The conformational transition pathway of ATP binding cassette transporter MsbA revealed by atomistic simulations

Journal of Biological Chemistry

Volumn 285, Issue 5, 2010, Pages 3053-3063

  Weng, Jing Wei ^a   Fan, Kang Nian ^a   Wang, Wen Ning ^a  

^a FUDAN UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ATOMISTIC SIMULATIONS; ATP BINDING CASSETTE TRANSPORTERS; ATP HYDROLYSIS; CONFORMATIONAL CHANGE; CONFORMATIONAL CONVERSION; CONFORMATIONAL TRANSITION PATHWAY; CONFORMATIONAL TRANSITIONS; DIMER INTERFACE; GRAM-NEGATIVE BACTERIA; INTEGRAL MEMBRANE PROTEINS; INTERACTION NETWORKS; MOLECULAR DYNAMICS TRAJECTORIES; MULTIDRUG-RESISTANCE ATP-BINDING CASSETTES; NUCLEOTIDE-BINDING DOMAIN; NUCLEOTIDE-BINDING SITES; SPATIOTEMPORAL ORDER; SUBSTRATE-BINDING SITES; TARGETED MOLECULAR DYNAMICS; TRANS-MEMBRANE DOMAINS; TRANSMEMBRANE HELICES;

ACTIVATION ANALYSIS; ADENOSINETRIPHOSPHATE; BACTERIA; BINDING ENERGY; BIOCHEMISTRY; BIOLOGICAL MEMBRANES; CELL MEMBRANES; CYTOLOGY; FACINGS; HYDROLYSIS; MOLECULAR DYNAMICS; NUCLEOTIDES; PROTEINS; SUBSTRATES;

BINDING SITES;

ABC TRANSPORTER; ABC TRANSPORTER MSB; ADENOSINE TRIPHOSPHATE; UNCLASSIFIED DRUG; BACTERIAL PROTEIN; MSBA PROTEIN, BACTERIA;

ARTICLE; BINDING SITE; BIOTRANSFORMATION; CONFORMATIONAL TRANSITION; CONSERVATION GENETICS; CYTOPLASM; DIMERIZATION; GENE REARRANGEMENT; HYDROLYSIS; MOLECULAR DYNAMICS; NUCLEOTIDE BINDING SITE; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FUNCTION; PROTEIN INTERACTION; SIGNAL TRANSDUCTION; SIMULATION; STRUCTURE ANALYSIS; TRIPLE HELIX; CELL MEMBRANE; CHEMISTRY; COMPUTER SIMULATION; CONFORMATION; LIPID BILAYER; METABOLISM; PROTEIN CONFORMATION; PROTEIN SECONDARY STRUCTURE; SALMONELLA TYPHIMURIUM; STATIC ELECTRICITY;

NEGIBACTERIA;

ADENOSINE TRIPHOSPHATE; ALLOSTERIC SITE; ATP-BINDING CASSETTE TRANSPORTERS; BACTERIAL PROTEINS; CELL MEMBRANE; COMPUTER SIMULATION; CYTOPLASM; DIMERIZATION; HYDROLYSIS; LIPID BILAYERS; MOLECULAR CONFORMATION; PROTEIN CONFORMATION; PROTEIN STRUCTURE, SECONDARY; SALMONELLA TYPHIMURIUM; STATIC ELECTRICITY;

EID: 77449137874     PISSN: 00219258     EISSN: 1083351X     Source Type: Journal    
DOI: 10.1074/jbc.M109.056432     Document Type: Article

References (64)

1. Dean, M., and Allikmets, R. (2001) J. Bioenerg. Biomembr. 33, 475-479
2. Hughes, A. L. (1994) Mol. Biol. Evol. 11, 899-910
3. Ling, V. (1992) Cancer 69, 2603-2609
4. Raviv, Y., Pollard, H. B., Bruggemann, E. P., Pastan, I., and Gottesman, M. M. (1990) J. Biol. Chem. 265, 3975-3980
5. Davidson, A. L., and Chen, J. (2004) Annu. Rev. Biochem. 73, 241-268
6. Jones, P. M., and George, A. M. (2004) Cell. Mol. Life Sci. 61, 682-699
7. van der Does, C., and Tampé, R. (2004) Biol. Chem. 385, 927-933
8. Aller, S. G., Yu, J., Ward, A., Weng, Y., Chittaboina, S., Zhuo, R., Harrell, P. M., Trinh, Y. T., Zhang, Q., Urbatsch, I. L., and Chang, G. (2009) Science 323, 1718-1722
9. Gerber, S., Comellas-Bigler, M., Goetz, B. A., and Locher, K. P. (2008) Science 321, 246-250
10. Hollenstein, K., Frei, D. C., and Locher, K. P. (2007) Nature 446, 213-216
11. Khare, D., Oldham, M. L., Orelle, C., Davidson, A. L., and Chen, J. (2009) Mol. Cell 33, 528-536
12. Pinkett, H. W., Lee, A. T., Lum, P., Locher, K. P., and Rees, D. C. (2007) Science 315, 373-377
13. Kadaba, N. S., Kaiser, J. T., Johnson, E., Lee, A., and Rees, D. C. (2008) Science 321, 250-253
14. Dawson, R. J., and Locher, K. P. (2006) Nature 443, 180-185
15. Locher, K. P., Lee, A. T., and Rees, D. C. (2002) Science 296, 1091-1098
16. Oldham, M. L., Khare, D., Quiocho, F. A., Davidson, A. L., and Chen, J. (2007) Nature 450, 515-521
17. Hollenstein, K., Dawson, R. J., and Locher, K. P. (2007) Curr. Opin. Struct. Biol. 17, 412-418
18. Moussatova, A., Kandt, C., O'Mara, M. L., and Tieleman, D. P. (2008) Biochim. Biophys. Acta 1778, 1757-1771
19. Oldham, M. L., Davidson, A. L., and Chen, J. (2008) Curr. Opin. Struct. Biol. 18, 726-733
20. Chen, J., Lu, G., Lin, J., Davidson, A. L., and Quiocho, F. A. (2003) Mol. Cell 12, 651-661
21. Smith, P. C., Karpowich, N., Millen, L., Moody, J. E., Rosen, J., Thomas, P. J., and Hunt, J. F. (2002) Mol. Cell 10, 139-149
22. Verdon, G., Albers, S. V., van Oosterwijk, N., Dijkstra, B. W., Driessen, A. J., and Thunnissen, A. M. (2003) J. Mol. Biol. 334, 255-267
23. Zaitseva, J., Jenewein, S., Jumpertz, T., Holland, I. B., and Schmitt, L. (2005) EMBO J. 24, 1901-1910
24. Lu, G., Westbrooks, J. M., Davidson, A. L., and Chen, J. (2005) Proc. Natl. Acad. Sci. U.S.A. 102, 17969-17974
25. Zaitseva, J., Oswald, C., Jumpertz, T., Jenewein, S., Wiedenmann, A., Holland, I. B., and Schmitt, L. (2006) EMBO J. 25, 3432-3443
26. Zhou, Z., White, K. A., Polissi, A., Georgopoulos, C., and Raetz, C. R. (1998) J. Biol. Chem. 273, 12466-12475
27. Woebking, B., Reuter, G., Shilling, R. A., Velamakanni, S., Shahi, S., Venter, H., Balakrishnan, L., and van Veen, H. W. (2005) J. Bacteriol. 187, 6363-6369
28. Reuter, G., Janvilisri, T., Venter, H., Shahi, S., Balakrishnan, L., and van Veen, H. W. (2003) J. Biol. Chem. 278, 35193-35198
29. Doerrler, W. T., Gibbons, H. S., and Raetz, C. R. H. (2004) J. Biol. Chem. 279, 45102-45109
30. Smriti, Zou, P., and McHaourab, H. S. (2009) J. Biol. Chem. 284, 13904-13913
31. Borbat, P. P., Surendhran, K., Bortolus, M., Zou, P., Freed, J. H., and Mc-Haourab, H. S. (2007) PLoS Biol. 5, e271
32. Buchaklian, A. H., Funk, A. L., and Klug, C. S. (2004) Biochemistry 43, 8600-8606
33. Buchaklian, A. H., and Klug, C. S. (2006) Biochemistry 45, 12539-12546
34. Dong, J., Yang, G., and McHaourab, H. S. (2005) Science 308, 1023-1028
35. Ward, A., Reyes, C. L., Yu, J., Roth, C. B., and Chang, G. (2007) Proc. Natl. Acad. Sci. U.S.A. 104, 19005-19010
36. Jones, P. M., and George, A. M. (2007) J. Biol. Chem. 282, 22793-22803
37. Wen, P. C., and Tajkhorshid, E. (2008) Biophys. J. 95, 5100-5110
38. Sonne, J., Kandt, C., Peters, G. H., Hansen, F. Y., Jensen, M. Ø., and Tieleman, D. P. (2007) Biophys. J. 92, 2727-2734
39. Cheng, X. L., Wang, H. L., Grant, B., Sine, S. M., and McCammon, J. A. (2006) PLoS Comput. Biol. 2, e134
40. Compoint, M., Picaud, F., Ramseyer, C., and Girardet, C. (2005) J. Chem. Phys. 122, 134707
41. Kong, Y., Shen, Y., Warth, T. E., and Ma, J. (2002) Proc. Natl. Acad. Sci. U.S.A. 99, 5999-6004
42. Ma, J., and Karplus, M. (1997) Proc. Natl. Acad. Sci. U.S.A. 94, 11905-11910
43. van der Vaart, A., Ma, J., and Karplus, M. (2004) Biophys. J. 87, 562-573
44. Phillips, J. C., Braun, R., Wang, W., Gumbart, J., Tajkhorshid, E., Villa, E., Chipot, C., Skeel, R. D., Kalé, L., and Schulten, K. (2005) J. Comput. Chem. 26, 1781-1802
45. MacKerell, A. D., Jr., Feig, M., and Brooks, C. L., 3rd (2004) J. Am. Chem. Soc. 126, 698-699
46. Feller, S. E., Zhang, Y. H., Pastor, R. W., and Brooks, B. R. (1995) J. Chem. Phys. 103, 4613-4621
47. Martyna, G. J., Tobias, D. J., and Klein, M. L. (1994) J. Chem. Phys. 101, 4177-4189
48. Humphrey, W., Dalke, A., and Schulten, K. (1996) J. Mol. Graph 14, 33-38
49. Kandt, C., Ash, W. L., and Tieleman, D. P. (2007) Methods 41, 475-488
50. Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W., and Klein, M. L. (1983) J. Chem. Phys. 79, 926-935
51. Ryckaert, J. P., Ciccotti, G., and Berendsen, H. J. C. (1977) J. Comput. Phys. 23, 327-341
52. Schlitter, J., Engels, M., Kruger, P., Jacoby, E., and Wollmer, A. (1993) Mol. Simul. 10, 291-308
53. Westfahl, K. M., Merten, J. A., Buchaklian, A. H., and Klug, C. S. (2008) Biochemistry 47, 13878-13886
54. Oancea, G., O'Mara, M. L., Bennett, W. F.., Tieleman, D. P., Abele, R., and Tampé, R. (2009) Proc. Natl. Acad. Sci. U.S.A. 106, 5551-5556
55. Doyle, D. A. (2004) Trends Neurosci. 27, 298-302
56. Grottesi, A., Domene, C., Hall, B., and Sansom, M. S. P. (2005) Biochemistry 44, 14586-14594
57. Law, R. J., Tieleman, D. P., and Sansom, M. S. P. (2003) Biophys. J. 84, 14-27
58. Sansom, M. S., and Weinstein, H. (2000) Trends Pharmacol. Sci. 21, 445-451
59. Choe, S., and Sun, S. X. (2005) J. Chem. Phys. 122, 244912
60. Huang, H., Ozkirimli, E., and Post, C. B. (2009) J. Chem. Theory Comput. 5, 1304-1314
61. Apostolakis, J., Ferrara, P., and Caflisch, A. (1999) J. Chem. Phys. 110, 2099-2108
62. Law, R. J., Munson, K., Sachs, G., and Lightstone, F. C. (2008) Biophys. J. 95, 2739-2749
63. Marco, E., Foucaud, M., Langer, I., Escrieut, C., Tikhonova, I. G., and Fourmy, D. (2007) J. Biol. Chem. 282, 28779-28790
64. Swift, R. V., and McCammon, J. A. (2008) Biochemistry 47, 4102-4111