Staff Publications

Staff Publications

  • external user (warningwarning)
  • Log in as
  • language uk
  • About

    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

    We have a manual that explains all the features 

    Records 1 - 8 / 8

    • help
    • print

      Print search results

    • export

      Export search results

    Check title to add to marked list
    Structural and mechanistic insight into N-glycan processing by endo-a-mannosidase
    Thompson, A.J. ; Williams, R.J. ; Hakki, Z. ; Alonzi, D.S. ; Wennekes, T. ; Gloster, T.M. ; Songsrirote, K. ; Thomas-Oates, E. ; Wrodnigg, T.M. ; Spreitz, J. ; Stütz, A.E. ; Butters, T.D. ; Williams, S.J. ; Davies, G.J. - \ 2012
    Proceedings of the National Academy of Sciences of the United States of America 109 (2012)3. - ISSN 0027-8424 - p. 781 - 786.
    asparagine-linked oligosaccharides - glucosidase-ii-deficient - glycoprotein-biosynthesis - endomannosidase pathway - endoplasmic-reticulum - glycoside hydrolases - quality-control - inhibitors - cells - classification
    N-linked glycans play key roles in protein folding, stability, and function. Biosynthetic modification of N-linked glycans, within the endoplasmic reticulum, features sequential trimming and readornment steps. One unusual enzyme, endo-a-mannosidase, cleaves mannoside linkages internally within an N-linked glycan chain, short circuiting the classical N-glycan biosynthetic pathway. Here, using two bacterial orthologs, we present the first structural and mechanistic dissection of endo-a-mannosidase. Structures solved at resolutions 1.7–2.1 Å reveal a (ß/a)8 barrel fold in which the catalytic center is present in a long substrate-binding groove, consistent with cleavage within the N-glycan chain. Enzymatic cleavage of authentic Glc1/3Man9GlcNAc2 yields Glc1/3-Man. Using the bespoke substrate a-Glc-1,3-a-Man fluoride, the enzyme was shown to act with retention of anomeric configuration. Complexes with the established endo-a-mannosidase inhibitor a-Glc-1,3-deoxymannonojirimycin and a newly developed inhibitor, a-Glc-1,3-isofagomine, and with the reducing-end product a-1,2-mannobiose structurally define the -2 to +2 subsites of the enzyme. These structural and mechanistic data provide a foundation upon which to develop new enzyme inhibitors targeting the hijacking of N-glycan synthesis in viral disease and cancer.
    The occurrence of internal (1,5)-linked arabinofuranose and arabinopyranose residues in arabinogalactan side chains from soybean pectic substances
    Huisman, M.M.H. ; Brüll, L.P. ; Thomas-Oates, J.E. ; Haverkamp, J. ; Schols, H.A. ; Voragen, A.G.J. - \ 2001
    Carbohydrate Research : an international journal 330 (2001). - ISSN 0008-6215 - p. 103 - 114.
    CDTA-extractable soybean pectic substances were subjected to enzymatic digestion with arabinogalactan degrading enzymes yielding a resistant polymeric pectic backbone and arabino-, galacto-, and arabinogalacto-oligomers. The complex digest was fractionated using size-exclusion chromatography. Monosaccharide composition analysis, HPAEC fractionation and MALDI-TOF MS analysis of the resulting fractions showed that each contained a mixture of oligosaccharides of essentially the same degree of polymerisation, composed of only arabinose and galactose. MALDI-TOF MS analysis was used for molecular mass screening of oligosaccharides in underivatised HPAEC fractions. The monosaccharide sequence and the branching pattern of oligosaccharides (degree of polymerisation from 4 to 8) were determined using linkage analysis and ES-CID tandem MS analysis of the per-O-methylated oligosaccharides in each of the HPAEC fractions. These analyses indicated the presence of common linear (1¿4)-linked galacto-oligosaccharides, and both linear and branched arabino-oligosaccharides. In addition, the results unambiguously showed the presence of oligosaccharides containing (1¿4)-linked galactose residues bearing an arabinopyranose residue as the non-reducing terminal residue, and a mixture of linear oligosaccharides constructed of (1¿4)-linked galactose residues interspersed with an internal (1¿5)-linked arabinofuranose residue. The consequences of these two new structural features of pectic arabinogalactan side chains are discussed
    Spectral characterization of fluorescent 5-iodoacetamidotetramethylrhodamine and its N-acetylcysteine derivative
    Zandvoort, M.A.M.J. van; Vossen, D.L.J. ; Ginkel, G. van; Torre, R. ; Bartolini, P. ; Ricci, M. ; Thomas-Oates, J. ; Zuilhof, H. - \ 1999
    Physical Chemistry Chemical Physics 1 (1999)19. - ISSN 1463-9076 - p. 4571 - 4582.
    This study describes a spectroscopic characterization of the fluorescent probe 5-iodoacetamidotetramethylrhodamine and its N-acetylcysteine derivative in various solvents. The monomeric character and the purity of the two compounds was established in ethanol, ethanol-water, water, dimethylformamide, dimethyl sulfoxide, glycerol, polyvinylalcohol and nitrocellulose films, using a combination of absorption and fluorescence spectroscopy and mass spectrometry. In all the polar solvents studied here, the probes were present in the open form only and thus, from the spectral parameters, the natural lifetime and Forster distance in those solvents could be calculated. Fluorescence lifetimes were determined and the homogeneity of probe distribution in both stretched and unstretched polymer films was checked. For this, a combination of confocal microscopy and polarized fluorescence experiments was used. Finally, applying angle-resolved fluorescence depolarization for immobilized molecules in uniaxially stretched polymer films, the orientation of both rhodamines in stretched polyvinylalcohol films was examined and the orientation of the transition dipole moments within the molecular frame was determined. There were no differences between the 5-isomer and its N-acetylcysteine derivative, but a strong environmental dependence of most optical properties was observed. This dependence was especially intriguing for the difference angle between the absorption and emission dipole moment. The implications of our results and suggestions for future research are discussed.
    alpha-D-Glcp-(1-1)-ß-D-Galp-containing oligosaccharides, novel products from lactose by the action of ß-galactosidase
    Fransen, C.T.M. ; Laere, K.M.J. van; Wijk, A.A.C. van; Brüll, L.P. ; Dignum, M. ; Thomas-Oates, J.E. ; Haverkamp, J. ; Schols, H.A. ; Voragen, A.G.J. ; Kamerling, J.P. ; Vliegenthart, J.F.G. - \ 1998
    Carbohydrate Research : an international journal 314 (1998). - ISSN 0008-6215 - p. 101 - 114.
    Alpha-D-Glcp-(1<->1)-beta-D-Galp containing oligosaccharides, a new class of oligosaccharides produced by beta-galactosidase form lactose as substrate.
    Fransen, C.T.M. ; Laere, K.M.J. van; Wijk, A.A.C. van; Brull, L.P. ; Dignum, M. ; Thomas-Oates, J. ; Haverkamp, J. ; Schols, H.A. ; Voragen, A.G.J. - \ 1998
    In: Proceedings of the International Carbohydrate Symposium, San Diego, USA (1998) AO028
    Rapid molecular mass and structural determination of plant cell wall-derived oligosaccharides using off-line high-performance anion-exchange chromatography/mass spectrometry.
    Brull, L. ; Huisman, M. ; Schols, H. ; Voragen, F. ; Critchley, G. ; Thomas-Oates, J. ; Haverkamp, J. - \ 1998
    Journal of Mass Spectrometry 33 (1998). - ISSN 1076-5174 - p. 713 - 720.
    Dimers of a GFG hexasaccharide occur in apple fruit xyloglucan.
    Spronk, B.A. ; Rademaker, G.J. ; Haverkamp, J. ; Thomas-Oates, E. ; Vincken, J.P. ; Voragen, A.G.J. ; Kamerling, J.P. ; Vliegenthart, J.F.G. - \ 1998
    Carbohydrate Research : an international journal 305 (1998). - ISSN 0008-6215 - p. 233 - 242.
    Fast molecular weight determination of plant cell wall oligosaccharides using off-line high performance anion exchange chromatography - electrospray ionisation mass spectrometry.
    Bröll, L. ; Thomas-Oates, J. ; Haverkamp, J. ; Huisman, M. ; Schols, H. ; Voragen, A.G.J. - \ 1997
    Eurocarb (1997). - p. B5 - B5.
    Check title to add to marked list

    Show 20 50 100 records per page

     
    Please log in to use this service. Login as Wageningen University & Research user or guest user in upper right hand corner of this page.