title: A MARTINI extension for Pseudomonas aeruginosa PAO1 lipopolysaccharide.
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.
authors.affiliation: Physics Department, Brock University, St. Catharines, Ontario L2S 3S1, Canada. Electronic address: bv07ay@brocku.ca.
authors.forename: Brad
authors.initials: B
authors.lastname: Van Oosten
authors.affiliation: Physics Department, Brock University, St. Catharines, Ontario L2S 3S1, Canada.
authors.forename: Thad A
authors.initials: TA
authors.lastname: Harroun
mesh_terms: D002462:Cell Membrane / Q000737:chemistry*; D057927:Hydrophobic and Hydrophilic Interactions; D008051:Lipid Bilayers / Q000737:chemistry*; D008070:Lipopolysaccharides / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D033363:Neutron Diffraction; D010714:Phosphatidylethanolamines / Q000737:chemistry*; D011550:Pseudomonas aeruginosa / Q000737:chemistry*; D053838:Scattering, Small Angle; D055672:Static Electricity; D013816:Thermodynamics
chemical_list: D008051:Lipid Bilayers; D008070:Lipopolysaccharides; D010714:Phosphatidylethanolamines; C483858:phosphatidylethanolamine
keywords: Coarse grain; GROMACS; Lipopolysaccharide; MARTINI; Molecular dynamics; P. aeruginosa; POPE