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The Application of NMR Spectroscopy to Functional Glycomics

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 600))

Abstract

Glycomics which is the study of saccharides and genes responsible for their formation requires the continuous development of rapid and sensitive methods for the identification of glycan structures. It involves glycoanalysis which relies upon the development of methods for determining the structure and interactions of carbohydrates. For the application of functional glycomics to microbial virulence, carbohydrates and their associated metabolic and carbohydrate processing enzymes and respective genes can be identified and exploited as targets for drug discovery, glyco-engineering, vaccine design, and detection and diagnosis of diseases. Glycomics also encompasses the detailed understanding of carbohydrate–protein interactions and this knowledge can be applied to research efforts focused toward the development of vaccines and immunological therapies to alleviate infectious diseases.

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References

  1. Twine, S. M., Paul, C. J., Vinogradov, E., McNally, D. J., Brisson, J. -R., Mullen, J. A., McMullin, D. R., Jarrell, H. C., Austin, J. W., Kelly, J. F., and Logan, S. M. (2008) Flagellar glycosylation in Clostridium botulinum. FEBS J. 275, 4428–4444.

    Article  CAS  PubMed  Google Scholar 

  2. McNally, D. J., Schoenhofen, I. C., Houliston, R. S., Khieu, N. H., Whitfield, D. M., Logan, S. M., Jarrell, H. C., and Brisson, J. -R. (2008) CMP-pseudaminic acid is a natural potent inhibitor of PseB, the first enzyme of the pseudaminic acid pathway in Campylobacter jejuni and Helicobacter pylori. ChemMedChem. 3, 55–59.

    Article  CAS  PubMed  Google Scholar 

  3. McNally, D. J., Lamoureux, M. P., Karlyshev, A. V., Fiori, L. M., Li, J., Thacker, G., Coleman, R. A., Khieu, N. H., Wren, B. W., Brisson, J. -R., Jarrell, H. C., and Szymanski, C. M. (2007) Commonality and biosynthesis of the O-methyl phosphoramidate capsule modification in Campylobacter jejuni. J. Biol. Chem. 282, 28566–28576.

    Article  CAS  PubMed  Google Scholar 

  4. McNally, D. J., Schoenhofen, I. C., Mulrooney, E. F., Whitfield, D. M., Vinogradov, E., Lam, J. S., Logan, S. M., and Brisson, J. -R. (2006) Identification of labile UDP-ketosugars in Helicobacter pylori, Campylobacter jejuni and Pseudomonas aeruginosa: key metabolites used to make glycan virulence factors. Chembiochem. 7, 1865–1868.

    Article  CAS  PubMed  Google Scholar 

  5. Schoenhofen, I. C., McNally, D. J., Vinogradov, E., Whitfield, D., Young, N. M., Dick, S., Wakarchuk, W. W., Brisson, J. -R., and Logan, S. M. (2006) Functional characterization of dehydratase/aminotransferase pairs from Helicobacter and Campylobacter: enzymes distinguishing the pseudaminic acid and bacillosamine biosynthetic pathways. J. Biol. Chem. 281, 723–732.

    Article  CAS  PubMed  Google Scholar 

  6. McNally, D. J., Jarrell, H. C., Li, J., Khieu, N. H., Vinogradov, E., Szymanski, C. M., and Brisson, J. -R. (2005) The HS:1 serostrain of Campylobacter jejuni has a complex teichoic acid-like capsular polysaccharide with nonstoichiometric fructofuranose branches and O-methyl phosphoramidate groups. FEBS J. 272, 4407–4422.

    Article  CAS  PubMed  Google Scholar 

  7. Szymanski, C. M., St Michael, F., Jarrell, H. C., Li, J., Gilbert, M., Larocque, S., Vinogradov, E., and Brisson, J. -R. (2003) Detection of conserved N-linked glycans and phase-variable lipooligosaccharides and capsules from campylobacter cells by mass spectrometry and high resolution magic angle spinning NMR spectroscopy. J. Biol. Chem. 278, 24509–24520.

    Article  CAS  PubMed  Google Scholar 

  8. McNally, D. J., Hui, J. P., Aubry, A. J., Mui, K. K., Guerry, P., Brisson, J. -R., Logan, S. M., and Soo, E. C. (2006) Functional characterization of the flagellar glycosylation locus in Campylobacter jejuni 81-176 using a focused metabolomics approach. J. Biol. Chem. 281, 18489–18498.

    Article  CAS  PubMed  Google Scholar 

  9. Morris, G. M., Goodsell, D. S., Halliday, R. S., Huey, R., Hart, W. E., Belew, R. K., and Olson, A. J. (1998) Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. J. Comput. Chem. 19, 1639–1662.

    Article  CAS  Google Scholar 

  10. Moseley, H. N., Curto, E. V., and Krishna, N. R. (1995) Complete relaxation and conformational exchange matrix (CORCEMA) analysis of NOESY spectra of interacting systems; two-dimensional transferred NOESY. J. Magn. Reson. B 108, 243–261.

    Article  CAS  PubMed  Google Scholar 

  11. Jayalakshmi, V. and Krishna, N. R. (2002) Complete relaxation and conformational exchange matrix (CORCEMA) analysis of intermolecular saturation transfer effects in reversibly forming ligand-receptor complexes. J. Magn. Reson. 155, 106–118.

    Article  CAS  PubMed  Google Scholar 

  12. Jayalakshmi, V. and Rama, K. N. (2004) CORCEMA refinement of the bound ligand conformation within the protein binding pocket in reversibly forming weak complexes using STD-NMR intensities. J. Magn. Reson. 168, 36–45.

    Article  CAS  PubMed  Google Scholar 

  13. Brisson, J. -R., Sue, S. C., Wu, W. G., McManus, G., Nghia, P. T., and Uhrin, D. (2002) NMR of carbohydrates: 1D homonuclear selective methods, in NMR Spectroscopy of Glycoconjugates (Jimenez-Barbero, J. and Peters, T., Eds.) pp. 59–93, Wiley-VCH, Weinhem, Germany.

    Chapter  Google Scholar 

  14. Duus, J. O., Gotfredsen, C. H., and Bock, K. (2000) Carbohydrate structural determination by NMR spectroscopy: modern methods and limitations. Chem. Rev. 100, 4589–4614.

    Article  CAS  PubMed  Google Scholar 

  15. Uhrin, D. and Brisson, J. -R. (2000) Structure determination of microbial polysaccharides by high resolution NMR spectroscopy, in NMR in Microbiology: Theory And Applications (Barbotin, J. N. and Portais, J. C., Eds.) pp. 165–190, Horizon Scientific Press, Wymondham, U.K.

    Google Scholar 

  16. Kogan, G. and Uhrin, D. (2000) Current NMR methods in the structural elucidation of polysaccharides, in New Advances in Analytical Chemistry (Atta, u. R., Ed.) pp. 73–134, Harwood Academic, Amsterdam.

    Google Scholar 

  17. Darveau, R. P. and Hancock, R. E. (1983) Procedure for isolation of bacterial lipopolysaccharides from both smooth and rough Pseudomonas aeruginosa and Salmonella typhimurium strains. J. Bacteriol. 155, 831–838.

    CAS  PubMed  Google Scholar 

  18. Huebner, J., Wang, Y., Krueger, W. A., Madoff, L. C., Martirosian, G., Boisot, S., Goldmann, D. A., Kasper, D. L., Tzianabos, A. O., and Pier, G. B. (1999) Isolation and chemical characterization of a capsular polysaccharide antigen shared by clinical isolates of Enterococcus faecalis and vancomycin-resistant Enterococcus faecium. Infect. Immun. 67, 1213–1219.

    CAS  PubMed  Google Scholar 

  19. Hsieh, Y. C., Liang, S. M., Tsai, W. L., Chen, Y. H., Liu, T. Y., and Liang, C. M. (2003) Study of capsular polysaccharide from Vibrio parahaemolyticus. Infect. Immun. 71, 3329–3336.

    Article  CAS  PubMed  Google Scholar 

  20. Ishiyama, N., Creuzenet, C., Miller, W. L., Demendi, M., Anderson, E. M., Harauz, G., Lam, J. S., and Berghuis, A. M. (2006) Structural studies of FlaA1 from Helicobacter pylori reveal the mechanism for inverting 4,6-dehydratase activity. J. Biol. Chem. 281, 24489–24495.

    Article  CAS  PubMed  Google Scholar 

  21. Gasteiger, J. and Marsili, M. (1980) Iterative partial equalization of orbital electronegativity – a rapid access to atomic charges. Tetrahedron. 36, 3219–3228

    Article  CAS  Google Scholar 

  22. Monteiro, C., Neyret, S., Leforestier, J., and du Penhoat, C. H. (2000) Solution conformation of various uridine diphosphoglucose salts as probed by NMR spectroscopy. Carbohydr. Res. 329, 141–155.

    Article  CAS  PubMed  Google Scholar 

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© 2010 Humana Press

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Brisson, JR. et al. (2010). The Application of NMR Spectroscopy to Functional Glycomics. In: Li, J. (eds) Functional Glycomics. Methods in Molecular Biology, vol 600. Humana Press. https://doi.org/10.1007/978-1-60761-454-8_11

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  • DOI: https://doi.org/10.1007/978-1-60761-454-8_11

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  • Publisher Name: Humana Press

  • Print ISBN: 978-1-60761-453-1

  • Online ISBN: 978-1-60761-454-8

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