title: Interaction of E. coli outer-membrane protein A with sugars on the receptors of the brain microvascular endothelial cells.
abstract: Esherichia coli, the most common gram-negative bacteria, can penetrate the brain microvascular endothelial cells (BMECs) during the neonatal period to cause meningitis with significant morbidity and mortality. Experimental studies have shown that outer-membrane protein A (OmpA) of E. coli plays a key role in the initial steps of the invasion process by binding to specific sugar moieties present on the glycoproteins of BMEC. These experiments also show that polymers of chitobiose (GlcNAcbeta1-4GlcNAc) block the invasion, while epitopes substituted with the L-fucosyl group do not. We used HierDock computational technique that consists of a hierarchy of coarse grain docking method with molecular dynamics (MD) to predict the binding sites and energies of interactions of GlcNAcbeta1-4GlcNAc and other sugars with OmpA. The results suggest two important binding sites for the interaction of carbohydrate epitopes of BMEC glycoproteins to OmpA. We identify one site as the binding pocket for chitobiose (GlcNAcbeta1-4GlcNAc) in OmpA, while the second region (including loops 1 and 2) may be important for recognition of specific sugars. We find that the site involving loops 1 and 2 has relative binding energies that correlate well with experimental observations. This theoretical study elucidates the interaction sites of chitobiose with OmpA and the binding site predictions made in this article are testable either by mutation studies or invasion assays. These results can be further extended in suggesting possible peptide antagonists and drug design for therapeutic strategies.
authors.affiliation: Materials and Process Simulation Center (MC 139-74), California Institute of Technology, Pasadena, California 91125, USA.
authors.forename: Deepshikha
authors.initials: D
authors.lastname: Datta
authors.forename: Nagarajan
authors.initials: N
authors.lastname: Vaidehi
authors.forename: Wely B
authors.initials: WB
authors.lastname: Floriano
authors.forename: Kwang S
authors.initials: KS
authors.lastname: Kim
authors.forename: Nemani V
authors.initials: NV
authors.lastname: Prasadarao
authors.forename: William A
authors.initials: WA
authors.lastname: Goddard
mesh_terms: D001425:Bacterial Outer Membrane Proteins / Q000737:chemistry / Q000378:metabolism*; D001665:Binding Sites; D001921:Brain / Q000098:blood supply*; D050260:Carbohydrate Metabolism; D002241:Carbohydrates / Q000737:chemistry; D019295:Computational Biology; D004187:Disaccharides / Q000737:chemistry / Q000378:metabolism; D004730:Endothelium, Vascular / Q000166:cytology* / Q000378:metabolism*; D008024:Ligands; D008833:Microcirculation; D008958:Models, Molecular; D018583:Pliability; D011956:Receptors, Cell Surface / Q000378:metabolism*; D012984:Software; D013816:Thermodynamics
chemical_list: D001425:Bacterial Outer Membrane Proteins; D002241:Carbohydrates; D004187:Disaccharides; D008024:Ligands; D011956:Receptors, Cell Surface; C078167:OMPA outer membrane proteins; C032438:chitobiose