Molecular dynamics simulations of Pseudomonas aeruginosa PelB barrel on different membranes under various conditions

The pathogen Pseudomonas aeruginosa enhances its virulence and antibiotic resistance upon formation of durable biofilms. The exopolysaccharides Pel, Psl and alginate essentially contribute to the biofilm matrix, but their secretion mechanisms are barely understood. Here, we reveal the unique architecture of the outer membrane complex PelBC for Pel secretion, where the essential periplasmic ring of twelve lipoproteins PelC is mounted on top of the nanodisc-embedded β-barrel PelB. In this study, we investigated the dynamics of PelB, especially the extracellular loops PlugS and PlugO, as well as the membrane interactions and tunnel opening in different conditions. The systems were created via CHARMM-GUI web server in atomistic resolution with the CHARMM36m force field. The PelB β-barrel was simulated in different membranes under various conditions:70%/30% POPC/POPG membrane, which mimics the experimental nanodicsmore realistic membranes with LPS for E.coli and P. aeruginosaat pH 3.5 and pH 7.4 with 150 mM NaCl and 25 °Cat 37 °C in 150 mM KClat 25 °C in 150 mM NaCl with and without 100 mM CaCl2PlugO and PlugS mutant at 25 °C in 150 mM NaCl for the 70%/30% POPC/POPG membraneIn the zip file, we provided the input files for simulations with GROMACS (gro, tpr, top, mdp, force field files) as well as end and tunnel structures of PelB (PDB files).