Molecular dynamics simulations of an α-(2 → 8)-linked sialic acid tetramer in vacuum and solvent

Journal of Molecular Structure: THEOCHEM

Volumn 395-396, Issue 1-3, 1997, Pages 375-388

  Venable, Richard M ^a   Bizik, Frantisek ^a   Henderson, Terry J ^a   Egan, William ^a  

^a CENTER FOR BIOLOGICS EVALUATION AND RESEARCH   (United States)

Author keywords

Molecular dynamics simulations; Solvent; Vacuum; (2 8) linked sialic acid tetramer

Indexed keywords

EID: 0000865044     PISSN: 01661280     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0166-1280(96)04865-8     Document Type: Article

References (31)

1. J.B. Robbins, R. Schneerson, W. Egan, W. Vann and D.T. Liu, in H. Smith, J.J. Skehel and M.J. Turner (Eds.), The Molecular Basis of Microbial Pathogenicity, Verlag Chemie, Weinheim, 1980, pp. 115-132.
2. A.K. Bhattacharjee, H.J. Jennings, C.P. Kenny, A. Martin and I.C.P. Smith, J. Biol. Chem., 250 (1975) 1926-1932.
3. G. Kogan, D. Uhrin, J.-R. Brisson, L.C. Paoletti, D.L. Kasper, C. Vonhunolstein, G. Orefici and H.J. Jennings, J. Carbohydr. Chem., 13 (1994) 1071-1078.
4. A. Sutton, R. Schneerson, S. Kendall-Morris and J.B. Robbins, Infect. Immun., 35 (1982) 95-104.
5. K.A. Joiner, Annu. Rev. Microbiol., 42 (1988) 201-230.
6. J. Finne, V. Finne, H. Deagostino-Bazin and C. Goridis, Biochem. Biophys. Res. Commun., 112 (1983) 482-487.
7. A.D. Perera, C.F. Lagenaur and T.M. Plant, Endocrinology, 133 (1993) 2729-2735.
8. A. Varki, Glycobiology, 3 (1993) 97-130.
9. W. Egan, in J.S. Cohen (Ed.), Magnetic Resonance in Biology, Vol. 1, Wiley, New York, 1980, pp. 197-258.
10. J.C. Lindon, J.G. Vinter, M.R. Lifely and C. Moreno, Carbohydr. Res., 133 (1984) 59-74.
11. F. Michon, J.-R. Brisson and H.J. Jennings, Biochemistry, 26 (1987) 8399-8405.
12. J.-R. Brisson, H. Baumann, A. Imberty, S. Pérez and H.J. Jennings, Biochemistry, 31 (1992) 4996-5004.
13. R. Yamasaki and B. Bacon, Biochemistry, 30 (1991) 851-857.
14. H. Baumann, J.-R. Brisson, F. Michon, R. Pon and H.J. Jennings, Biochemistry, 32 (1993) 4007-4013.
15. S.V. Evans, B.W. Sigurskjoid, H.J. Jennings, J.-R. Brisson, R. To, E. Altman, F. Frosch, C. Weisgerber, H. Kratzin, S. Klebert, M. Vaesen, D. Bitter-Suermann, D.R. Rose, N.M. Young and D.R. Bundle, Biochemistry, 34 (1995) 6737-6744.
16. B.R. Brooks, R.E. Bruccoleri, B.D. Olafson, D.J. States, S. Swaminathan and M. Karplus, J. Comp. Chem., 4 (1983) 187-217.
17. Molecular Simulations, Inc., Release of parameter set, PAR-M30A.PRM for Quanta/CHARMM, Molecular Simulations, Inc., San Diego, CA, March 31, 1992.
18. J.L. Flippen, Acta Crystallogr., Sect. B: Struct. Crystallogr. Cryst. Chem., 29 (1973) 1881-1886.
19. G.S. Manning, Acc. Chem. Res., 12 (1979) 443-449.
20. K.K. Irikura, B. Tidor, B.R. Brooks and M. Karplus, Science, 229 (1985) 571-572.
21. L. Verlet, Phys. Rev., 159 (1967) 98-103.
22. S. Vijayakumar, G. Ravishanker, R.F. Pratt and D.L. Beveridge, J. Am. Chem. Soc., 117 (1995) 1722-1730.
23. W.L. Jorgensen, J. Chandrasekhar, J.D. Madura, R.W. Impey and M.L. Klein, J. Chem. Phys., 79 (1983) 926-935.
24. B.J. Hardy, W. Egan and G. Widmalm, Intern. J. Biol. Macromol., 17 (1995) 149-160.
25. G. Widmalm, R.A. Byrd and W. Egan, Carbohydr. Res., 229 (1992) 195-211.
26. C.A.G. Haasnoot, F.A.A.M. DeLeeuw and C. Altona, Tetrahedron, 36 (1980) 2783-2792.
27. I. Tvaroska and S. Pérez, Carbohydr. Res., 149 (1986) 389-410.
28. T.J. Henderson, R.W. Venable and W. Egan, unpublished results; presented in part at the 209th National ACS Meeting, Anaheim, CA, April, 1995.
29. R.W. Pastor, in V. Renugopalakrishnan, P.R. Carey, I.C.P. Smith, S.G. Huang and A.C. Storer (Eds.), Proteins: Structure, Dynamics, and Design, ESCOM, Leiden, 1991, pp. 229-233.
30. Y. Zhang and R.W. Pastor, Molecular Simulations, 13 (1994) 25-38.
31. H. Kooijman, L.M.J. Kroon-Batenburg, J. Kroon, J.N. Breg and J. De Boer, Acta Crystallogr., Sect. C, 46 (1990) 407-410.