| 1. |
- Perepelov, Andrei V., et al.
(författare)
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Structure and genetics of the O-antigen of Escherichia coli O169 related to the O-antigen of Shigella boydii type 6
- 2015
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Ingår i: Carbohydrate Research. - : Elsevier BV. - 0008-6215 .- 1873-426X. ; 414, s. 46-50
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Tidskriftsartikel (refereegranskat)abstract
- The O-polysaccharide (O-antigen) of Escherichia coli O169 was studied by sugar analysis along with 1D and 2D H-1 and C-13 NMR spectroscopy. The following structure of the branched hexasaccharide repeating unit was established: [GRAPHICS] The O-polysaccharide of E. coli O169 differs from that of Shigella boydii type 6 only in the presence of a side-chain glucose residue. A comparison of the O-antigen biosynthesis gene clusters between the galF to gnd genes in the genomes of the two bacteria revealed their close relationship. The glycosyltransferase gene responsible for the formation of the beta-D-Glcp-(1 -> 6)-alpha-D-Galp linkage in the O-antigen was identified in the gene cluster.
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| 2. |
- Daikoku, S., et al.
(författare)
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Synthesis and structural investigation of a series of mannose-containing oligosaccharides using mass spectrometry
- 2018
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Ingår i: Organic and biomolecular chemistry. - : Royal Society of Chemistry (RSC). - 1477-0520 .- 1477-0539. ; 16:2, s. 228-238
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Tidskriftsartikel (refereegranskat)abstract
- A series of compounds associated with naturally occurring and biologically relevant glycans consisting of alpha-mannosides were prepared and analyzed using collision-induced dissociation (CID), energy-resolved mass spectrometry (ERMS), and H-1 nuclear magnetic resonance spectroscopy. The CID experiments of sodiated species of disaccharides and ERMS experiments revealed that the order of stability of mannosyl linkages was as follows: 6-linked > 4-linked >= 2-linked > 3-linked mannosyl residues. Analysis of linear trisaccharides revealed that the order observed in disaccharides could be applied to higher glycans. A branched trisaccharide showed a distinct dissociation pattern with two constituting disaccharide ions. The estimation of the content of this ion mixture was possible using the disaccharide spectra. The hydrolysis of mannose linkages at 3- and 6-positions in the branched trisaccharide revealed that the 3-linkage was cleaved twice as fast as the 6-linkage. It was observed that the solution-phase hydrolysis and gas-phase dissociation have similar energetics.
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| 3. |
- Furevi, Axel, et al.
(författare)
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Structural analysis of the O-antigen polysaccharide from Escherichia coli O188
- 2020
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Ingår i: Carbohydrate Research. - : Elsevier BV. - 0008-6215 .- 1873-426X. ; 498
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Tidskriftsartikel (refereegranskat)abstract
- The structure of the O-antigen from Escherichia coli reference strain O188 (E. coli O188:H10) has been investigated. The lipopolysaccharide shows a typical nonrandom modal chain-length distribution and the sugar and absolute configuration analysis revealed D-Man, D-Glc, D-GlcN and D-GlcA as major components. The structure of the O-specific polysaccharide was determined using one- and two-dimensional H-1 and C-13 NMR spectroscopy experiments, where inter-residue correlations were identified by H-1,C-13-heteronuclear multiple-bond correlation and H-1,H-1-NOESY experiments, which revealed that it consists of pentasaccharide repeating units with the -> 4)-beta-D-GlcpA-(1 -> 2)-beta-D-Manp-(1 -> 4)-beta-D-Manp-(1 -> 3)-beta-D-GlcpNAc-(1 -> following structure: vertical bar alpha-D-Galp-(1 -> 3) Biosynthetic aspects and NMR analysis are consistent with the presented structure as the biological repeating unit. The O-antigen of Shigella boydii type 16 differs only in that it carries O-acetyl groups to similar to 50% at O6 of the branchpoint mannose residues. A molecular model of the E. coli O188 O-antigen containing 20 repeating units extends similar to 100 angstrom, which is similar to the height of the periplasmic portion of polysaccharide co-polymerase Wzz proteins that regulate the O-antigen chain length of lipopolysaccharides in the Wzx/Wzy biosynthetic pathway.
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| 4. |
- Goulart, Paula N., et al.
(författare)
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The importance of orientation of exocyclic groups in a naphthoxyloside : A specific rotation calculation study
- 2017
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Ingår i: Journal of Physical Organic Chemistry. - : John Wiley & Sons. - 0894-3230 .- 1099-1395. ; 30:12
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Tidskriftsartikel (refereegranskat)abstract
- 2-Naphthyl -d-xylopyranoside (XylNap) inhibits -1,4-galactosyltransferase 7 (4GalT7) and thereby growth of tumor cells both in vitro and in vivo. The binding pocket of 4GalT7 has a defined orientation of hydrogen bond acceptors and hydrophobic moiety. Knowing the orientation of the hydroxyl and naphthyl groups of this molecule would help in the development of more efficient inhibitors. In this work, we have tried, for the first time, to determine the exocyclic hydroxyl and aglycon groups orientation of XylNap, using ab initio descriptions, and calculation of the specific rotation values, in methanol solutions, using 2 different solvent descriptions: a dielectric continuum approach (polarizable continuum model [PCM]) and a microsolvated+continuum approach (MS+PCM). In the PCM approach, [](D)=-59 deg/(dm(g/cm(3))) whereas for the MS+PCM approach [](D)=-29 deg/(dm(g/cm(3))). The latter is in excellent agreement with the experimentally determined value in methanol solution, viz, [](D)=-30 deg/(dm(g/cm(3))). This agreement allows us to say that the hydroxyl groups have similar orientations in xylose and XylNap, and the naphthyl group has a very well-defined dihedral angle value in the most abundant conformations.
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| 5. |
- Muheim, Claudio, et al.
(författare)
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Identification of a Fragment-Based Scaffold that Inhibits the Glycosyltransferase WaaG from Escherichia coli
- 2016
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Ingår i: Antibiotics. - : MDPI AG. - 2079-6382. ; 5:1
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Tidskriftsartikel (refereegranskat)abstract
- WaaG is a glycosyltransferase that is involved in the biosynthesis of lipopolysaccharide in Gram-negative bacteria. Inhibitors of WaaG are highly sought after as they could be used to inhibit the biosynthesis of the core region of lipopolysaccharide, which would improve the uptake of antibiotics. Herein, we establish an activity assay for WaaG using C-14-labeled UDP-glucose and LPS purified from a increment waaG strain of Escherichia coli. We noted that addition of the lipids phosphatidylglycerol (PG) and cardiolipin (CL), as well as the detergent 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate (CHAPS) increased activity. We then use the assay to determine if three molecular scaffolds, which bind to WaaG, could inhibit its activity in vitro. We show that 4-(2-amino-1,3-thiazol-4-yl)phenol inhibits WaaG (IC50 1.0 mM), but that the other scaffolds do not. This study represents an important step towards an inhibitor of WaaG by fragment-based lead discovery.
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| 6. |
- Riu, Federico, et al.
(författare)
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A Lead-Based Fragment Library Screening of the Glycosyltransferase WaaG from Escherichia coli
- 2022
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Ingår i: Pharmaceuticals. - : MDPI AG. - 1424-8247. ; 15:2
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Tidskriftsartikel (refereegranskat)abstract
- Glucosyl transferase I (WaaG) in E. coli catalyzes the transfer of an α-d-glucosyl group to the inner core of the lipopolysaccharide (LPS) and plays an important role in the biogenesis of the outer membrane. If its activity could be inhibited, the integrity of the outer membrane would be compromised and the bacterium would be susceptible to antibiotics that are normally prevented from entering the cell. Herein, three libraries of molecules (A, B and C) were docked in the binding pocket of WaaG, utilizing the docking binding affinity as a filter to select fragment-based compounds for further investigations. From the results of the docking procedure, a selection of compounds was investigated by molecular dynamics (MD) simulations to obtain binding free energy (BFE) and KD values for ligands as an evaluation for the binding to WaaG. Derivatives of 1,3-thiazoles (A7 and A4) from library A and 1,3,4-thiadiazole (B33) from library B displayed a promising profile of BFE, with KD < mM, viz., 0.11, 0.62 and 0.04 mM, respectively. Further root-mean-square-deviation (RMSD), electrostatic/van der Waals contribution to the binding and H-bond interactions displayed a favorable profile for ligands A4 and B33. Mannose and/or heptose-containing disaccharides C1–C4, representing sub-structures of the inner core of the LPS, were also investigated by MD simulations, and compound C42− showed a calculated KD = 0.4 µM. In the presence of UDP-Glc2−, the best-docked pose of disaccharide C42− is proximate to the glucose-binding site of WaaG. A study of the variation in angle and distance was performed on the different portions of WaaG (N-, the C- domains and the hinge region). The Spearman correlation coefficient between the two variables was close to unity, where both variables increase in the same way, suggesting a conformational rearrangement of the protein during the MD simulation, revealing molecular motions of the enzyme that may be part of the catalytic cycle. Selected compounds were also analyzed by Saturation Transfer Difference (STD) NMR experiments. STD effects were notable for the 1,3-thiazole derivatives A4, A8 and A15 with the apo form of the protein as well as in the presence of UDP for A4.
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| 7. |
- Söderström, Bill, et al.
(författare)
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An OregonGreen488-labelled d-amino acid for visualizing peptidoglycan by super-resolution STED nanoscopy
- 2020
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Ingår i: Microbiology. - : Microbiology Society. - 1350-0872 .- 1465-2080. ; 166:12, s. 1129-1135
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Tidskriftsartikel (refereegranskat)abstract
- Fluorescent o amino acids (FDAAs) are molecular probes that are widely used for labelling the peptidoglycan layer of bacteria. When added to growing cells they are incorporated into the stem peptide by a transpeptidase reaction, allowing the timing and localization of peptidoglycan synthesis to be determined by fluorescence microscopy. Herein we describe the chemical synthesis of an Oregon Green 488 labelled FDAA (OGDA). We also demonstrate that OGDA can be efficiently incorporated into the PG of Grampositive and some Gramnegative bacteria, and imaged by superresolution stimulated emission depletion (STED) nanoscopy at a resolution well below 100 nm.
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| 8. |
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