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Journal of Biomolecular NMR

, Volume 35, Issue 2, pp 89–101 | Cite as

Molecular conformations of a disaccharide investigated using NMR spectroscopy

  • Clas Landersjö
  • Baltzar Stevensson
  • Robert Eklund
  • Jennie Östervall
  • Peter Söderman
  • Göran Widmalm
  • Arnold Maliniak
Article

Abstract

The molecular structure of \(\upalpha\)-l-Rhap-(1→ 2)-\(\upalpha\)-l-Rhap-OMe has been investigated using conformation sensitive NMR parameters: cross-relaxation rates, scalar 3 J CH couplings and residual dipolar couplings obtained in a dilute liquid crystalline phase. The order matrices of the two sugar residues are different, which indicates that the molecule cannot exist in a single conformation. The conformational distribution function, \(P(\upphi,\uppsi)\), related to the two glycosidic linkage torsion angles \(\upphi\) and \(\uppsi\) was constructed using the APME method, valid in the low orientational order limit. The APME approach is based on the additive potential (AP) and maximum entropy (ME) models. The analyses of the trajectories generated in molecular dynamics and Langevin dynamics (LD) computer simulations gave support to the distribution functions constructed from the experimental NMR parameters. It is shown that at least two conformational regions are populated on the Ramachandran map and that these regions exhibit very different molecular order.

Keywords

carbohydrates conformation NMR spectroscopy residual dipolar couplings oligosaccharides 

Abbreviations

R2R

\(\upalpha\)-l-Rhap-(1→ 2)-\(\upalpha\)-l-Rhap-OMe

RDC

residual dipolar couplings

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Notes

Acknowledgements

This work was supported by grants from the Carl Trygger Foundation, the Swedish Research Council, the Magnus Bergvall Foundation, and SIDA/SAREC. We thank the Center for Parallel Computers, KTH, Stockholm, for putting computer facilities at our disposal and Dr. Johan Weigelt for helpful discussions. Finally, we thank a reviewer for useful comments on the analysis of the experimental data.

Supplementary material

References

  1. Berardi R., Spinozzi F., Zannoni C. (1998). J. Chem. Phys. 109: 3742–3759CrossRefADSGoogle Scholar
  2. Berendsen H.J.C., Postma J.P.M., van Gunsteren W.F., DiNola A., Haak J.R. (1984). J. Chem. Phys. 81: 3684–3690CrossRefADSGoogle Scholar
  3. Brink D.M., Satchler G.R. (1993) Angular Momentum. Clarendon Press, OxfordGoogle Scholar
  4. Brooks B.R., Bruccoleri R.E., Olafson B.D., States D.J., Swaminathan S., Karplus M. (1983). J. Comput. Chem. 4:187–217CrossRefGoogle Scholar
  5. Castellani F., van Rossum B., Diehl A., Schubert M., Rehbein K., Oschkinat H. (2002). Nature 420: 98–102CrossRefADSGoogle Scholar
  6. Catalano D., Di Bari L., Veracini C.A., Shilstone G.N., Zannoni C. (1991). J. Chem. Phys. 94: 3928–3935CrossRefADSGoogle Scholar
  7. Cloran F., Carmichael I., Serianni A.S. (1999). J. Am. Chem. Soc. 121: 9843–9851CrossRefGoogle Scholar
  8. Delaglio F., Grzesiek S., Vuister G.W., Zhu G., Pfeifer J., Bax A. (1995). J. Biomol. NMR 6: 277–293CrossRefGoogle Scholar
  9. Delaglio F., Wu Z., Bax A. (2001). J. Magn. Reson. 149: 276–281CrossRefADSGoogle Scholar
  10. Eklund R., Widmalm G. (2003). Carbohydr. Res. 338: 393–398CrossRefGoogle Scholar
  11. Emsley J.W., Luckhurst G.R., Stockley C.P. (1982). Proc. R. Soc. Lond. A 381: 117–138ADSCrossRefGoogle Scholar
  12. Fung B.M. (2002). Prog. Nucl. Magn. Reson. Spectrosc. 41: 171–186CrossRefGoogle Scholar
  13. Hardy B.J., Bystricky S., Kovac P., Widmalm G. (1997). Biopolymers 41: 83–96CrossRefGoogle Scholar
  14. Hockney R.W. (1970). Meth. Comput. Phys. 9: 136–211Google Scholar
  15. Jansson P.-E., Kenne L., Widmalm G. (1991). Acta Chem. Scand. 45: 517–522CrossRefGoogle Scholar
  16. Keepers J.W., James T.L.J. (1984). Magn. Reson. 57: 404–426Google Scholar
  17. Kjellberg A., Widmalm G. (1999). Biopolymers 50: 391–399CrossRefGoogle Scholar
  18. Kroon-Batenburg L.M.J., Kroon J., Leeflang B.R., Vliegenthart J.F.G. (1993). Carbohydr. Res. 245: 21–42CrossRefGoogle Scholar
  19. Lemieux R.U., Koto S. (1974). Tetrahedron 30: 1933–1944CrossRefGoogle Scholar
  20. Loncharich R.J., Brooks B.R., Pastor R.W. (1992). Biopolymers 32: 523–535CrossRefGoogle Scholar
  21. Lycknert K., Helander A., Oscarson S., Kenne L, Widmalm G. (2004). Carbohydr. Res. 339: 1331–1338CrossRefGoogle Scholar
  22. MacKerell Jr. A.D., Bashford D., Bellott M., Dunbrack Jr. R.L., Evanseck J.D., Field M.J., Fischer S., Gao J., Guo H., Ha S., Joseph-McCarthy D., Kushnir L., Kuczera K., Lau F.T.K., Mattos C., Michnick S., Ngo T., Nguyen T.D., Prodhom B., Reiher III W.E., Roux B., Schlenkrich M., Smith J.C., Stote R., Straub J., Watanabe M., Wiórkiewicz-Kuczera J., Yin D., Karplus M. (1998). J. Phys. Chem. B 102: 3586–3616CrossRefGoogle Scholar
  23. Merlet D., Emsley J.W., Lesot P., Courtieu J. (1999). J. Chem. Phys. 111: 6890–6896CrossRefADSGoogle Scholar
  24. Norberg T., Oscarson S., Szönyi M. (1986). Carbohydr. Res. 156: 214–217CrossRefGoogle Scholar
  25. O’Neil-Cabello E., Bryce D.L., Nikonowicz E.P., Bax A. (2004). J. Am. Chem. Soc. 126: 66–67CrossRefGoogle Scholar
  26. Otting G., Rückert M., Levitt M.H., Moshref A. (2000). J. Biomol. NMR 16: 343–346CrossRefGoogle Scholar
  27. Prestegard J.H., Al-Hashimi H.M., Tolman H.M. (2000). Quart. Rev. Biophys. 33: 371–424CrossRefGoogle Scholar
  28. Steinbach P.J., Brooks B.R. (1994). J. Comput. Chem. 15: 667–683CrossRefGoogle Scholar
  29. Stevensson B., Landersjö C., Widmalm G., Maliniak A. (2002). J. Am. Chem. Soc. 124: 5946–5947CrossRefGoogle Scholar
  30. Stevensson B., Sandström D., Maliniak A. (2003). J. Chem. Phys. 119: 2738–2746CrossRefADSGoogle Scholar
  31. Söderman P., Oscarson S., Widmalm G. (1998). Carbohydr. Res. 312: 233–237CrossRefGoogle Scholar
  32. Thaning, J., Stevensson, B. and Maliniak, A. (2005) J. Chem. Phys. 123, 044507-1-6Google Scholar
  33. Thomas P.D., Basus V.J., James T.L. (1991). Proc. Natl. Acad. Sci. USA 88: 1237–1241CrossRefADSGoogle Scholar
  34. Tjandra, N. and Bax, A. (1997a) J. Magn. Reson. 124, 512–515Google Scholar
  35. Tjandra, N. and Bax, A. (1997b) Science 278, 1111–1114Google Scholar
  36. Tolman J.R., Al-Hashimi H.M., Kay L.E., Prestegard J.H. (2001). J. Am. Chem. Soc. 123: 1416–1424CrossRefGoogle Scholar
  37. van Buuren B.N.M., Schleucher J., Wittmann V., Griesinger C., Schwalbe H., Wijmenga S.S. (2004). Angew. Chem. Int. Ed. 43: 187–192CrossRefGoogle Scholar
  38. Wang C., Arthur G., Palmer A.G. III (2003). Magn. Reson. Chem. 41: 866–876CrossRefGoogle Scholar
  39. Widmalm G., Byrd R.A., Egan W. (1992). Carbohydr. Res. 229: 195–211CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, Inc. 2006

Authors and Affiliations

  • Clas Landersjö
    • 1
  • Baltzar Stevensson
    • 2
  • Robert Eklund
    • 1
  • Jennie Östervall
    • 1
    • 2
  • Peter Söderman
    • 1
  • Göran Widmalm
    • 1
  • Arnold Maliniak
    • 2
  1. 1.Arrhenius Laboratory, Department of Organic ChemistryStockholm UniversityStockholmSweden
  2. 2.Arrhenius Laboratory, Division of Physical ChemistryStockholm UniversityStockholmSweden

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