Full length vpu from hiv-1: Combining molecular dynamics simulations with nmr spectroscopy

Journal of Biomolecular Structure and Dynamics

Volumn 23, Issue 5, 2006, Pages 485-496

  Lemaitre, V ^a,c   Willbold, D ^d   Watts, A ^a   Fischer, W B ^a,b  

^a UNIVERSITY OF OXFORD   (United Kingdom)

^b UNIVERSITY OF OXFORD   (United Kingdom)

^c NESTLÉ RESEARCH CENTER   (Switzerland)

^d HEINRICH HEINE UNIVERSITY   (Germany)

Author keywords

HIV 1; Membrane protein; Molecular dynamics simulations; NMR spectroscopy; Vpu

Indexed keywords

AMINO ACID; VPU PROTEIN;

ALPHA HELIX; ARTICLE; CARBOXY TERMINAL SEQUENCE; CONFORMATIONAL TRANSITION; CYTOPLASM; LIPID BILAYER; MOLECULAR DYNAMICS; MOLECULAR MODEL; NONHUMAN; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FUNCTION; PROTEIN PHOSPHORYLATION; PROTEIN STRUCTURE; SIMULATION; STRUCTURE ANALYSIS;

HUMAN IMMUNODEFICIENCY VIRUS 1; SIMIAN IMMUNODEFICIENCY VIRUS;

EID: 33645296283     PISSN: 07391102     EISSN: 15380254     Source Type: Journal    
DOI: 10.1080/07391102.2006.10507074     Document Type: Article

References (52)

1. Campbell, I. D., and Downing, A. K., 1998. Nature Struc. Biol. NMR Supplement,:496–499.
2. Campbell, I. D., 2003. Biochem. Soc. Trans., 31:1107–1114.
3. Biggin, P. C., Roosild, T., and Choe, S., 2000. Curr. Opin. Struc. Biol., 10:456–461.
4. Ma, C., Marassi, F. M., Jones, D. H., Straus, S. K., Bour, S., Strebel, K., Schubert, U., Oblatt-Montal, M., Montal, M., and Opella, S. J., 2002. Prot. Sci., 11:546–557.
5. Fischer, W. B., 2003. FEBS Lett., 552:39–46.
6. Fischer, W. B., 2005. Viral Membrane Proteins:Structure, Function and Drug Design, Vol. 1. New York:Kluwer Academic/Plenum Publisher.
7. Strebel, K., Klimkait, T., and Martin, M. A., 1988. Science, 241:1221–1223.
8. Cohen, E. A., Terwilliger, E. F., Sodroski, J. G., and Haseltine, W. A., 1988. Nature, 334:532–534.
9. Huet, T., Cheynier, R., Meyerhans, A., and Roelants, G., 1990. Nature, 345:356–359.
10. Courgnaud, V., Salemi, M., Pourrut, X., Mpoudi-Ngole, E., Abela, B., Auzel, P., Bibollet-Ruche, F., Hahn, B., Vandamme, A.-M., Delaporte, E., and Peeters, M., 2002. J. Virol., 76:8298–8309.
11. Courgnaud, V., Abela, B., Pourrut, X., Mpoudi-Ngole, E., Loul, S., Delaporte, E., and Peeters, M., 2003. J. Virol., 77:12523–12534.
12. Klimkait, T., Strebel, K., Hoggan, M. D., Martin, M. A., and Orenstein, J. M., 1990. J. Virol., 64:621–629.
13. Willey, R. L., Maldarelli, F., Martin, M. A., and Strebel, K., 1992. J. Virol., 66:7193–7200.
14. Kimura, T., Nishikawa, M., and Ohyama, A., 1994. J. Biochem., 115:1010–1020.
15. Schubert, U., Bour, S., Ferrer-Montiel, A. V., Montal, M., Maldarelli, F., and Strebel, K., 1996. J. Virol., 70:809–819.
16. Levesque, K., Finzi, A., Binette, J., and Cohen, E. A., 2004. Curr. Hiv Res., 2:51–59.
17. Ewart, G. D., Sutherland, T., Gage, P. W., and Cox, G. B., 1996. J. Virol., 70:7108–7115.
18. Kochendörfer, G. G., Jones, D. H., Lee, S., Oblatt-Montal, M., Opella, S. J., and Montal, M., 2004. J. Am. Chem. Soc., 126:2439–2446.
19. Bour, S., Schubert, U., and Strebel, K., 1995. J. Virol., 69:1510–1520.
20. Schubert, U., Ferrer-Montiel, A. V., Oblatt-Montal, M., Henklein, P., Strebel, K., and Montal, M., 1996. FEBS Lett., 398:12–18.
21. Montal, M., 2003. FEBS Lett., 552:47–53.
22. Wray, V., Federau, T., Henklein, P., Klabunde, S., Kunert, O., Schomburg, D., and Schubert, U., 1995. Int. J. Peptide Protein Res., 45:35–43.
23. Federau, T., Schubert, U., Floßdorf, J., Henklein, P., Schomburg, D., and Wray, V., 1996. Int. J. Peptide Protein Res., 47:297–310.
24. Willbold, D., Hoffmann, S., and Rösch, P., 1997. Eur. J. Biochem., 245:581–588.
25. Park, S. H., Mrse, A. A., Nevzorov, A. A., Mesleh, M. F., Oblatt-Montal, M., Montal, M., and Opella, S. J., 2003. J. Mol. Biol., 333:409–424.
26. Kukol, A., and Arkin, I. T., 1999. Biophys. J., 77:1594–1601.
27. Marassi, F. M., Ma, C., Gratkowski, H., Straus, S. K., Strebel, K., Oblatt-Montal, M., Montal, M., and Opella, S. J., 1999. Proc. Natl. Acad. Sci. Usa, 96:14336–14341.
28. Coadou, G., Evrard-Todeschi, N., Gharbi-Benarous, J., Benarous, R., and Girault, J.-P., 2002. Int. J. Biol. Macromolecues, 30:23–40.
29. Coadou, G., Gharbi-Benarous, J., Megy, S., Bertho, G., Evrard-Todeschi, N., Segeral, E., Benarous, R., and Giraudat, J.-P., 2003. Biochemistry, 42:14741–14751.
30. Sramala, I., Lemaitre, V., Faraldo-Gomez, J. D., Vincent, S., Watts, A., and Fischer, W. B., 2003. Biophys. J., 84:3276–3284.
31. van Aalten, D. M.F., Bywater, R., Findlay, J. B., Hendlich, M., Hooft, R. W., and Vriend, G., 1996. J. Comput. Aided Mol. Des., 10:255–262.
32. Tieleman, D. P., Berendsen, H. J. C., and Sansom, M. S. P., 1999. Biophys. J., 76:3186–3191.
33. Tieleman, D. P., Berendsen, H. J. C., and Sansom, M. S. P., 1999. Biophys. J., 76:1757–1769.
34. Tieleman, D. P., Sansom, M. S. P., and Berendsen, H. J. C., 1999. Biophys. J., 76:40–49.
35. Lindahl, E., Hess, B., and Van der Spoel, D., 2001. J. Mol. Mod., 7:306–317.
36. Berendsen, H. J. C., Griegera, J. R., and Straatsma, T. P., 1987. J. Phys. Chem., 91:6269–6271.
37. Kabsch, W., and Sander, C., 1983. Biopolymers, 22:2577–2637.
38. Berger, O., Edholm, O., and Jähnig, F., 1997. Biophys. J., 72:2002–2013.
39. Sun, F., 2003. J. Mol. Model., 9:114–123.
40. Vetter, I. R., and Wittinghofer, A., 2001. Science, 294:1299–1304.
41. Cordes, F. S., Tustian, A., Sansom, M. S. P., Watts, A., and Fischer, W. B., 2002. Biochemistry, 41:7359–7365.
42. Heller, H., Schaefer, M., and Schulten, K., 1993. J. Phys. Chem., 97:8343–8360.
43. Tieleman, D. P., and Berendsen, H. J. C., 1996. J. Chem. Phys., 105:4871–4880.
44. Jakobsson, E., 1997. Trends Biochem. Sci., 22:339–354.
45. Hofsäss, C., Lindahl, E., and Edholm, O., 2003. Biophys. J., 84:2192–2206.
46. Böckmann, R. A., Hac, A., Heimburg, T., and Grubmüller, H., 2003. Biophys. J., 85:16471655
47. Mukhopadhyay, P., Monticelli, L., and Tieleman, D. P., 2004. Biophys. J., 86:1601–1609.
48. Coadou, G., Evrard-Todeschi, N., Gharbi-Benarous, J., Benarous, R., and Girault, J.-P. 2001. C. R. Acad. Sci. Paris, Chemie/Chemistry, 4:751–758.
49. Henklein, P., Kinder, R., Schubert, U., and Bechinger, B., 2000. FEBS Lett., 482:220–224.
50. Zheng, S., Strzalka, J., Ma, C., Opella, S. J., Ocko, B. M., and Blasie, J. K., 2001. Biophys. J., 80:1837–1850.
51. Fischer, W. B., Forrest, L. R., Smith, G. R., and Sansom, M. S. P., 2000. Biopolymers, 53:529538
52. Wray, V., Kinder, R., Federau, T., Henklein, P., Bechinger, B., and Schubert, U., 1999. Biochemistry, 38:5272–5282.