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

]

NCBI PubMed ID: 36802606
Publication DOI: 10.1021/acs.jcim.3c00072
Journal NLM ID: 101230060
Publisher: Washington, D.C.: American Chemical Society
Correspondence: G. Widmalm <goran.widmalm

su.se>; W. Im <wonpil

lehigh.edu>
Institutions: School of Mathematics, Physics and Statistics, Shanghai University of Engineering Science, Shanghai 201620, China, Department of Biological Sciences, Department of Chemistry, and Department of Bioengineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States, Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-10691 Stockholm, Sweden

Capsule is one of the common virulence factors in Gram-negative bacteria protecting pathogens from host defenses and consists of long-chain capsular polysaccharides (CPS) anchored in the outer membrane (OM). Elucidating structural properties of CPS is important to understand its biological functions as well as the OM properties. However, the outer leaflet of the OM in current simulation studies is represented exclusively by LPS due to the complexity and diversity of CPS. In this work, representative Escherichia coli CPS, KLPS (a lipid A-linked form) and KPG (a phosphatidylglycerol-linked form), are modeled and incorporated into various symmetric bilayers with co-existing LPS in different ratios. All-atom molecular dynamics simulations of these systems have been conducted to characterize various bilayer properties. Incorporation of KLPS makes the acyl chains of LPS more rigid and ordered, while incorporation of KPG makes them less ordered and flexible. These results are consistent with the calculated area per lipid (APL) of LPS, in which the APL of LPS becomes smaller when KLPS is incorporated, whereas it gets larger when KPG is included. Torsional analysis reveals that the influence of the CPS presence on the conformational distributions of the glycosidic linkages of LPS is small, and minor differences are also detected for the inner and outer regions of the CPS. Combined with previously modeled enterobacterial common antigens (ECAs) in the form of mixed bilayers, this work provides more realistic OM models as well as the basis for characterization of interactions between the OM and OM proteins

Lipopolysaccharide, capsular polysaccharide, polysaccharides

Structure type: oligomer
Location inside paper: Fig. 1A, EcO9
Aglycon: lipid A
Compound class: LPS
Contained glycoepitopes: IEDB_115576,IEDB_120354,IEDB_123890,IEDB_130650,IEDB_130659,IEDB_130670,IEDB_130701,IEDB_131186,IEDB_133751,IEDB_135813,IEDB_135818,IEDB_136104,IEDB_136906,IEDB_137340,IEDB_137472,IEDB_140088,IEDB_140116,IEDB_141111,IEDB_141794,IEDB_141795,IEDB_141807,IEDB_141830,IEDB_142488,IEDB_143632,IEDB_144983,IEDB_144998,IEDB_146664,IEDB_151528,IEDB_151531,IEDB_152206,IEDB_153543,IEDB_153756,IEDB_164174,IEDB_164175,IEDB_164176,IEDB_164480,IEDB_174840,IEDB_190606,IEDB_2189047,IEDB_226811,IEDB_241100,IEDB_76933,IEDB_983930,IEDB_983931,SB_136,SB_192,SB_196,SB_197,SB_44,SB_67,SB_7,SB_72

Methods: conformation analysis, MD simulations, CHARMM-GUI Membrane Builder
3D data: molecular modeling, 3D data

Related record ID(s): 20265, 20267, 20268, 20269, 20270, 20271, 22234
NCBI Taxonomy refs (TaxIDs): 1010797
Show glycosyltransferases

There is only one chemically distinct structure:

CC(=O)N[C@H]1[C@H](O[C@@H]2[C@@H](O)[C@H](O[C@H]3[C@H](O)[C@@H](CO)O[C@H](O[C@H]4[C@H](O)[C@@H](CO)O[C@H](O[C@@H]5[C@H](O)[C@@H](O[C@@H]6[C@H](O)[C@@H](O[C@@H]7[C@H](O[C@]8(C(=O)O)C[C@@H](O)[C@@H](O)[C@@H]([C@H](O)CO)O8)C[C@](O)(C(=O)O)O[C@@H]7[C@H](O)CO)O[C@H]([C@@H](O)CO)[C@H]6OP(=O)(O)OP(=O)(O)OCCN)O[C@H]([C@@H](O)CO[C@H]6O[C@H]([C@@H](O)CO)[C@@H](O)[C@H](O)[C@@H]6O)[C@H]5OP(=O)(O)O)[C@@H]4O)[C@@H]3O[C@H]3O[C@H](CO)[C@H](O)[C@H](O)[C@H]3O[C@H]3O[C@H](CO)[C@H](O)[C@H](O)[C@H]3O)O[C@H](CO)[C@H]2O)O[C@H](CO)[C@@H](O)[C@@H]1O[C@H]1O[C@H](CO)[C@@H](O)[C@H](O[C@H]2O[C@H](CO)[C@@H](O)[C@H](O[C@H]3O[C@H](CO)[C@@H](O)[C@H](O[C@H]4O[C@H](CO)[C@@H](O)[C@H](O)[C@@H]4O[C@H]4O[C@H](CO)[C@@H](O)[C@H](O)[C@@H]4O[C@H]4O[C@H](CO)[C@@H](O)[C@H](O)[C@@H]4O[C@H]4O[C@H](CO)[C@@H](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]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]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]8O[C@H]8O[C@H](CO)[C@@H](O)[C@H](O)[C@@H]8O[C@H]8O[C@H](CO)[C@@H](O)[C@H](O)[C@@H]8O[C@H]8O[C@H](CO)[C@@H](O)[C@H](O[C@H]9O[C@H](CO)[C@@H](O)[C@H](O[C@H]%10O[C@H](CO)[C@@H](O)[C@H](O)[C@@H]%10O[C@H]%10O[C@H](CO)[C@@H](O)[C@H](O)[C@@H]%10O[C@H]%10O[C@H](CO)[C@@H](O)[C@H](O)[C@@H]%10O[C@H]%10O[C@H](CO)[C@@H](O)[C@H](O[C@H]%11O[C@H](CO)[C@@H](O)[C@H](O[C@H]%12O[C@H](CO)[C@@H](O)[C@H](O)[C@@H]%12O[C@H]%12O[C@H](CO)[C@@H](O)[C@H](O)[C@@H]%12O[C@H]%12O[C@H](CO)[C@@H](O)[C@H](O)[C@@H]%12O[C@H]%12O[C@H](CO)[C@@H](O)[C@H](O[C@H]%13O[C@H](CO)[C@@H](O)[C@H](O)[C@@H]%13O)[C@@H]%12O)[C@@H]%11O)[C@@H]%10O)[C@@H]9O)[C@@H]8O)[C@@H]7O)[C@@H]6O)[C@@H]5O)[C@@H]4O)[C@@H]3O)[C@@H]2O)[C@@H]1O

SVG MW SMILES 3D mol Ionize