A MARTINI extension for Pseudomonas aeruginosa PAO1 lipopolysaccharide

J Mol Graph Model. 2016 Jan:63:125-33. doi: 10.1016/j.jmgm.2015.12.002. Epub 2015 Dec 15.

Abstract

We report a course-grained, large scale simulation of the outer membrane from Pseudomonas aeruginosa. Using the MARTINI force field approach of 4-to-1 atom mapping, we simulate an asymmetrically constructed bilayer with over 1100 rough lipopolysaccharide (LPS) and 3100 16:0-18:1-phosphatidylethanolamine. We achieve 90-fold improvement in computational efficiency on a system much larger than reasonable for all-atom simulation. We also compare a coarse-grained LPS/LPS bilayer simulation with known parameters determined from neutron diffraction.

Keywords: Coarse grain; GROMACS; Lipopolysaccharide; MARTINI; Molecular dynamics; P. aeruginosa; POPE.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cell Membrane / chemistry*
  • Hydrophobic and Hydrophilic Interactions
  • Lipid Bilayers / chemistry*
  • Lipopolysaccharides / chemistry*
  • Molecular Dynamics Simulation
  • Neutron Diffraction
  • Phosphatidylethanolamines / chemistry*
  • Pseudomonas aeruginosa / chemistry*
  • Scattering, Small Angle
  • Static Electricity
  • Thermodynamics

Substances

  • Lipid Bilayers
  • Lipopolysaccharides
  • Phosphatidylethanolamines
  • phosphatidylethanolamine