title: MD Simulations of Lipid A Phosphoethanol Transferase from Neisseria meningitidis (NmEptA) in pure DPPE and mixed PE/PG bilayer
author: Karmen Condic-Jurkic
description: MD simulations of a full-length Lipid A phosphoethanolamine transferase from Neisseria meningitidis (NmEptA, PDB code: 5FGN). NmEptA decorates lipid A with phosphoethanolamine (PEA) by transferring the moiety from phosphoethanolamine (PE) lipids found in the bacterial membrane, resulting with the reduced negative charge of the bacterial surface and increased colistin resistance. The full publication can be found here: doi: 10.1073/pnas.1612927114The uploaded files contain total of 9 independent simulations of NmEptA embedded in two membrane models - pure DPPE bilayer and mixed PE/PG bilayer. A set of three simulations were carried out in DPPE bilayer ar 298 K and three at 310 K, while another set of triplicates was run in a bilayer containing 80% PE and 20% PG lipids at 298 K. A detailed description of MD setup is uploaded in a separate file and the input files used to run the simulations are also provided (.mdp). All the simulations were carried out using GROMACS 3.3.3 engine in conjunction with GROMOS 54a7 force field. Links to the lipid parameters used in these simulations are given below.The uploaded files contain:* The starting structure of NmEptA embedded in the DPPE bilayer (NmEptA_DPPE_Zn.gro) and the mixed PE/PG bilayer (NmEptA_PEPG_Zn.gro).* Set of trajectories in DPPE bilayer and the corresponding input mdp files at 298 K (NmEptA_DPPE_run1-3-298K.xtc/mdp) and at 310 K (NmEptA_DPPE_run1-3-310K.xtc/mdp).* Set of trajectories in PE/PG bilayer and the corresponding mdp files run at 298 K (NmEptA_PEPG_run1-3-298K.xtc/mdp).* PPoPE lipid paramteres (PPoPE.itp) and the equilibrated mixed PE/PG bilayer snapshot (80_PPoPE-20_DMPG.pdb).* MD simulation protocol (MD_Setup.pdf) 