Iron(II) triggered conformational changes in Escherichia coli fur upon DNA binding: a study using molecular modeling

Journal of Molecular Graphics and Modelling

Volumn 25, Issue 2, 2006, Pages 234-246

  Hamed, Mazen Y ^a   Al jabour, Salih ^a  

^a BIRZEIT UNIVERSITY   (Palestine)

Author keywords

Corepressor; DNA; Ferric; Protein; Regulation; Repressor; Uptake

Indexed keywords

COREPRESSOR; ENERGY MINIMIZATION; HOMOLOGY MODELING; MOLECULAR MODELING; REPRESSOR;

CONCENTRATION (PROCESS); DIMERS; DNA; HYDROPHOBICITY; IRON; MOLECULAR DYNAMICS; PROTEINS;

BACTERIA;

DNA; FERROUS ION; FUR PROTEIN; HELIX LOOP HELIX PROTEIN; REPRESSOR PROTEIN; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ARTICLE; AT RICH SEQUENCE; CONFORMATIONAL TRANSITION; DIMERIZATION; ESCHERICHIA COLI; MOLECULAR MODEL; NONHUMAN; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PRIORITY JOURNAL; PROTEIN DNA BINDING; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE; PSEUDOMONAS AERUGINOSA; RHIZOBIUM LEGUMINOSARUM; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY;

AMINO ACID SEQUENCE; BACTERIAL PROTEINS; COMPUTER SIMULATION; DIMERIZATION; DNA, BACTERIAL; DNA-BINDING PROTEINS; HELIX-TURN-HELIX MOTIFS; IRON; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN STRUCTURE, SECONDARY; REPRESSOR PROTEINS; SEQUENCE HOMOLOGY, AMINO ACID;

ESCHERICHIA COLI;

EID: 33748426375     PISSN: 10933263     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmgm.2005.12.010     Document Type: Article

References (47)

1. Bagg A., and Neilands J.B. Biochemistry 26 (1987) 5471-5477
2. Escolar L., Perez-Martin J., and de Lorenzo V. J. Mol. Biol. 283 3 (1998) 537-547
3. Hamed Y.M. J. Inorg. Biochem. 51 594 (1993) 1-2
4. Hamed M.Y., and Neilands J.B. J. Inorg. Biochem. 53 4 (1994) 235-248
5. Hamed M.Y., Neilands J.B., and Huynh V. J. Inorg. Biochem. 50 3 (1993) 193-210
6. Coy M., Doyle C., Besser J., and Neilands B.J. BioMetals 7 (1993) 292-298
7. Jacquament L., Dole F., Jeandey C., Oddou J.L., Perret E., La Pape L., Aberdam D., Hazemann J.L., Michaud-Soret I., and Latour J.M. J. Am. Chem. Soc. 122 (2000) 394-395
8. Neilands J.B. Can. J. Microbiol. 38 7 (1992) 728-733
9. Le Cam E., Frechon D., Barray M., Fourcade A., and Delain E. Proc. Natl Acad. Sci. U.S.A. 91 25 (1994) 11816-11820
10. Frechon D., and Le Cam E. Biochem. Biophys. Res. Commun. 201 1 (1994) 346-355
11. Coy M. Biochem. Biophys. Res. Commun. 212 3 (1995) 784-792
12. Coy M., and Neilands J.B. Biochemistry 30 33 (1991) 8201-8210
13. Saito T., and Williams R.J.P. Eur. J. Biochem. 197 (1991) 43-47
14. Saito T., Womlad M.R., and Williams R.J.P. Eur. J. Biochem. 197 (1991) 29-39
15. Saito T., Williams R.J.P., and Duly D. Eur. J. Biochem. 197 (1991) 39-42
16. Kolade O.O., Bellini P., Wexler M., Johnston A.W.B., Grossmann J.G., and Hemmings A.M. Biometals 30 4 (2002) 771-774
17. Pohl E., Haller J.C., Mijovilovich A., Meyer-Klaucke W., German E., and Vesil M.L. Mol. Microbiol. 47 4 (2003) 903-915
18. Jacquamet L., Aberdam D., Adrait A., Hazemann J.L., Latour J.M., and Michaud-Soret I. Biochemistry 37 (1998) 2564-2571
19. Zheleznova E.E., Crosa J.H., and Brennan R.G. J. Bacteriol. 182 21 (2000) 6264-6267
20. Schmitt M.P., Twiddy E.M., and Holmes R.K. Proc. Natl. Acad. Sci. USA. 89 10 (1992) 7576-7580
21. Reidhaar-Olsin J.F., and Sauer R.T. Proteins: Struct. Funct. Genet. 7 (1990) 306-316
22. Qiu X., Verlinde C.L.M.J., Zhang S., Schmitt M.P., Holmes R.K., and Hol W.G.J. Structure 3 1 (1995) 87-100
23. Jacquamet L., Dole F., Jeandey C., Oddou J.L., Perret E., Le Pape L., Aberdam D., Hazemann J.L., Michaud-Soret I., and Latour J.M. J. Am. Chem. Soc. 122 (2000) 394-395
24. Wisedchaisri G., Holmes R.K., and Hol W.G.J. J. Mol. Biol. 342 4 (2004) 1155-1169
25. Brennan R.G., and Matthews B.W. TIBS 80 (1988) 6513-6517
26. Barondeau D., and Getzoff E.D. Curr. Opin. Struct. Biol. 14 6 (2004) 765-774
27. Case D.A., Pearlman D.A., Caldwell J.W., Cheatham III T.E., Wang J., Ross W.S., Simmerling C.L., Darden T.A., Merz K.M., Stanton R.V., Cheng A.L., Vencent J.J., Crowley M., Tsui V., Gohlke H., Radmer R.J., Duan Y., Pitera J., Massova I., Seibel G.L., Singh U.C., Weiner P.K., and Kollman P.A. Amber, 7 (2002), University of California, San Francisco
28. Pearlman D.A., Case D.A., Caldwell J.W., Ross W.R., Cheatham T.E., DeBolt I.I.I.S., Ferguson D., Seibel G., and Kollman P. Comp. Phys. Commun. 91 (1995) 1-41
29. DeLano W.L. The PyMol Molecular Graphics System on the World Wide Web (2002)
30. Torsten S., Jürgen K., Nicolas G., and Manuel C.P. SWISS-MODEL: an automated protein homology-modeling server. Nucleic Acids Res. 31 13 (2003) 3381-3385
31. Kelley L.A., MacCallum R.M., and Sternberg M.J.E. Enhanced genome annotation using structural profiles in the program 3D-PSSM. J. Mol. Biol. 299 2 (2000) 501-522
32. M.M. Garrett, S.G. David, H. Ruth, E.H. William, H. Scott, B. Rik, J.O. Arthur, Automated docking of flexible ligands to receptors (Autodock). Molecular Graphics Laboratory, Department of Molecular Biology, 10550 North Torrey Pines Road, La Jolla, CA (2002) 92037-1000, Version 3.0.5.
33. Zheleznova E.E., Crosa J.H., and Brennan R.G. J. Bacteriol. 182 21 (2000) 6264-6267
34. Althaus E.W., Outten C.E., Olson K.E., Cao H., and O'Halloran T.V. Biochemistry 38 (1999) 6559-6569
35. Lesser G.J., and Rose G.D. Proteins: Struct. Funct. Genet. 8 (1990) 6-13
36. Schiffer C.a., Calwell J.W., Kollman P.A., and Stroud R.M. Proteins: Struct. Funct. Genet. 8 (1990) 30-43
37. Akke M., and Forsen S. Proteins: Struct. Funct. Genet. 8 (1990) 23-29
38. De Peredo A.G., Saint-Pierre C., Latour J.M., Michaud-Soret I., and Forest E. J. Mol. Biol. 310 (2001) 83-91
39. Fuangthong M., and Helmann J.D. Am. Soc. Microbiol. 185 21 (2003) 6348-6357
40. Huffman J.L., and Brennan R.G. Curr. Opin. Struct. Biol. 12 1 (2002) 98-106
41. Lavrrar J.L., Christoffersen C.A., and McIontosh M.A. J. Mol. Biol. 322 (2002) 983-995
42. de-Lorenzo V., Giovannini F., Herrero M., and Neilands J.B. J. Mol. Biol. 203 (1987) 875-884
43. Bsat N., and Helmann J.D. J. Bacteriol. 181 14 (1999) 4299-4307
44. Escolar L., Perez-Martin J., and de Lorenzo V. J. Bacteriol. 181 20 (1999) 6223-6229
45. Adrait A., Jacquamet L., Le Pape L., de Peredo A.G., Aberdam D., Hazemann J.L., Latour J.M., and Michaud-Soret I. Biochemistry 38 (1999) 6248-6260
46. Baichoo N., and Helmann J.D. J. Bacteriol. 184 21 (2002) 5826-5832
47. Ouali M., and King R.D. Cascaded multiple classifiers for secondary structure prediction. Prot. Sci. 9 (2000) 1162-1176