Interdomain flexibility and pH-induced conformational changes of AcrA revealed by molecular dynamics simulations

Journal of Physical Chemistry B

Volumn 116, Issue 10, 2012, Pages 3411-3420

  Wang, Beibei ^a   Weng, Jingwei ^a   Fan, Kangnian ^a   Wang, Wenning ^a  

^a FUDAN UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

CELL MEMBRANES; DRUG INTERACTIONS; DYNAMICS; HYDROGEN BONDS; PH;

ATOMISTIC SIMULATIONS; CONFORMATIONAL CHANGE; CONFORMATIONAL DYNAMICS; CONFORMATIONAL FLEXIBILITY; EFFLUX PUMPS; EPR STUDIES; HOMOLOGY MODELING; HYDROGEN BOND INTERACTION; INNER MEMBRANES; INTER-DOMAIN; MEMBRANE FUSION; MOLECULAR DYNAMICS SIMULATIONS; OUTER MEMBRANE PROTEIN; PERIPLASM; PH VALUE; POINT MUTATIONS;

MOLECULAR DYNAMICS;

EID: 84863391966     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp212221v     Document Type: Article

References (38)

1. Zgurskaya, H. I.; Nikaido, H. Mol. Microbiol. 2000, 37, 219
2. Murakami, S. Curr. Opin. Struct. Biol. 2008, 18, 459
3. Murakami, S.; Nakashima, R.; Yamashita, E.; Matsumoto, T.; Yamaguchi, A. Nature 2006, 443, 173
4. Murakami, S.; Nakashima, R.; Yamashita, E.; Yamaguchi, A. Nature 2002, 419, 587
5. Sennhauser, G.; Amstutz, P.; Briand, C.; Storchenegger, O.; Grutter, M. G. PLoS Biol. 2007, 5, 106
6. Seeger, M. A.; Schiefner, A.; Eicher, T.; Verrey, F.; Diederichs, K.; Pos, K. M. Science 2006, 313, 1295
7. Yu, E. W.; McDermott, G.; Zgurskaya, H. I.; Nikaido, H.; Koshland, D. E. Science 2003, 300, 976
8. Federici, L.; Walas, F.; Luisi, B. Curr. Sci. 2004, 87, 190
9. Koronakis, V.; Eswaran, J.; Hughes, C. Annu. Rev. Biochem. 2004, 73, 467
10. Koronakis, V.; Sharff, A.; Koronakis, E.; Luisi, B.; Hughes, C. Nature 2000, 405, 914
11. Lobedanz, S.; Bokma, E.; Symmons, M. F.; Koronakis, E.; Hughes, C.; Koronakis, V. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 4612
12. Gerken, H.; Misra, R. Mol. Microbiol. 2004, 54, 620
13. Husain, F.; Humbard, M.; Misra, R. J. Bacteriol. 2004, 186, 8533
14. Elkins, C. A.; Nikaido, H. J. Bacteriol. 2003, 185, 5349
15. Ge, Q.; Yamada, Y.; Zgurskaya, H. J. Bacteriol. 2009, 191, 4365
16. Zgurskaya, H. I.; Nikaido, H. J. Mol. Biol. 1999, 285, 409
17. Mikolosko, J.; Bobyk, K.; Zgurskaya, H. I.; Ghosh, P. Structure 2006, 14, 577
18. Symmons, M. F.; Bokma, E.; Koronakis, E.; Hughes, C.; Koronakis, V. Proc. Natl. Acad. Sci. U.S.A. 2009, 106, 7173
19. Tikhonova, E. B.; Zgurskaya, H. I. J. Biol. Chem. 2004, 279, 32116
20. Zgurskaya, H. I.; Nikaido, H. J. Bacteriol. 2000, 182, 4264
21. Bagai, I.; Liu, W.; Rensing, C.; Blackburn, N. J.; McEvoy, M. M. J. Biol. Chem. 2007, 282, 35695
22. Ferguson, K. M.; Lemmon, M. A.; Schlessinger, J.; Sigler, P. B. Cell 1995, 83, 1037
23. Ingelman, M.; Bianchi, V.; Eklund, H. J. Mol. Biol. 1997, 268, 147
24. Borges-Walmsley, M. I.; Beauchamp, J.; Kelly, S. M.; Jumel, K.; Candlish, D.; Harding, S. E.; Price, N. C.; Walmsley, A. R. J. Biol. Chem. 2003, 278, 12903
25. Vaccaro, L.; Koronakis, V.; Sansom, M. S. P. Biophys. J. 2006, 91, 558
26. Ip, H.; Stratton, K.; Zgurskaya, H.; Liu, J. J. Biol. Chem. 2003, 278, 50474
27. Xu, Y.; Lee, M.; Moeller, A.; Song, S.; Yoon, B.-Y.; Kim, H.-M.; Jun, S.-Y.; Lee, K.; Ha, N.-C. J. Biol. Chem. 2011, 286, 17910
28. Tikhonova, E. B.; Yamada, Y.; Zgurskaya, H. I. Chem. Biol. 2011, 18, 454
29. Arnold, K.; Bordoli, L.; Kopp, J.; Schwede, T. Bioinformatics 2006, 22, 195
30. Phillips, J. C.; Braun, R.; Wang, W.; Gumbart, J.; Tajkhorshid, E.; Villa, E.; Chipot, C.; Skeel, R. D.; Kale, L.; Schulten, K. J. Comput. Chem. 2005, 26, 1781
31. MacKerell, A. D.; Feig, M.; Brooks, C. L. J. Am. Chem. Soc. 2004, 126, 698
32. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. J. Chem. Phys. 1983, 79, 926
33. Darden, T.; York, D.; Pedersen, L. J. Chem. Phys. 1993, 98, 10089
34. Humphrey, W.; Dalke, A.; Schulten, K. J. Mol. Graphics 1996, 14, 33
35. Gordon, J. C.; Myers, J. B.; Folta, T.; Shoja, V.; Heath, L. S.; Onufriev, A. Nucleic Acids Res. 2005, 33, W368
36. Daura, X.; Gademann, K.; Jaun, B.; Seebach, D.; van Gunsteren, W. F.; Mark, A. E. Angew. Chem., Int. Ed. 1999, 38, 236
37. Higgins, M. K.; Bokma, E.; Koronakis, E.; Hughes, C.; Koronakis, V. Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 9994
38. Wilks, J. C.; Slonczewski, J. L. J. Bacteriol. 2007, 189, 5601