Conformational flexibility and dynamics of two (1→6)-Linked disaccharides related to an oligosaccharide epitope expressed on malignant tumour cells

Chemistry - A European Journal

Volumn 15, Issue 35, 2009, Pages 8886-8894

  Olsson, Ulrika ^a   Säwén, Elin ^a   Stenutz, Roland ^a   Widmalm, Göran ^a  

^a STOCKHOLM UNIVERSITY   (Sweden)

Author keywords

Carbohydrates enzymes; Molecular dynamics; Nmr spectroscopy; Torsion angles

Indexed keywords

ANOMERICS; ANTIPERIPLANAR; CONFORMATIONAL ANALYSIS; CONFORMATIONAL FLEXIBILITY; CONFORMATIONAL STATE; COUPLING CONSTANTS; EXPERIMENTAL OBSERVATION; FORCE FIELDS; GLYCOSYL TRANSFERASE; MD SIMULATION; MOLECULAR DYNAMICS SIMULATIONS; NMR SPECTROSCOPY; OLIGOSACCHARIDE EPITOPES; POPULATION DISTRIBUTION; SITE-SPECIFIC; SPECTRAL DISPERSIONS; SPECTRAL OVERLAP; TORSION ANGLE; TORSION ANGLES; TUMOUR CELLS;

CARBOHYDRATES; CATALYSTS; CONFORMATIONS; DYNAMICS; ENZYMES; LABELS; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; POLYSACCHARIDES; TUMORS;

TORSIONAL STRESS;

EPITOPE; OLIGOSACCHARIDE;

ARTICLE; CHEMISTRY; COMPUTER SIMULATION; CONFORMATION; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY;

CARBOHYDRATE CONFORMATION; COMPUTER SIMULATION; EPITOPES; MAGNETIC RESONANCE SPECTROSCOPY; OLIGOSACCHARIDES;

EID: 69749105434     PISSN: 09476539     EISSN: 15213765     Source Type: Journal    
DOI: 10.1002/chem.200900507     Document Type: Article

References (77)

1. R. G. Spiro, Glycobiology 2002, 12, 43R-56R.
2. R. Apweiler, H. Hermjakob, N. Sharon, Biochim. Biophys. Acta 1999, 1473, 4-8.
3. T. S. Raju, B. J. Scallon, Biochem. Biophys Res Commun. 2006, 341, 797.
4. Essentials of Glycobiology (Eds.: A. Varki, R. Cummings, J. Esko, H. Freeze, G. Hart, J. Marth), Cold Spring Harbor Laboratory Press, Cold Spring Harbor, 1999.
5. A. Helenius, M. Aebi, Annu. Rev. Biochem. 2004, 73, 1019-1049.
6. R. D. Cummings, I. S. Trowbridge, S. Kornfeld, J. Biol. Chem. 1982, 257, 13421-13427.
7. S. C. Hubbard, J. Biol. Chem. 1987, 262, 16403-16411.
8. L. Chen, W. Zhang, N. Fregien, M. Pierce, Oncogene 1998, 17, 2087-2093.
9. K. Murata, E. Miyoshi, M. Kameyama, O. Ishikawa, T. Kabuto, Y. Sasaki, M. Hiratsuka, H. Ohigashi, S. Ishiguro, S. Ito, H. Honda, F. Takemura, N. Taniguchi, S. Imaoka, Clin. Cancer Res 2000, 6, 1772-1777.
10. J. W. Dennis, J. Pawling, P. Cheung, E. Partridge, M. Demetriou, Biochim. Biophys. Acta 2002, 1573, 414-422.
11. P. Cheung, J. Pawling, E. A. Partridge, B. Sukhu, M. Grynpas, J. W. Dennis, Glycobiology 2007, 17, 828-837.
12. M. Przybylo, D. Martuszewska, E. Pochese, D. Hojalukowicz, A. Lityñska, Biochim. Biophys Acta 2007, 1770, 1427-1435.
13. O. P. Srivastava, O. Hindsgaul, M. Shoreibah, M. Pierce, Carbohydr. Res 1988, 179, 137-161.
14. K. Bock, J. O. Duus, O. Hindsgaul, I. Lindh, Carbohydr. Res. 1992, 228, 1-20.
15. Z. Ma, J. Zhang, F. Kong, Tetrahedron: Asymmetry 2003, 14, 2595-2603.
16. S. H. Khan, K. L. Matta, Carbohydr. Res. 1993, 243, 29-42.
17. S. Ogawa, T. Furuya, H. Tsunoda, O. Hindsgaul, K. Slangier, M. M. Paleic, Carbohydr. Res. 1995, 271, 197-205.
18. M. Kaneko, O. Kanie, T. Kajimoto, C.-H. Wong, Bioorg. Med. Chem. Lett. 1997, 7, 2809-2812.
19. M. A. Macnaughtan, M. Kamar. G. Alvarez-Manilla, A. Venot, J. Glushka, J. M. Pierce, J. H. Prestegard, J. Mol. Biol 2007, 366, 1266-1281.
20. R. Stenutz, I. Carmichael, G. Widmalm, A. S. Serianni, J. Org. Chem. 2002, 67, 949-958.
21. C. Thibaudeau, R. Stenutz, B. Hertz, T. Klepach, S. Zhao, Q. Wu, I. Carmichael, A. S. Serianni, J. Am. Chem. Soc. 2004, 126, 15668-15685.
22. P. D. Thomas, V. J. Basus, T. L. James, Proc. Natl Acad. Sci. USA 1991, 88, 1237-1241.
23. M. Nilges, G. M. Clore, A. M. Gronenborn, N. Piel, L. W. McLaughlin, Biochemistry 1987, 26, 3734-3744.
24. S. G. Hyberts, G. Wagner, J. Magn. Reson. 1989, 81, 418-422.
25. J. D. Baleja, J. Moult, B. D. Sykes, J. Magn. Reson. 1990, 87, 375-384.
26. J. Fejzo, A. M. Krezel, W. M. Westler, S. Macura, J. L. Markley, J. Magn. Reson. 1991, 92, 651-657.
27. A. M. Dixon, G. Widmalm, T. E. Bull, J. Magn. Reson. 2000, 147, 266-272.
28. D. Neuhaus, M. Williamson, The Nuclear Overhauser Effect in Structural and Conformational Analysis, VCH, Weinheim, 1989.
29. A. A. Bothner-By, R. L. Stephens, J.-m. Lee, C. D. Warren, R. W. Jeanloz, J. Am. Chem. Soc. 1984, 106, 811-813.
30. T. E. Bull, Prog. Nucl. Magn. Reson. Spectrosc. 1992, 24, 377-410.
31. T.-L. Hwang, A. J. Shaka, J Am. Chem. Soc. 1992, 114, 3157-3159.
32. T.-L. Hwang, M. Kadkhodaei, A. Mohebbi, A. J. Shaka, Magn. Reson. Chem. 1992, 30, S24-S34.
33. T.-L. Hwang, A. J. Shaka, J. Magn. Reson. Ser. B 1993, 102, 155-165.
34. D. G. Davis, J. Am. Chem. Soc. 1987, 109, 3471-3472.
35. K. Stott, J. Keeler, Q. Van, A. J. Shaka, J. Magn. Reson. 1997, 125, 302-324.
36. A. Kjellberg, G. Widmalm, Biopolymers 1999, 50, 391-399.
37. P. J. Garegg, T. Norberg, Acta Chem. Scand. 1979, 33, 116-118.
38. P. Konradsson, U. E. Udodong, F.-B. Reid, Tetrahedron Lett. 1990, 57, 4313-4316.
39. H. Hori, Y. Nishida, H. Ohrui, H. Meguro, J. Carbohydr. Chem. 1990, 9, 601-618.
40. B. A. Spronk, A. Rivera-Sagredo, J. P. Kamerling, J. F. G. Vliegenthart, Carbohydr. Res. 1995, 273, 11-26.
41. K. Lycknert, M. Edblad, A. Imberty, G. Widmalm, Biochemistry 2004, 43, 9647-9654.
42. S. Wolfe, Acc. Chem. Res 1972, 5, 102-111.
43. O. Hassel, B. Ottar, Acta Chem. Scand. 1947, 1, 929-943.
44. J.-R. Brisson, J. P. Carver, Biochemistry 1983, 22, 1362-1368.
45. J.-R. Brisson, J. P. Carver, Biochemistry 1983, 22, 3680-3686.
46. S. W. Homans, R. A. Dwek, J. Boyd, M. Mahmoudian, W. G. Richards, T. W. Rademacher, Biochemistry 1986, 25, 6342-6350.
47. D. A. Cumming, R. N. Shah, J. J. Krepinsky, A. A. Grey, J. P. Carver, Biochemistry 1987, 26, 6655-6663.
48. D. A. Cumming, J. P. Carver, Biochemistry 1987, 26, 6664-6676.
49. D. A. Cumming, J. P. Carver, Biochemistry 1987, 26, 6676-6683.
50. S. W. Homans, R. A. Dwek, T. W. Rademacher, Biochemistry 1987, 26, 6553-6560.
51. H. Hori, Y. Nishida, H. Ohrui, H. Meguro, J. Uzawa, Tetrahedron Lett. 1988, 29, 4457-4460.
52. E. W. Wooten, R. Bazzo, C. J. Edge, S. Zamze, R. A. Dwek, T. W. Rademacher, Eur. Biophys. J. 1990, 18, 139-148.
53. E. W. Sayers, J. H. Prestegard, Biophys. J. 2000, 79, 3313-3329.
54. A. Almond, J. Øuus, J. Biomol. NMR 2001, 20, 351-363.
55. J. P. M. Lommerse, J. J. M. van Rooijen, L. M. J. Kroon-Batenburg, J. P. Kamerling, J. F. G. Vliegenthart, Carbohydr. Res. 2002, 337, 2279-2299.
56. M. K. Dowd, A. D. French, P. J. Reilly, J. Carbohydr. Chem. 1995, 14, 589-600.
57. A. Bernardi, A. Colombo, I. Sánchez-Medina, Carbohydr. Res. 2004, 339, 967-973.
58. F. Cloran, I. Carmichael, A. S. Serianni, J Am. Chem. Soc. 1999, 121, 9843-9851.
59. T. Lütteke, M. Frank, C.-W. von der Lieth, Carbohydr. Res. 2004, 339, 1015-1020.
60. T. Lutteke, M. Frank, C.-W. von der Lieth, Nucleic Acids Res. 2005, 33, D242-D246.
61. http ://www.glycosciences.de/tools/glytorsion/.
62. T. Rundlöf, A. Kjellberg, C. Damberg, T. Nishida, G. Widmalm, Magn. Reson. Chem. 1998, 36, 839-847.
63. B. Bose, S. Zhao, R. Stenutz, F. Cloran, P. B. Bondo, G. Bondo, B. Hertz, I. Carmichael, A. S. Serianni, J. Am. Chem. Soc. 1998, 120, 11158-11173.
64. L. Mäler, G. Widmalm, J. Kowalewski, J. Biomol. NMR 1996, 7, 1-7.
65. R. K. Ness, J. R. Fletcher, C. S. Hudson, J. Am. Chem. Soc. 1959, 81, 2200-2205.
66. M. H. El-Badri, D. Willenbring, D. J. Tantillo, J. Gervay-Hauge, J. Org. Chem. 2007, 72, 4663-4672.
67. N. Khiar, I. Fernández, C. S. Araújo, J.-A. Rodríguez, B. Suárez, E. Alvarez, J. Org. Chem. 2003, 68, 1433-1442.
68. R. Laatikainen, M. Niemitz, U. Weber, J. Sundelin, T. Hassinen, J. Väpsäläinen, J. Magn. Reson. Ser. A 1996, 120, 1-10.
69. W. Komiñski, D. Nanz, J. Magn. Reson. 2000, 142, 294-299.
70. B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swami-nathan, M. Karplus, J. Comput. Chem. 1983, 4, 187-217.
71. A. D. MacKerell, Jr., D. Bashford, M. Bellott, R. L. Dunbrack, Jr., J. D. Evanseck, M. J. Field, S. Fischer, J. Gao, H. Guo, S. Ha, D. Joseph-McCarthy, L. Kushnir, K. Kuczera, F. T. K. Lau, C. Mattos, S. Michnick, T. Ngo, T. D. Nguyen, B. Prodhom, W. E. Reiher III, B. Roux, M. Schlenkrich, J. C. Smith, R. Stote, J. Straub, M. Watanabe, J. Wiórkiewicz-Kuczera, D. Yin, M. Karplus, J. Phys. Chem. B 1998, 102, 3586-3616.
72. R. Eklund, G. Widmalm, Carbohydr. Res 2003, 338, 393-398.
73. E. Neria, S. Fischer, M. Karplus, J. Chem. Phys 1996, 105, 1902-1921.
74. R. W. Hockney, Methods Comput. Phys 1970, 9, 136-211.
75. J. P. Ryckaert, G. Ciccotti, H. J. C. Berendsen, J. Comput. Phys. 1977, 23, 327-341.
76. P. J. Steinbach, B. R. Brooks, J. Comput. Chem. 1994, 15, 667-683.
77. H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren, A. DiNola, J. R. Haak, J. Chem. Phys. 1984, 81, 3684-3690.