PGL-BCG-TUB

This repository contains all the data produced regarding the study of DIM PGL TUB and PGL BCG in a unique membrane environnement. The simulations of phase transition of 4-membrane systems are gathered in different repositories :- DIM : https://doi.org/10.5281/zenodo.15276372- PGL TUB : https://doi.org/10.5281/zenodo.15276359- PGL BCG : https://doi.org/10.5281/zenodo.15276346It also contains the Scripts necessary to reproduce Fig2 Fig3 Fig4 of the corresponding article (DOI to come soon), and MARTINI3 parameters of DIM, PGL TUB and PGL BCG mycobacterial lipids.Below, a short description of the methodology : We conducted all simulations building on our previous work on PDIM . The atomistic MD simulations were carried out with the Amber16 software (http://ambermd.org) using the Lipid17 force field in combination with the general AMBER force field (GAFF2) . Using the CHARMM-GUI server (https://www.charmm-gui.org) , we built systems containing a bilayer of 300 lipid molecules, DMPC or POPC, with either 1 or 10 embedded molecules of PGL. The systems were solvated with TIP3P water. The membrane models were minimized by executing 2500 iterations using the steepest descent method, followed by 7500 iterations with the conjugate gradient method, with weakly restrained solute (k = 10 kcal/mol/Å2). Next, a short 100 ps MD run was performed on weakly restrained solute with the temperature increasing linearly from 0 to 303 K. The temperature was controlled using Langevin dynamics with the collision frequency parameter γ set to 1.0 ps−1 and a time step of 1 fs. Throughout the calculations, a cutoff of 10 Å was used for electrostatic interactions. We then proceeded with the equilibration of the system, consisting of 10 consecutive MD runs of 500 ps each, progressively releasing the restraints, at a constant temperature of 303 K with a time step of 2 fs. We finally carried out a 1.4 µs production run at a temperature of 303 K and a pressure of 1 bar. Langevin dynamics was used to control the temperature, with γ = 1.0 ps−1, while the pressure was controlled by the anisotropic Monte Carlo semi-isotropic barostat with the pressure relaxation time τp = 2 ps, with csurften = 3 and gamma_ten = 0. Bonds involving hydrogen were constrained with the SHAKE algorithm. We performed Coarse-Grained (CG) simulations using GROMACS 2020.2 with the Martini 3 force field . We built membrane systems made of pure DMPC, pure POPC or a mixture of DOPE/POPC (3:1), containing PDIM, PGL-BCG or PGL-Mtb, using the Martini insane tool. All systems were minimized and gradually equilibrated according to the protocol suggested by CHARMM-GUI Martini Maker . Coulomb interactions were treated using the reaction-field potential, and Lennard–Jones interactions were treated using shifted potentials with a cutoff radius of 1.1 nm. Pressure was maintained at 1 bar using the Parrinello–Rahman algorithm with a semi-isotropic pressure control. The temperature was kept at 310 K using the v-rescale algorithm. A time step of 20 fs was used.