title: Lipopolysaccharide membrane building and simulation.
abstract: While membrane simulations are widely employed to study the structure and dynamics of various lipid bilayers and membrane proteins in the bilayers, simulations of lipopolysaccharides (LPS) in membrane environments have been limited due to their structural complexity, difficulties in building LPS-membrane systems, and lack of the appropriate molecular force fields. In this work, as a first step to extend CHARMM-GUI Membrane Builder to incorporate LPS molecules and to explore their structures and dynamics in membrane environments using molecular dynamics simulations, we describe step-by-step procedures to build LPS bilayer systems using CHARMM and the recently developed CHARMM carbohydrate and lipid force fields. Such procedures are illustrated by building various bilayers of Escherichia coli R1.O6 LPS and the presentation of preliminary simulation results in terms of per-LPS area and density distributions of various components along the membrane normal.
authors.affiliation: Department of Molecular Biosciences and Center for Computational Biology, The University of Kansas, 2030 Becker Drive, Lawrence, KS, 66045, USA.
authors.forename: Sunhwan
authors.initials: S
authors.lastname: Jo
authors.forename: Emilia L
authors.initials: EL
authors.lastname: Wu
authors.forename: Danielle
authors.initials: D
authors.lastname: Stuhlsatz
authors.forename: Jeffery B
authors.initials: JB
authors.lastname: Klauda
authors.forename: Alexander D
authors.initials: AD
authors.lastname: MacKerell
authors.forename: Göran
authors.initials: G
authors.lastname: Widmalm
authors.forename: Wonpil
authors.initials: W
authors.lastname: Im
mesh_terms: D002462:Cell Membrane / Q000737:chemistry*; D004926:Escherichia coli / Q000378:metabolism; D006027:Glycosides / Q000737:chemistry; D008051:Lipid Bilayers / Q000737:chemistry; D008070:Lipopolysaccharides / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D013997:Time Factors
chemical_list: D006027:Glycosides; D008051:Lipid Bilayers; D008070:Lipopolysaccharides