title: A Glycam-Based Force Field for Simulations of Lipopolysaccharide Membranes: Parametrization and Validation.
abstract: Lipopolysaccharides (LPS) comprise the outermost layer of the Gram-negative bacteria cell envelope. Packed onto a lipid layer, the outer membrane displays remarkable physical-chemical differences compared to cell membranes. The carbohydrate-rich region confers a membrane asymmetry that underlies many biological processes such as endotoxicity, antibiotic resistance, and cell adhesion. Furthermore, unlike membrane proteins from other sources, integral outer-membrane proteins do not consist of transmembrane α helices; instead they consist of antiparallel β-barrels, which highlights the importance of the LPS membrane as a medium. In this work, we present an extension of the GLYCAM06 force field that has been specifically developed for LPS membranes using our Wolf2Pack program. This new set of parameters for lipopolysaccharide molecules expands the GLYCAM06 repertoire of monosaccharides to include phosphorylated N- and O-acetylglucosamine, 3-deoxy-d-manno-oct-2-ulosonic acid, l-glycero-D-manno-heptose and its O-carbamoylated variant, and N-alanine-d-galactosamine. A total of 1 μs of molecular dynamics simulations of the rough LPS membrane of Pseudomonas aeruginosa PA01 is used to showcase the added parameter set. The equilibration of the LPS membrane is shown to be significantly slower compared to phospholipid membranes, on the order of 500 ns. It is further shown that water molecules penetrate the hydrocarbon region up to the terminal methyl groups, much deeper than commonly observed for phospholipid bilayers, and in agreement with neutron diffraction measurements. A comparison of simulated structural, dynamical, and electrostatic properties against corresponding experimentally available data shows that the present parameter set reproduces well the overall structure and the permeability of LPS membranes in the liquid-crystalline phase.
authors.affiliation: Fraunhofer-Institute for Algorithms and Scientific Computing (SCAI), Department of Bioinformatics, Schloss Birlinghoven, 53754 Sankt Augustin, Germany.
authors.forename: Karl N
authors.initials: KN
authors.lastname: Kirschner
authors.affiliation: Department of Fundamental Chemistry, Federal University of Pernambuco, Cidade Universitária, Recife, PE 50740-560 Brazil.
authors.forename: Roberto D
authors.initials: RD
authors.lastname: Lins
authors.affiliation: Fraunhofer-Institute for Algorithms and Scientific Computing (SCAI), Department of Simulation Engineering, Schloss Birlinghoven, 53754 Sankt Augustin, Germany.
authors.forename: Astrid
authors.initials: A
authors.lastname: Maass
authors.affiliation: Department of Fundamental Chemistry, Federal University of Pernambuco, Cidade Universitária, Recife, PE 50740-560 Brazil.
authors.forename: Thereza A
authors.initials: TA
authors.lastname: Soares