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

]

NCBI PubMed ID: 32476421
Publication DOI: 10.1021/acs.jpcb.0c03353
Journal NLM ID: 101157530
Publisher: Washington, DC: American Chemical Society
Correspondence: Goran.Widmalm

su.se; 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, School of Computational Sciences, Korea Institute for Advanced Study, Seoul 02455, Republic of Korea

Enterobacterial common antigen (ECA) is a surface glycolipid shared by all members of the Enterobacteriaceae family. In addition to lipopolysaccharides (LPS), ECA is an important component in the outer membrane (OM) of Gram-negative bacteria, making the OM an effective, selective barrier against the permeation of toxic molecules. Previous modeling and simulation studies represented OMs exclusively with LPS in the outer leaflet. In this work, various ECA molecules were first modeled and incorporated into symmetric bilayers with LPS in different ratios, and all-atom molecular dynamics simulations were conducted to investigate the properties of the mixed bilayers mimicking OM outer leaflets. Dynamic and flexible conformational ensembles are sampled for each ECA/LPS system. Incorporation of ECALPS (an LPS core-linked form) and ECAPG (a phosphatidylglycerol-linked form) affects lipid packing and ECA/LPS distributions on the bilayer surface. Hydrophobic thickness and chain order parameter analyses indicate that incorporation of ECAPG makes the acyl chains of LPS more flexible and disordered and thus increases the area per lipid of LPS. The calculated area per lipid of each ECA/LPS provides a good estimate for building more realistic OMs with different ratios of ECA/LPS, which will be useful in order to characterize their interactions with outer membrane proteins in more realistic OMs.

Lipopolysaccharide, enterobacterial common antigen, engineering, outer membrane, molecular dynamics simulations

Structure type: oligomer
Location inside paper: p.5949, Fig.1, Fig.S1
Trivial name: ECA(LPS)
Compound class: LPS
Contained glycoepitopes: IEDB_120354,IEDB_123890,IEDB_130650,IEDB_130659,IEDB_130670,IEDB_131186,IEDB_133751,IEDB_135813,IEDB_135818,IEDB_136906,IEDB_137340,IEDB_137472,IEDB_140088,IEDB_141794,IEDB_141807,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_151528,IEDB_151531,IEDB_153543,IEDB_176772,IEDB_190606,IEDB_2189047,IEDB_226811,IEDB_534864,IEDB_983931,SB_192,SB_7

Methods: MD simulations, CHARMM-GUI Membrane Builder
Comments, role: structure of E. coli ECA in an endotoxin/LPS-associated form - ECA(LPS).
3D data: molecular modeling

Related record ID(s): 32104
NCBI Taxonomy refs (TaxIDs): 562
Show glycosyltransferases

There is only one chemically distinct structure:

CCCCCCCCCCCCCC(=O)O[C@H](CCCCCCCCCCC)CC(=O)O[C@H]1[C@H](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)OP(=O)(O)OCCN)[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]9O[C@H](C(=O)O)[C@@H](O[C@H]%10O[C@H](C)[C@H](NC(C)=O)[C@H](O[C@H]%11O[C@H](CO)[C@@H](O[C@@H]%12O[C@H](C(=O)O)[C@@H](O[C@H]%13O[C@H](C)[C@H](NC(C)=O)[C@H](O[C@H]%14O[C@H](CO)[C@@H](O[C@@H]%15O[C@H](C(=O)O)[C@@H](O[C@H]%16O[C@H](C)[C@H](NC(C)=O)[C@H](O[C@H]%17O[C@H](CO)[C@@H](O[C@@H]%18O[C@H](C(=O)O)[C@@H](O[C@H]%19O[C@H](C)[C@H](NC(C)=O)[C@H](O[C@H]%20O[C@H](CO)[C@@H](O[C@@H]%21O[C@H](C(=O)O)[C@@H](O[C@H]%22O[C@H](C)[C@H](NC(C)=O)[C@H](O[C@H]%23O[C@H](CO)[C@@H](O[C@@H]%24O[C@H](C(=O)O)[C@@H](O[C@H]%25O[C@H](C)[C@H](NC(C)=O)[C@H](O)[C@H]%25O)[C@H](O)[C@@H]%24NC(C)=O)[C@H](O)[C@H]%23NC(C)=O)[C@H]%22O)[C@H](O)[C@@H]%21NC(C)=O)[C@H](O)[C@H]%20NC(C)=O)[C@H]%19O)[C@H](O)[C@@H]%18NC(C)=O)[C@H](O)[C@H]%17NC(C)=O)[C@H]%16O)[C@H](O)[C@@H]%15NC(C)=O)[C@H](O)[C@H]%14NC(C)=O)[C@H]%13O)[C@H](O)[C@@H]%12NC(C)=O)[C@H](O)[C@H]%11NC(C)=O)[C@H]%10O)[C@H](O)[C@@H]9NC(C)=O)[C@H](O)[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)O[C@@H](OC[C@H]2O[C@H](OP(=O)(O)O)[C@H](NC(=O)C[C@H](O)CCCCCCCCCCC)[C@@H](OC(=O)C[C@H](O)CCCCCCCCCCC)[C@@H]2O)[C@@H]1NC(=O)C[C@@H](CCCCCCCCCCC)OC(=O)CCCCCCCCCCC

SVG MW SMILES 3D mol Ionize

Warning = sub-repeat ending at aDGlcpN: large unit count (9) was reduced to 5