the spontaneous dimerization on the membrane is observed, as a function of time (total interface and contribution of LukF and Hlg2 rim domains) (Fig. S4)
• angles: files with the histograms of the angle between LukF and the axis perpendicular to the membrane, for the simulation of the single LukF monomer and for that capturing the spontaneous dimerization on the membrane (Fig. 4); file with the angle between the LukF and the Hlg2 axis as a function of time in the replica where the spontaneous dimerization is observed (Fig. S6)
• HADDOCK_scores: files with the HADDOCK scores of the predicted LukF-Hlg2 dimers and their RMSD values computed with respect to the same dimer in the crystal pore. The data are reported for the four top-scored models of each cluster ( for both the HADDOCK models in the presence and in the absence of the LukF N-ter) (Fig. 5).
• RMSD: files with the RMSD as a function of time for the LukF and the Hlg2 monomers in the replica where the spontaneous dimerization on the membrane is observed (Fig. 2, Fig. S2, Fig. S3)
• RMSF: files with the RMSF of the LukF and the Hlg2 residues in the replica where the spontaneous dimerization on the membrane is observed and in the simulations of the single monomers (Fig. 2)
• interaction_persistences: files with H-bond (side chain + backbone and backbone only atoms) salt-bridge, and hydrophobic contact persistence matrices for the single LukF monomer simulated alone (299 x 299) and for the LukF-Hlg2 dimer (299+280 x 299+280) (Fig. 4, Fig. S7 + interactions reported in the manuscript)
• distance_protein_membrane: files with the minimum distance between each monomer and the membrane, in the last 200ns of the simulation of spontaneous dimerization on the membrane (Figure S9).
• distance_residues_interface: files with the distance between functionally relevant residues measured along the simulation of the HADDOCK dimer in the absence of LukF N-terminus (Figure S14).