Molecular dynamics-derived conformation and intramolecular interaction analysis of the N-acetyl-9-O-acetylneuraminic acid-containing ganglioside G(D1a) and NMR-based analysis of its binding to a human polyclonal immunoglobulin G fraction with selectivity for O-acetylated sialic acids

Glycobiology

Volumn 6, Issue 6, 1996, Pages 561-572

  Siebert, Hans Christian ^a   Von Der Lieth, Claus Wilhelm ^b   Dong, Xin ^a   Reuter, Gerd ^a   Schauer, Roland ^a   Gabius, Hans Joachim ^a   Vliegenthart, Johannes F G ^c  

^a UNIVERSITY OF MUNICH   (Germany)

^b GERMAN CANCER RESEARCH CENTER DKFZ   (Germany)

^c UTRECHT UNIVERSITY   (Netherlands)

Author keywords

Antibody; Conformation; Ganglioside; Molecular dynamics; NMR; Sialic acid

Indexed keywords

GANGLIOSIDE; GANGLIOSIDE GD 1A;

ACETYLATION; ANTIGEN BINDING; ARTICLE; CALCULATION; COMPUTER SIMULATION; DIELECTRIC CONSTANT; DRUG STRUCTURE; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PRIORITY JOURNAL; PROTEIN BINDING;

EID: 0029905621     PISSN: 09596658     EISSN: None     Source Type: Journal    
DOI: 10.1093/glycob/6.6.561-b     Document Type: Article

References (64)

1. 4Cer. Eur. J. Biochem., 225, 271-288.
2. 2+-independent sialic acid-binding lectin from human placenta with preferential affinity to O-acetyl sialic acids. J. Biol Chem., 264, 18673-18678.
3. Allinger, N.L., Kok, R.A. and Imam, M.R. (1988) Hydrogen bonding in MM2. J. Compt. Chem., 9, 591-595.
4. Asensio, J., Martin-Pastor, M. and Jimenez-Babero, J. (1995) The use of CVFF and CVFF91 force fields in conformational analysis of carbohydrate molecules. Comparison with AMBER molecular mechanics and dynamics calculations for methyl α-lactoside. Int. J. Biol. Macromol, 17, 137-148.
5. Balaji, P.V , Qasba, P.K. and Rao, V.S.R. (1993) Molecular dynamics simulations of asialo-glycoprotein. Biochemistry. 32, 12599-12611.
6. Balaji, P.V., Qasba, P.K. and Rao, V S.R (1994) Molecular dynamics simulations of high-mannose oligosaccharides. Glycobiology, 4, 497-515.
7. Burkert, U. and Allinger, N.L. (1982) Molecular Mechanics, American Chemical Society. Washington, DC.
8. D3, by human melanoma cells creates a unique antigenic epitope. Science, 225, 844-846.
9. Cheresh, D.A., Varki, A.P., Varki, N.M., Stallcup, W.B., Levine, J. and Reisfeld, R.A. (1984b) A monoclonal antibody recognizes an O-acetylated sialic acid in a human melanoma-associated ganglioside. J. Biol. Chem., 259, 7453-7459.
10. Eaton, H.L. and Hakomori, S. (1988) Conformation of micelle-bound gangliosides by 2D proton NMR spectroscopy. Third Chemical Congress of North America, Abstract CARS 91, Toronto.
11. Gabius, H.-J. (1996) Concepts of tumor lectinology. Cancer Invest., in press
12. Gabius, H.-J. and Gabius, S. (1996) Glycosciences: Status and Perspectives. Chapman & Hall, Weinheim.
13. Gabius, H.-J., Kayser, K. and Gabius, S. (1995) Protein-Zucker-Erkennung. Grundlagen und medizinische Anwendung am Beispiel der Tumorlektinologie. Naturwissenschaften, 82, 533-543.
14. DIa) containing terminal N-acetyl-9-0-acetylneurarminic acid in rat erythrocytes. Hoppe-Seyler's Z- Physiol. Chem., 365, 1247-1253.
15. Guenot, J. and Kollman, P.A. (1992) Molecular dynamics studies of DNA-binding protein: an evaluation of implicit and explicit solvent models for the molecular dynamics simulation of the Escherichia coli tip represser. Protein Sci., 1, 1185-1205.
16. Guenot, J. and Kollman, P.A. (1993) Conformational and energetic effects of truncating nonbonded interactions in an aqueous protein dynamics simulation. J. Comput. Chem., 14, 278-284.
17. Hagler, A.T., Huler, E. and Lifson, S (1974) Energy functions for peptides and proteins. Deviation of a consistent force field including the hydrogen bond for amide crystals. J. Am. Chem. Soc., 96, 5316-5327.
18. Hagler, A.T., Lifson, S. and Dauber, P. (1979a) Consistent force field studies of intermolecular forces in hydrogen-bonded crystals. 2. A benchmark for the objective comparison of alternative force fields. J Am. Chem. Soc., 101, 5122-5130.
19. Hagler, A.T., Dauber, P., and Lifson, S. ( 1979b) Consistent force field studies of intermolecular forces in hydrogen-bonded crystals. 3. The C = O H-O hydrogen bond and the analysis of the energetics and packing of carboxylic acids. J. Am. Chem. Soc., 101, 5131-5141.
20. Hakomori, S. (1990) Bifunctional role of glycosphingolipids. J. Biol. Chem., 265, 18713-18716.
21. Hakomori, S. (1991) New directions in cancer therapy based on aberrant expression of glycosphingolipids: anti-adhesion and ortho-signalling therapy. Cancer Cells, 3, 461-470.
22. Herrler, G., Rott, R., Klenk, H.D., Muller, H.P., Shukla, A.K. and Schauer, R. (1985) The receptor-destroying enzyme of influenza C virus is neuraminateO-acetylesterase. EMBO J., 4, 1503-1506.
23. Homans, S.W. (1990) A molecular mechanical force field for the conformational analysis of oligosaccharides: comparison of theoretical and crystal structures of Manα1-3 Manβ1-4 GlcNAc. Biochemistry, 92, 9110-9118.
24. Kelm, S , Schauer, R., Manuguerra, J C, Gross, H.-J. and Crocker, P. (1994) Modification of cell surface sialic acids modulate cell adhesion mediated by sialoadhesin and CD22. Glycoconjugate J., 11, 576-585.
25. Klein, A., Krishna, M., Varki, N.M. and Varki, A. (1994) 9-O-Acetylated sialic acids have widespread but selective expression. analysis using a chimeric dual-function probe derived from influenza C hemagglutinin-esterase. Proc. Natl. Acad. Sci. USA, 91, 7782-7786.
26. Kopitz, J. (1996) Glycolipids: structure and functions. In Gabius, H.-J. and Gabius, S. (eds.). Glycosciences; Status and Perspectives. Chapman & Hall, Weinheim, in press.
27. Kozár, T (1995) Force fields. First Electronic Glycoscience Conference.
28. Ledeen, R.W. and Yu, R.K. (1982) Gangliosides structure, isolation and analysis. Methods Enzymo., 83, 139-191.
29. Liliefors, M. (1983) MOLBUILD - an interactive computer graphics interface to molecular mechanics. J. Mol. Graphics, 1, 111-117.
30. Manzi, A.E., Sjoberg, E.R., Diaz, S. and Varki, A. (1990) Biosynthesis and turnover of O-acetyl and N-acetyl groups in the gangliosides of human melanoma cells. J. Biol. Chem., 265, 13091-13103.
31. Marti, J., Guàrdia, E., and Padró, J.A. (1994) Dielectric properties and infrared spectra of liquid water: influence of the dynamic cross correlations. J. Chem. Phys., 101, 10883-10891.
32. Mierke, D. and Kessler, H. (1992) Combined use of homo- and heteronuclear coupling constants as restraints in molecular dynamics simulations. Biopolymers. 32, 1277-1282.
33. Ogura, H., Furuhata, K., Sato, S., Anazawa, K., Itoh.M. and Shitory, Y. (1987) Synthesis of 9-O-acetyl- and 4-O-acetyl-sialic acids. Carbohydr. Res., 167, 77-86.
34. DIa headgroup transformations revealed by NMR spectroscopy. Biophys. J., 66, 1642-1652.
35. D3 is recognized by Cancer antennarius lecrin. J. Biol. Chem., 263, 2079-2086.
36. D3 recognized by antibodies in melanoma patients after active specific immunotherapy. Cancer Res., 49, 3891-3897.
37. Redinbaugh, M.E. and Campbell, W.H, (1985) Adaptation of the dye-binding protein assay to microtiter plates. Anal. Biochem.. 147, 144-147.
38. Reuter, G. and Schauer, R. (1987) Isolation and analysis of gangliosides with O-acetylated sialic acids. In Rahmann, H. (ed.). Gangliosides and Modulation of Neuronal Functions, NATO ASI Series H. Springer Verlag, Heidelberg, pp. 155-167.
39. Reuter, G., Pfeil, R., Stoll, S., Schauer, R., Kamerling, J.P., Versluis, C. and Vliegenthart, J.F.G. (1983) Identification of new sialic acids derived from glycoprotein of bovine submandibular gland.. Eur. J. Biochem., 134, 139-143.
40. Ritter, G., Livingston, P.O., Boosfeld, E., Wiegandt, H., Yu, R.K., Oettgen, H.F. and Old, L.J (1989) Development of melanoma vaccines: gangliosides as immunogens. In Oettgen, H.F. (ed.), Gangliosides and Cancer. VCH. Weinheim, pp. 301-313,
41. D3. Cancer Res., 50, 1403-1410.
42. D12. J. Am, Chem. Soc., 113, 3236-3246.
43. Sabesan, S., Bock, K. and Paulson, J.C. (1991b) Conformational analysis of sialyloligosaccharides. Carbohydr. Res., 218, 27-54.
44. Scarsdale, J.N., Prestegard, J.H. and Yu, R.K. (1990) NMR and computational studies of interactions between remote residues in gangliosides Biochemistry, 29, 9843-9855.
45. Schauer, R. (1979) Biosynthesis of sialic acids. Methods Enzymol, 50, 374-386
46. Schauer, R. (1982) Chemistry, metabolism and biological functions of sialic acids. Adv. Carbohydr. Chem. Biochem., 40, 131-234.
47. Schauer, R., Kelm, S., Reuter, G., Roggentin, P. and Shaw, L. (1995) Biochemistry and role of sialic acids. In Rosenberg.A. (ed.). Biology of the Sialic Acids. Plenum Press, New York, pp. 7-67
48. Schultze, B., Zimmer, G. and Herrler, G. ( 1993) Viral lectins for the detection of 9-O-acetylated sialic acid on glycoproteins and glycolipids. In Gabius, H.-J. and Gabius, S. (eds.), Lectins and Glycobiology. Springer Verlag, Heidelberg, pp. 175-181.
49. Siebert, H C. (1990) Konformationsanalyse verschiedener Ganglioside mit Hilfe von 1-Kemresonanzmethoden und Computerberechnungen. Ph.D. Thesis, University of Heidelberg.
50. M3 gangliosides containing different sialic acid residues as revealed by NOE-based distance-mapping, and molecular mechanics and molecular dynamics calculations. Biochemistry, 31, 6962-6971.
51. Siebert, H.-C., Kaptein, R. and Vliegenthart, J.F.G (1993) Study of oligosaccharide-lectin interaction by various nuclear magnetic resonance (NMR) techniques and computational methods. In Gabius, H.-J. and Gabius, S. (eds), Lectins and Glycobiology, Springer Verlag, Heidelberg, pp. 105-116.
52. Siebert, H-C., Gilleron, M., Kaltner, H., von der Lieth, C.-W., Kozár.T., Bovin, N.V., Korchagina, E.Y., Vliegenthart, J F.G. and Gabius H-J. (1996a) NMR-based, molecular dynamics- and random walk molecular mechanics-supported study of conformational aspects of a carbohydrate ligand (Galβ1.2Galβl-R) for an animal galectin in the free and in the bound state. Biochem. Biophys. Res. Commun., 219, 205-212.
53. Siebert, H.-C., von der Lieth, C.-W., Gilleron, M., Reuter, G., Wittmann, J., Vliegenthart, J.F.G and Gabius, H.-J. (1996b) Carbohydrate-protein interaction. In Gabius, H.-J. and Gabius, S. (eds.). Glycosciences: Status and Perspectives. Chapman & Hall, Weinheim, in press.
54. D2 is an acceptor for ganglioside O-acetyltransferase in human melanoma cells. J. Biol. Chem., 267, 16200-16211.
55. Sjoberg, E.R., Powell, L.D., KIein, A. and Varki, A. (1994) Natural ligands of B cell adhesion molecule CD22b can be masked by 9-O-acetylation of sialic acids. J. Cell Biol. 126, 549-562.
56. Sun, Y. and Kollman, P.A. (1992) Conformational sampling and ensemble generation by molecular dynamics simulations: 18-Crown-6 as a test case. J. Comput. Chem., 13, 33-40.
57. D3. J. Biol. Chem., 260, 14556-14563.
58. Varki, A. (1992) Diversity in the sialic acids. Glycobiology, 2, 25-40.
59. von der Lieth, C.-W, Schmitz, M., Poppe, L., Hauck, M. and Dabrowski, J. (1989) CARBHYD - ein computergrafisches Interface zur Konstruktion. Wiedergabe und Konformationsberechnung von Poly- und Oligosacchariden. In Gauglitz, G. (ed.). Software-Entwicklung in der Chemie 3. Springer Verlag. Heidelberg, pp. 371-378.
60. von der Lieth, C.-W., Kozar, T. and Hull, W.E. (1996) A (critical) survey of modeling protocols use to explore the conformational space of oligosaccharides. J. Mol. Struct. (Theochem), in press.
61. Zeng, F.-Y. and Gabius, H.-J. (1992) Sialic acid-binding proteins: characterization, biological function and application. Z Naturforsch., 47c, 641-653.
62. Zeng, F-Y., Wegenka, U. and Gabius, H.-J. (1992) Purification and properties of a fucoidan-binding protein from human placenta and its identification as immunoglobulin G. Int. J. Biochem., 24, 1329-1340.
63. Zimmer, G., Reuter, G. and Schauer, R. (1992) Use of influenza C virus for detection of 9-O-acetylated sialic acids on immobilized glycoconjugates by esterase activity. Eur. J. Biochem., 204, 209-215.
64. Zimmer, G., Suguri.T., Reuter, G., Yu, R.K., Schauer, R. and Herrler, G. (1994) Modification of sialic acids by 9-O-acetylation is detected in human leukocytes using the lectin property of influenza C virus. Glycobiology, 4, 343-349.