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Taxonomic group: bacteria / Proteobacteria (Phylum: Proteobacteria)
Associated disease: infection due to Escherichia coli [ICD11: XN6P4

]

NCBI PubMed ID: 25753722
Publication DOI: 10.1007/978-1-4939-2343-4_24
Journal NLM ID: 9214969
Publisher: Springer
Correspondence: wonpil

ku.edu
Institutions: Department of Molecular Biosciences and Center for Computational Biology, The University of Kansas, 2030 Becker Drive, Lawrence, KS, 66045, USA, Department of Chemical and Biomolecular Engineering, The University of Maryland, 2113 Chemical and Nuclear Engineering, College Park, MD 20742, USA, Department of Organic Chemistry and Stockholm Center for Biomembrane Research, Arrhenius Laboratory, Stockholm University, S106-91 Stockholm, Sweden

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.

molecular, Escherichia coli, lipid A, glycan, Computational Biology, E.coli, bilayer, molecular dynamics simulation, O6 antigen, R1 core

Structure type: oligomer
Location inside paper: fig.1
Compound class: LPS
Contained glycoepitopes: IEDB_130648,IEDB_130650,IEDB_130659,IEDB_130670,IEDB_131186,IEDB_133751,IEDB_135394,IEDB_135515,IEDB_135813,IEDB_135818,IEDB_136906,IEDB_137340,IEDB_137472,IEDB_137473,IEDB_137485,IEDB_1391961,IEDB_140088,IEDB_141584,IEDB_141794,IEDB_141807,IEDB_142488,IEDB_144983,IEDB_144998,IEDB_146664,IEDB_150908,IEDB_151528,IEDB_151531,IEDB_152206,IEDB_153543,IEDB_176772,IEDB_190606,IEDB_2189047,IEDB_226811,IEDB_885822,IEDB_983930,IEDB_983931,SB_192,SB_44,SB_7,SB_72

Methods: MD simulations, CHARMM-GUI Membrane Builder
3D data: 3D data

NCBI Taxonomy refs (TaxIDs): 217992
Show glycosyltransferases

There is only one chemically distinct structure:

CCCCCCCCCCCCCC(=O)OC(CCCCCCCCCCC)CC(=O)N[C@H]1[C@H](OC[C@H]2O[C@H](OP(=O)(O)O)[C@H](NC(=O)CC(O)CCCCCCCCCCC)[C@@H](OC(=O)CC(O)CCCCCCCCCCC)[C@@H]2O)O[C@H](CO[C@]2(C(=O)O)C[C@@H](O[C@]3(C(=O)O)C[C@@H](O)[C@@H](O)[C@@H]([C@H](O)CO)O3)[C@@H](O[C@H]3O[C@H]([C@@H](O)CO)[C@@H](OP(=O)(O)O)[C@H](O[C@H]4O[C@H]([C@@H](O)CO[C@H]5O[C@H]([C@@H](O)CO)[C@@H](O)[C@H](O)[C@@H]5O)[C@@H](OP(=O)(O)O)[C@H](O[C@H]5O[C@H](CO)[C@@H](O)[C@H](O[C@H]6O[C@H](CO)[C@@H](O)[C@H](O[C@@H]7O[C@H](CO)[C@@H](O)[C@H](O[C@@H]8O[C@H](CO)[C@@H](O)[C@H](O[C@@H]9O[C@H](CO)[C@@H](O[C@@H]%10O[C@H](CO)[C@@H](O)[C@H](O[C@H]%11O[C@H](CO)[C@H](O[C@H]%12O[C@H](CO)[C@@H](O)[C@H](O[C@@H]%13O[C@H](CO)[C@@H](O[C@@H]%14O[C@H](CO)[C@@H](O)[C@H](O[C@H]%15O[C@H](CO)[C@H](O)[C@H](O)[C@H]%15NC(C)=O)[C@@H]%14O[C@@H]%14O[C@H](CO)[C@@H](O)[C@H](O)[C@H]%14O)[C@H](O)[C@@H]%13O)[C@H]%12NC(C)=O)[C@H](O)[C@H]%11NC(C)=O)[C@@H]%10O[C@@H]%10O[C@H](CO)[C@@H](O)[C@H](O)[C@H]%10O)[C@H](O)[C@@H]9O)[C@H]8NC(C)=O)[C@H]7O)[C@H]6O[C@H]6O[C@H](CO)[C@H](O)[C@H](O)[C@H]6O[C@H]6O[C@H](CO)[C@H](O)[C@H](O)[C@H]6O)[C@H]5O)[C@@H]4O)[C@@H]3O)[C@@H]([C@H](O)CO)O2)[C@@H](OP(=O)(O)O)[C@@H]1OC(=O)CC(CCCCCCCCCCC)OC(=O)CCCCCCCCCCCCC

SVG MW SMILES 3D mol Ionize