Dynamics of ganglioside headgroup in lipid environment: Molecular dynamics simulations of GM1 embedded in dodecylphosphocholine micelle

Journal of Physical Chemistry B

Volumn 105, Issue 29, 2001, Pages 7033-7041

  Vasudevan, Sheeja V ^a   Balaji, Petety V ^a  

^a INDIAN INSTITUTE OF TECHNOLOGY BOMBAY   (India)

Author keywords

[No Author keywords available]

Indexed keywords

CRYPTICITY;

COMPUTER SIMULATION; CONFORMATIONS; LIPIDS; MICELLES; PROTEINS;

MOLECULAR DYNAMICS;

EID: 0035954988     PISSN: 10895647     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp0027952     Document Type: Article

References (66)

1. Evans, S.V.; MacKenzie, C.R. J. Mol. Recognit. 1999, 12, 155.
2. Fishman, P.H.; Pacuszka, T.; Oralandi, P. A Adv. Lipid Res. 1993, 25, 165.
3. Schengrund, C.-L. Biol. Signals 1995, 4, 1.
4. Nohara, K.; Kunimoto, M.; Fujimaki, H. J. Biochem. 1998, 124, 194.
5. Ladisch, S.; Chang, F.; Li, R.; Cogen, P.; Johnson, D. Cancer Lett. 1997, 120, 71.
6. Yohe, H.C.; Ye, S.; Reinhold: B.B.; Reinhold: V.N. Glycobiology 1997, 7, 1215.
7. Simons, K.; Ikonen, E. Nature 1997, 387, 569.
8. Sears, C.L.; Kaper, J.B. Microbiol. Rev. 1996, 60, 167.
9. Merritt, E.A.; Hoi, W.G. J. Curr. Opin. Struct. Biol. 1995, 5, 165.
10. Pascher, I.; Sundell, S. Chem. Phys. Lipids 1977, 20, 175.
11. Nyholm, P.G.; Pascher, I.; Sundell, S. Chem. Phys. Lipids 1990, 52, 1.
12. Abrahamsson, S.; Dahlen, B.; Pascher, I. Acta Crystallogr. 1977, B33, 2008.
13. Skarjune, R.; Oldfield, E. Biochemistry 1982, 21, 3154.
14. Jarell, H.C.; Jovall, P.A.; Giziewicz, J.B.; Turner, L.A.; Ian Smith, C.P. Biochemistry 1987, 26, 1805.
15. Nyholm, P.-G.; Pascher, I. Biochemistry 1993, 32, 1225.
16. Stromberg, N.; Nyholm, P.G.; Pascher, I.; Normark, S. Proc. Natl. Acad. Sci. (U.S.A.) 1991, 88, 9340.
17. Pacuszka, T.; Fishman, P.H. J. Biol. Chem. 1990, 265, 7673.
18. Fishman, P.H.; Pacuszka, T.; Hom, B.; Moss, J. J. Biol. Chem. 1980, 255, 7657.
19. Schengrund, C.-L.; Ringler, N.J. J. Biol. Chem. 1989, 264, 13233.
20. Siebert, H.-C.; Reuter, G.; Schauer, R.; von der Leith, C.-W.; Dabrowski, J. Biochemistry 1992, 31, 6962.
21. Poppe, L.; Halbeek, H. van; Acquotti, D.; Sonnino, S. Biophys. J. 1994, 66, 1642.
22. Singh, D.M.; Shan, X.; Davis, J.H.; Jones, D.H.; Grant, C.W.M. Biochemistry 1995, 34, 451.
23. Beswick, V.; Guerois, R.; Cordier-Ochssenbein, F.; Coic, Y.M.; Tam, H.D.; Tostain, J.; Noel, J.P.; Sanson, A.; Neumann, J.M. Eur. Biophys. J. 1998, 28, 48.
24. Kloosterman, D.A.; Goodwin, J.T.; Burton, P.S.; Conradi, R.A.; Stockman, B.J.; Scahill, T.A.; Blinn, J.R. Biopolymers 2000, 53, 396.
25. Jarvet, J.; Zdunek, J.; Damberg, P.; Graslund, A. Biochemistry 1997, 36, 8153.
26. Mercurio, E.; Pellegrini, M.; Mierke, D.F. Biopolymers 1997, 42, 759.
27. Chorev, M.; Gurrath, M.; Behar, V.; Mammi, S.; Tonello, A.; Peggion, E. Biopolymers 1995, 36, 473.
28. Wymore, T.; Wong, T.C. Biophys. J. 1999, 76, 1213.
29. Goldstein, H. Classical Mechanics, 2nd ed.; Addison-Wesley Inc.: London, 1980; Chapter 5.
30. Hoffmann, H.; Ulbricht, W. In Thermodynamic data for biochemistry and biotechnology; Springer-Verlag: Berlin, 1986; Chapter 12, p 298.
31. Lanterwein, J.; Bosch, C.; Brown, L.R.; Wuthrich, K. Biochim. Biophys. Acta 1979, 556, 244.
32. Jones, M.N.; Chapman, D. In Micelles, monolayers and biomembranes; Wiley-Liss: New York, 1995; Chapter 3, p 80.
33. Berendson, H.J.C.; van der Spoel, D.; van Drunen, R. Comput. Phys. Commun. 1995, 91, 43.
34. Van der Spoel, D.; van Buuren, A.R.; Apol, E.; Meulenhoff, P.J.; Tielman, D.P.; Sijbers, A.L.T.M.; Hess, B.; Feenstra, K.A.; Lindahl, E.; van Drunen, R.; Berendsen, H.J.C. Gromacs User Manual version 2.0; The Netherlands; http://md.chem.rug.nl/~gmx; 1999.
35. Sayle, R. RASMOL molecular visualisation program; Biomolecular structures group, Glaxo Research and Development, Greenford, Middlesex, 1994.
36. van Gunsteren, W.F.; Billeter, S.R.; Dusubg, A.A.; Hunenberger, P.H.; Kruger, P.; Mark, A.E.; Scott, W.R.P.; Tironi, I.G. Biomolecular Simulation: The GROMOS96 manual and user guide; Zurich, Switzerland: Hochschulverlag AG an der ETH Zurich, 1996.
37. Chiu, S.-W.; Clark, M.; Balaji, V.; Subramaniam, S.; Scott, H.L.; Jakobosson, E. Biophys. J. 1995, 69, 1230.
38. Hess, B.; Bekker, H.; Berendsen, H.J.C.; Fraaije, J.G.E.M. J. Comput. Chem. 1997, 18, 1463.
39. Ran, V.S.R.; Qasba, P.K.; Balaji, P.V.; Chandrasekaran, R. Conformation of Carbohydrates; Harwood Academic: Singapore, 1998; Chapter 4.
40. Park, H.J.; Han, S.J.; Kang, Y.K. Biopolymers 1997, 42, 19.
41. Sabesan, S.; Bock, K.; Lemieux, R.U. Can. J. Chem. 1984, 62, 1034.
42. Sabesan, S.; Duus, J.; Fukunaga, T.; Bock, K.; Ludvigsen, S. J. Am. Chem. Soc. 1991, 113, 3236.
43. Siebert, H.; Reuter, G.; Schauer R.; von der Leith, C.-W.; Dabrowski, J. Biochemistry 1992, 31, 6962.
44. Acquotti, D.; Poppe, L.; Darbrowski, J.; von der Lieth, C.-W.; Sonnino, S.; Tettamanti, G. J. Am. Chem. Soc. 1990, 112, 7772.
45. Acquotti, D.; Cantu, L.; Ragg, E.; Sonnino, S. Eur. J. Biochem. 1994, 225, 271.
46. Imberty, A.; Mikros, E.; Koca, J.; Mollicone, R.; Oriol, R.; Perez, S. Glycoconj. J. 1995, 12, 331.
47. Yan, Z.-Y.; Bush, A. Biopolymers 1990, 29, 799.
48. Kobayashi, H.; Kitamura, S.; Ozaki, T.; Yamaguchi, M.; Kuge, T. Chem. Express 1989, 4, 213.
49. Yadav, J.S.; Luger, P. Carbohydr. Res. 1983, 119, 57.
50. Veluraja, K. Studies on the conformations of gangliosides. Ph.D. Thesis, Indian Institute of Science, Bangalore; 1983.
51. Veluraja, K.; Rao, V.S.R. Carbohydr. Polym. 1983, 4, 357.
52. Poppe, L.; Dabrowski, J.; von der Lieth, C.-W.; Numata, M.; Ogawa, T. Eur. J. Biochem. 1989, 180, 337.
53. Wynn, C.H.; Marsden A.; Robson B. J. Theor. Biol. 1986, 119, 81.
54. May, A.P.; Robinson, R.C.; Vinson, M.; Crocker, P.R.; Jones, E.Y. Mol. Cell. Recogn. 1998, 1, 719.
55. Stehle, T.; Yan, Y.; Benjamin, T.L.; Harrison, S.C. Nature 1994, 369, 160.
56. Eisen, M.B.; Sabesan, S.; Skehel, J.J.; Wiley, D.C. Virology 1997, 232, 19.
57. Wright, C.S. J. Mol. Biol. 1990, 215, 635.
58. Merritt, E.A.; Sarfaty, S.; van der Akker, F.; L'Hoit, C.; Martial, J.A.; Hol, W.G. J. Prot. Sci. 1994, 3, 166.
59. Wymore, T.; Gao, X.F.; Wong, T.C. J. Mol. Struct. 1999, 485-486, 195.
60. Tieleman, D.P.; Van Der Spoel, D.; Berendsen, H.J.C. J. Phys. Chem. 2000, 104, 6380S.
61. Dill, K.A.; Flory, P.J. Proc. Natl. Acad. Sci. (U.S.A.) 1981, 78, 676.
62. Kairash, A.; Boyd; B.; Lingwood, C.A. J. Biol. Chem. 1994, 269, 11138.
63. Homans, S.W. Glycobiology 1993, 3, 551.
64. Qasba, P.K.; Balaji, P.V.; Rao, V.S.R. Glycobiology 1994, 4, 805.
65. Poveda, A.; Jimenez-Barbero, J. Chem. Soc. Rev. 1998, 27, 133.
66. von der Lieth, C.-W.; Siebert, H.-C.; Kozar, T.; Burchert, M.; Frank, M.; Gilleron, M.; Kaltner, H.; Kayser, G.; Tajkhorshid, E.; Bovin, N.V.; Vliegenthart, J.F.G.; Gabius, H.-J. Acta Anat. 1998, 161, 91.