Molecular dynamics simulation of conformational flexibility of alamethicin fragments in aqueous and membranous environment

Journal of Biomolecular Structure and Dynamics

Volumn 14, Issue 3, 1996, Pages 303-316

  Kothekar, V ^a   Mahajan, K ^a   Raha, K ^a   Gupta, D ^a  

^a ALL INDIA INSTITUTE OF MEDICAL SCIENCES   (India)

Author keywords

[No Author keywords available]

Indexed keywords

ALAMETHICIN;

AMINO ACID SEQUENCE; ARTICLE; CHANNEL GATING; CRYSTAL STRUCTURE; LIPID BILAYER; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; PRIORITY JOURNAL; PROTEIN CONFORMATION;

EID: 0030463441     PISSN: 07391102     EISSN: 15380254     Source Type: Journal    
DOI: 10.1080/07391102.1996.10508126     Document Type: Article

References (70)

1. Payne, J. W., Jakes, R., and Hartley, B. S., 1970. Biochem. J., 117:757–766.
2. Mueller, P., and Rudin, D. O., 1968. Nature, 217:713–719.
3. Gisin, B. F., Kobayashi, S., Davis, D. G., and Hall, J. E., 1977. Proc. 5th Am. Peptide Symp. Edited by:Goodman, E. D., and Meienhojer, M., 215–218. (Wiley New York)
4. Pandey, R. C., Cook, J. C., and Rinehart, K. L.J., 1977. Am. Chem. Soc., 99:8469–8483.
5. Eisenberg, M., Hall, J. E., and Mead, C. A., 1973. J. Membrane Biol., 14:143–176.
6. Gordon, L. G.M., and Hayden, D. A., 1975. Phil, Trans. R. Soc., B270:433–447.
7. Bohein, G., and Kolb, H. A., 1978. J. Membrane Biol., 38:99–150.
8. Latorre, R., and Donovan, J. J., 1980. Acta. Physiol. Scand. Suppl., 481:37–45.
9. Gordon, L. G.M., and Haydon, D. A., 1972. Biochem. Biophys. Acta., 255:1014–1018.
10. Boheim, G., 1974. J. Membrane Biol., 19:277–303.
11. Ritov, V. B., Murzakhmetova, M. K., Tverdislova, I. L., Menshikova, E. V., Butylin, A. A., Avakian, T. Yu, and Yakovenko, L. V., 1993. Biochem. Biophy. Acta., 1148:257–262.
12. Sethi, R., Dhalla, K. S., Shali, K. R., and Dhalla, N. S., 1993. Mol. Cell Biochem., 119:199–203.
13. Martin, D. R., and Williams, R. J.P., 1976. Biochem. J., 153:181–190.
14. Rinehart, K. L., Jr., Cook, J. C., Jr., Meng, H., Olson, K. L., and Pandey, R. C., 1977. Nature (London), 269:832–833.
15. Marshall, G. R., and Bosshard, H. E., 1972. Circ. Res. Suppl. 30th and 31st,:143–150.
16. Shamala, N., Nagaraj, R., and Balaram, P., 1977. Biochem. et Biophy. Res. Commun., 79:292–298.
17. Shamala, N., Nagaraj, R., and Balaram, P., 1978. J. Chem. Soc.,:996–997. Chem. Commun
18. Venkataramprasad, B. V., Shamala, N., Nagaraj, R., Chandrasekharan, R., and Balaram, P., 1979. Biopolymers, 18:1635–1646.
19. Turk, J., Neddleman, P., and Marshall, G. R., 1976. Mol. Pharmacol., 12:217–224.
20. Smith, G. D., Pletev, V. Z., Duax, W. L., Balasubramanian, T. M., Bosshord, H. L., Czerwinski, E. W., Kendrick, N. E., Mathews, F. S., and Marshall, G. R., 1981. J. Am. Chem. Soc., 103:1493–1501.
21. Butters, T., 1981. Angew Chem., 93:904–905.
22. McMullen, A. I., Mariborough, D. I., and Bayley, P. M., 1971. FEBS Lett., 16:278–280.
23. Jung, G., Dubishar, N., and Leibfritz, D., 1975. Eur. J. Biochem., 54:395–409.
24. Fox, R. O., and Richards, F. M., 1982. Nature (London), 300:325–330.
25. Nikiforvich, G. V. 1992. Int. J. Pept. & Protein Res., 44:513–531.
26. White, S. H., and Wimley, W. C., 1994. Curr. Opin. Struct. Biol., 4:79–86.
27. Kaiser, E. T., and Kezdy, F. J., 1983. Proc. Natl. Acad. Sci. USA., 80:1137–1143.
28. Kaiser, E. T., and Kezdy, F. J., 1987. Annual Review of Biophys. Chem., 16:561–581.
29. Jacob, R. E., and White, S. H., 1987. Biochemistry, 25:2605–2612. 26, 6127–6134 (1986
30. Brown, J. W., and Huestis, W. H., 1993. J. Phys. Chem., 97:2967–2973.
31. Reynaud, J. A., Grivet, J. P., and Trudelle, Y., 1993. Biochemistry, 32:4997–5008.
32. Schwyzer, R., Erne, D., and Rolka, K., 1986. Helv. Chim. Acta., 69:1789–1797.
33. Erne, D., Rolka, K., and Schwyzer, R., 1986. Helv. Chim. Acta., 69:1807–1816.
34. Chassaing, G., Convert, O., and Lavielle, S., 1986. Eur J. Biochem., 154:77–85.
35. Woolley, G. A., and Deber, C. M., 1987. Biopolymers, 26:S109–S121.
36. Sumner, S. C.J., Gallagher, K. S., Davis, D. G., Covell;, D. G., Jemigan, R. L., and Ferretti, J. A., 1990. J. Biomol. Struct. & Dynamics, 8:687–707.
37. Herbette, L. G., Trumbore, M., Chester, D. W., and Katz, A. M., 1988. J. Mol. Cell. Cardiol., 20:273–278.
38. Mason, R. P., and Chester, D. W., 1989. Biophys. J., 56:1193–1201.
39. Herbette, l. G., Vant Erve, Y. M.H., and Rohdes, D. G., 1989. J. Mol. Cell. Cardiol., 21:187–201.
40. Mason, P. R., Moring, J., and Herbette, L. G., 1990. Nucl. Med. Biol., 17:13–33.
41. Bauerle, H. D., and Seelig, J., 1991. Biochem., 30:7203–7211.
42. Egberts, S., and Berendsen, H. J.C., (Private communication)
43. Essex;, J. W., Hann, M. M., and Richards, W. G., 1994. Phil-Trans. R. Soc. Lond., B344:239–260.
44. Robinson, A. J., Richards, W. G., Thomas, P. J., and Hann, M. M., 1994. Biophys. J., 67:2345–2354.
45. Damodaran, K. V., and Merz, K. M., 1994. Biophys. J., 66:1076–1087.
46. Huang, P., Perez, J. J., and Loew, G. H., 1994. J. Biomol. Struct. & Dynamics, 11:927–955.
47. Huang, P., and Loew, G. H., 1995. J. Biomol. Struct. & Dynamics, 12:937–955.
48. Damodaran, K. V., Merz, K. M., and Gaber, B. P., 1995. Biophys. J., 69:1299–1308.
49. Damodaran, K. V., and Merz, K. M., 1995. J. Am. Chem. Soc., 117:6561–6571.
50. Kothekar, V., 1996. J. Biomole. Struct. & Dynamics, 13:601–613.
51. Bassolino-Klimas, D., Alper, H. E., and Stouch, T. R., 1993. Biochem., 32:12624–12637.
52. Alper, H. E., and Stouch, T. R., 1995. J. Phys. Chem., 99:5724–5731.
53. Huang, P., Bertaccini, E. D., and Loew, G. H., 1995. J. Biomol. Struct. & Dynamics, 12:725–754.
54. Robinson, A. J., Richards, W. G., Thomas, P. J., and Hann, M. M., 1995. Biophys. J., 66:164–170.
55. Woolf, T. B., and Roux, B., 1994. Proc. Natl. Acad. Sci. USA, 91:11631–11635.
56. Pearlman, D. A., Case, D. A., Caldwell, J. C., Seibel, G. L., Singh, U. C., Weiner, P., and Kollman, P. A., 1993. AMBER 4.0 UCFS version
57. Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W., and Klein, M. L., 1983. J. Chem. Phys., 79:926–935.
58. Sundaralingam, M., 1972. Ann. N. Y. Acad. Sci. USA, 195:324–355.
59. Pearson, R. H., and Pascher, I., 1979. Nature (Lond), 281:499–501.
60. Mrigank, Royyuru, A. K., and Kothekar, V., 1986. FEBS Lett., 195:203–207.
61. De Young, L. R., and Dill, K. A., 1988. Biochemistry, 27:5281–5289.
62. Lewis, B. A., and Engelman, D. M., 1983. J. Molec. Biol., 166:211–217.
63. Kothekar, V., Biosciences (in Press)
64. Pople, J. A., Santry, D. P., and Segal, G. A., 1965. J. Chem. Phys., 43:129–135.
65. Weiner, S. J., Kollman, P. A., Case, D. A., Chandra Singh, U., Ghio, C., Alagona, G., Profeta, S., and Weiner, P. J., 1984. J. Am. Chem. Soc., 106:765–784.
66. Seelig, A., and Seelig, J., 1974. Biochem., 13:4839–4845.
67. Oldfield, E., Meadows, M., Rice, D., and Jacob, R., 1978. Biochem., 17:2727–2740.
68. Meier, P., Ohmes, E., Kothe, G, Blume, A., Weldner, J., and Eibl, H. J., 1983. J. Phys. Chem., 87:4904–4912.
69. De Loof, H., Harvey, S. C., Segrest, J. P., and Pastor, R. W., 1991. Biochem., 30:2099–2113.
70. Kothekar, V., and Kotwal, A., 1992. Ind. J. Biochem. & Biophys., 29:322–329.