Table of Contents
International Journal of Carbohydrate Chemistry
Volume 2012, Article ID 725271, 7 pages
Research Article

Conformational Search on the Lewis X Structure by Molecular Dynamic: Study of Tri- and Pentasaccharide

Laboratory of Natural Products and Bio Actives, Department of Chemistry, Faculty of Sciences, Aboubakr Belkaid University, Tlemcen 13000, Algeria

Received 4 July 2011; Revised 7 October 2011; Accepted 12 October 2011

Academic Editor: Yuriy A. Knirel

Copyright © 2012 N. Khebichat et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. A. Imberty and S. Perez, “Structure, conformation, and dynamics of bioactive oligosaccharides: theoretical approaches and experimental validations,” Chemical Reviews, vol. 100, no. 12, pp. 4567–4588, 2000. View at Publisher · View at Google Scholar · View at Scopus
  2. Y. Luo, F. Barbault, C. Gourmala et al., “Cellular interaction through LewisX cluster: theoretical studies,” Journal of Molecular Modeling, vol. 14, no. 10, pp. 901–910, 2008. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  3. E. A. Kabat, “Immunochemical studies on the carbohydrate moiety of water-soluble blood group A, B, H, Lea, and Leb substances and their precursor I antigens,” in Carbohydrates in Solution, H. Isbell, Ed., vol. 117, pp. 334–355, American Chemical Society, Washington, DC, USA, 1973. View at Google Scholar
  4. W. M. Watkins, “Biochemistry and genetics of the ABO, Lewis, and P blood group systems,” in Advances in Human Genetics, H. Harris and K. Hirsch-Horn, Eds., vol. 10, pp. 1–136, Plenum Press, New York, NY, USA, 10th edition, 1980. View at Google Scholar
  5. S. I. Hakomori, “Antigen structure and genetic basis of histo-blood groups A, B and O: their changes associated with human cancer,” Biochimica et Biophysica Acta, vol. 1473, no. 1, pp. 247–266, 1999. View at Publisher · View at Google Scholar · View at Scopus
  6. F. Bizik and I. Tvaroska, “Conformational analysis of disaccharide fragments of blood group determinants in solution by molecular modelling,” Chemical Papers, vol. 49, no. 4, pp. 202–214, 1995. View at Google Scholar
  7. A. Imberty, E. Mikros, J. Koca, R. Mollicone, R. Oriol, and S. Perez, “Computer simulation of histo-blood group oligosaccharides: energy maps of all constituting disaccharides and potential energy surfaces of 14 ABH and Lewis carbohydrate antigens,” Glycoconjugate Journal, vol. 12, no. 3, pp. 331–349, 1995. View at Publisher · View at Google Scholar · View at Scopus
  8. T. Kozar and C.-W. von der Lieth, “Efficient modelling protocols for oligosaccharides: from vacuum to solvent,” Glycoconjugate Journal, vol. 14, no. 8, pp. 925–933, 1997. View at Publisher · View at Google Scholar · View at Scopus
  9. D. Case, T. Darden, T. Cheatham et al., “AMBER,” University of California, CA, USA, 10th edition, 2006. View at Google Scholar
  10. R. J. Woods, R. A. Dwek, C. J. Edge, and B. Fraser-Reid, “Glycam biomolecule builder,”
  11. C. Gourmala, Y. Luo, F. Barbault et al., “Elucidation of the LewisX-LewisX carbohydrate interaction with molecular dynamics simulations: a glycosynapse model,” Journal of Molecular Structure, vol. 821, no. 1–3, pp. 22–29, 2007. View at Publisher · View at Google Scholar · View at Scopus
  12. J. P. Ryckaert, G. Ciccotti, and H. J. C. Berendsen, “Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes,” Journal of Computational Physics, vol. 23, no. 3, pp. 327–341, 1977. View at Publisher · View at Google Scholar · View at Scopus
  13. H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren, A. Dinola, and J. R. Haak, “Molecular dynamics with coupling to an external bath,” The Journal of Chemical Physics, vol. 81, no. 8, article 3684, 7 pages, 1984. View at Publisher · View at Google Scholar · View at Scopus
  14. E. Y. Yoon, “A conformational study of linkage positions in oligosaccharides investigated by 2-D NMR spectroscopy and molecular modeling,” Bulletin of the Korean Chemical Society, vol. 24, no. 3, pp. 339–344, 2003. View at Google Scholar
  15. J. A. McCammon and S. C. Harvey, Dynamics of Proteins and Nucleic Acids, Cambridge University Press, Cambridge, UK, 1987.
  16. E. B. Philip and W. Helge, Structural Boinformatics, 1st edition, 2003.