Transmembrane domains of viral ion channel proteins: A molecular dynamics simulation study

Biopolymers

Volumn 53, Issue 7, 2000, Pages 529-538

  Fischer, Wolfgang B ^a   Forrest, Lucy R ^a   Smith, Graham R ^a   Sansom, Mark S P ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

Alphahelix propensity; Hydrogen bonding; Hydrophobic mismatch; Lipid bilayer; Molecular dynamics simulation; Transmembrane alpha helix; Viral ion channel

Indexed keywords

COMPUTER SIMULATION; HYDROGEN BONDS; HYDROPHOBICITY; MOLECULAR DYNAMICS; SOLUTIONS; VIRUSES;

ALPHA-HELIX PROPENSITY; TRANSMEMBRANE ALPHA-HELIX; VIRAL ION CHANNEL;

PROTEINS;

ION CHANNEL PROTEIN; MEMBRANE PROTEIN; UNCLASSIFIED DRUG;

ALPHA HELIX; ARTICLE; INFLUENZA VIRUS; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; NONHUMAN; PHOSPHOLIPID BILAYER; PROTEIN DOMAIN; PROTEIN INTERACTION; SIMULATION;

AMINO ACID SEQUENCE; COMPUTER SIMULATION; GENE PRODUCTS, VPU; GLYCOPROTEINS; HIV-1; HYDROGEN BONDING; IMAGE PROCESSING, COMPUTER-ASSISTED; INFLUENZA B VIRUS; INFLUENZAVIRUS C; ION CHANNELS; LIPID BILAYERS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN STRUCTURE, SECONDARY; VIRAL MATRIX PROTEINS; VIRAL PROTEINS;

HIV 1; INFLUENZA VIRUS; RNA VIRUSES;

EID: 0034097318     PISSN: 00063525     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0282(200006)53:7<529::AID-BIP1>3.0.CO;2-6     Document Type: Article

References (56)

1. Sansom, M. S. P. Quart Rev Biophys 1993, 26, 365-421.
2. Tieleman, D. P.; Berendsen, H. J. C.; Sansom, M. S. P. Biophys J 1999, 76, 1757-1769.
3. Unwin, N. Nature 1995, 373, 37-43.
4. Doyle, D. A.; Cabral, J. M.; Pfützner, R. A.; Kuo, A.; Gulbis, J. M.; Cohen, S. L.; Cahit, B. T.; MacKinnon, R. Science 1998, 280, 69-77.
5. Chang, G.; Spencer, R. H.; Lee, A. T.; Barclay, M. T.; Rees, D. C. Science 1998, 282, 2220-2226.
6. Popot, J. L.; Engelman, D. M. Biochem 1990, 29, 4031-4037.
7. Lamb, R. A.; Pinto, L. H. Virol 1997, 229, 1-24.
8. Sansom, M. S. P.; Forrest, L. R.; Bull, R. Bioessays 1998, 20, 992-1000.
9. Kovacs, F. A.; Song, Z.; Wang, J.; Cross, T. A. Biophys J 1999, 76, A126.
10. Kukol, A.; Adams, P. D.; Rice, L. M.; Brünger, A. T.; Arkin, I. T. J Mol Biol 1999, 286, 951-962.
11. Sansom, M. S. P. Curr Opin Struct Biol 1998, 8, 237-244.
12. Duff, K. C.; Ashley, R. H. Virol 1992, 190, 485-489.
13. Duff, K. C.; Kelly, S. M.; Price, N. C.; Bradshaw, J. P. FEBS Lett 1992, 311, 256-258.
14. Duff, K. C.; Gilchrist, P. J.; Saxena, A. M.; Bradshaw, J. P. Virol 1994, 202, 287-293.
15. Sansom, M. S. P. Prog Biophys Mol Biol 1991, 55, 139-236.
16. Pinto, L. H.; Holsinger, L. J.; Lamb, R. A. Cell 1992, 69, 517-528.
17. Chizhmakov, I. V.; Geraghty, F. M.; Ogden, D. C.; Hayhurst, A.; Antoniou, M.; Hay, A. J. J Physiol 1996, 494, 329-336.
18. Shimbo, K.; Brassard, D. L.; Lamb, R. A.; Pinto, L. H. Biophys J 1996, 70, 1335-1346.
19. Hay, A. J.; Wolstenholme, A. J.; Skehel, J. J.; Smith, M. H. EMBO J 1985, 4, 3021-3024.
20. Wang, C.; Takeuchi, K.; Pinto, L. H.; Lamb, R. A. J Virol 1993, 67, 5585-5594.
21. Brassard, D. L.; Leser, G. P.; Lamb, R. A. Virol 1996, 220, 350-360.
22. Pekosz, A.; Lamb, R. A. Virol 1997, 237, 439-451.
23. Hongo, S.; Sugawara, K.; Muraki, Y.; Matsuzaki, Y.; Takashita, E.; Kitame, F.; Nakamura, K. J Virol 1999, 73, 46-50.
24. Betakova, T.; Nermut, M.; Hay, A. J Gen Virol 1996, 77, 2689-2694.
25. Hongo, S.; Sugawara, K.; Muraki, Y.; Kitame, F.; Nakamura, K. J Virol 1997, 71, 2786-2792.
26. Sunstrom, N. A.; Prekumar, L. S.; Prekumar, A.; Ewart, G.; Cox, G. B.; Gage, P. W. J Memb Biol 1996, 150, 127-132.
27. Chizhmakov, I.; Ogden, D.; Betakova, T.; Phillips, A.; Hay, A. Biophys J 1998, 74, A319.
28. Maldarelli, F.; Chen, M. Y.; Willey, R. L.; Strebel, K. J Virol 1993, 67, 5056-5061.
29. Schubert, U.; Bour, S.; Ferrer-Montiel, A. V.; Montal, M.; Maldarelli, F.; Strebel, K. J Virol 1996, 70, 809-819.
30. Paul, M.; Mazumder, S.; Raja, N.; Jabbar, M. A. J Virol 1998, 72, 1270-1279.
31. Friborg, J.; Ladha, A.; Goettlinger, H.; Haseltine, W. A.; Cohen, E. A. J AIDS Hum Retroviruses 1995, 8, 10-22.
32. Schubert, U.; Strebel, K. J Virol 1994, 68, 2260-2271.
33. Ewart, G. D.; Sutherland, T.; Gage, P. W.; Cox, G. B. J Virol 1996, 70, 7108-7115.
34. Schubert, U.; Ferrer-Montiel, A. V.; Oblatt-Montal, M.; Henklein, P.; Strebel, K.; Montal, M. FEBS Lett 1996, 398, 12-18.
35. Coady, M. J.; Daniel, N. G.; Tiganos, E.; Allain, B.; Friborg, J.; Lapointe, J. Y.; Cohen, E. A. Virol 1998, 244, 39-49.
36. Forrest, L. R.; Tieleman, D. P.; Sansom, M. S. P. Biophys J 1999, 76, 1886-1896.
37. Daura, X.; Jaun, B.; Seebach, D.; van Gunsteren, W. F.; Mark, A. E. J Mol Biol 1998, 280, 925-932.
38. Duan, Y.; Kollman, P. A. Science 1998, 282, 740-744.
39. Jones, D. T.; Taylor, W. R.; Thornton, J. M. Biochem 1994, 33, 3038-3049.
40. Cserzo, M.; Bernassau, J.-M.; Simon, I.; Maigret, B. J Mol Biol 1994, 243, 388-396.
41. Persson, B.; Argos, P. J Mol Biol 1994, 237, 182-192.
42. von Heijne, G. V. J Mol Biol 1992, 225, 487-494.
43. Rost, B.; Fariselli, P.; Casadio, R. Prot Sci 1996, 5, 1704-1718.
44. Brünger, A. T. X-PLOR Version 3.1. A System for X-ray Crystallography and NMR. (Yale Univ Press, CT), 1992.
45. Kerr, I. D.; Sankararamakrishnan, R.; Smart, O. S.; Sansom, M. S. P. Biophys J 1994, 67, 1501-1515.
46. Tieleman, D. P.; Sansom, M. S. P.; Berendsen, H. J. C. Biophys J 1999, 76, 40-49.
47. Kabsch, W.; Sander, C. Biopoly 1983, 22, 2577-2637.
48. Woolf, T. B. Biophys J 1996, 70, A377.
49. Li, S. C.; Deber, C. M. FEBS Lett 1992, 311, 217-220.
50. Hayward, S.; Berendsen, H. J. C. Proteins: Struc Func Genet 1998, 30, 144-154.
51. Deber, C. M.; Li, S.-C. Biopoly 1995, 37, 295-318.
52. Koshi, J. M.; Bruno, W. J. Proteins: Struct Func Genet 1999, 34, 333-340.
53. de Planque, M. R. R.; Greathouse, D. V.; Koeppe II, R. E.; Schaefer, H.; Marsh, D.; Killian, J. A. Biochem 1998, 37, 9333-9345.
54. Webb, R. J.; East, J. M.; Sharma, R. P.; Lee, A. J. Biochem 1998, 37, 673-679.
55. Mouritsen, O. G.; Bloom, M. Ann Rev Biophys Biomol Struct 1993, 22, 145-171.
56. Kabsch, W.; Sander, C. Biopoly 1983, 22, 2577-2637.