A MARTINI extension for Pseudomonas aeruginosa PAO1 lipopolysaccharide

• An MD model of a lipopolysaccharide was created as an extension to MARTINI.
• The model was tested with MARTINI's polarized and non polarized water models.
• Comparison was made with all-atom simulations as well as neutron scattering data.
• The membrane structure was well reproduced by the coarse grained model.
• A computational efficiency of 92× greater than all-atom simulations was achieved.

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.

Figure optionsDownload high-quality image (460 K)Download as PowerPoint slide