Probing the binding of the coumarin drugs using peptide fragments of DNA gyrase B protein

Journal of Peptide Research

Volumn 65, Issue 5, 2005, Pages 502-511

  Garrido, S S ^a   Scatigno, A C ^b   Trovatti, E ^a   Carvalho, D C ^a   Marchetto, R ^a  

^a SÃO PAULO STATE UNIVERSITY UNESP   (Brazil)

^b UNIVERSIDADE DO OESTE DE SANTA CATARINA   (Brazil)

Author keywords

Affinity chromatography; Coumarins; DNA gyrase; Fluorescence; Peptide synthesis; Quenching

Indexed keywords

COUMARIN ANTICOAGULANT; DNA TOPOISOMERASE (ATP HYDROLYSING) B; NOVOBIOCIN;

AFFINITY CHROMATOGRAPHY; ARTICLE; BINDING SITE; COMPLEX FORMATION; DNA SUPERCOILING; DRUG BINDING; ENZYME ACTIVITY; ENZYME SUBUNIT; NONPHOTOCHEMICAL QUENCHING; PEPTIDE SYNTHESIS; PRIORITY JOURNAL; PROTEIN BINDING; TARGET CELL;

ADENOSINE TRIPHOSPHATE; AMINO ACID SEQUENCE; ARGININE; BINDING SITES; BINDING, COMPETITIVE; CHROMATOGRAPHY, AFFINITY; COUMARINS; DNA GYRASE; DRUG DESIGN; ESCHERICHIA COLI PROTEINS; MAGNESIUM; MOLECULAR SEQUENCE DATA; NOVOBIOCIN; PEPTIDE FRAGMENTS;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI;

EID: 18344372591     PISSN: 1397002X     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1399-3011.2005.00264.x     Document Type: Article

References (35)

1. Reece, R.J. & Maxwell, A. (1991) DNA gyrase: structure and function. Crit. Rev. Biochem. Mol. Biol. 26, 335-375.
2. Wang, J.C. (1996) DNA topoisomerases. Annu. Rev. Biochem. 54, 665-697.
3. Wigley, D.B. (1995) Structure and mechanism of DNA gyrase. In: Nucleic Acids and Molecular Biology, Vol. 9 (Eckstein, F. & Lilley, D.M.J., eds), pp. 165-176. Springer-Verlag, Heidelberg, Berlin.
4. Reece, R.J. & Maxwell, A. (1989) Tryptic fragments of the Escherichia coli DNA gyrase A protein. J. Biol. Chem. 164, 19648-19653.
5. Reece, R.J. & Maxwell, A. (1991) Probing the limits of the DNA breakage-reunion domain of the Escherichia coli DNA gyrase A protein. J. Biol. Chem. 266, 3540-3546.
6. Wigley, D.B., Davies, G.J., Dodson, E.J., Maxwell, A. & Dodson, G. (1991) Crystal structure of an N-terminal fragment of the DNA gyrase B protein. Nature 351, 624-629.
7. Ali, J.A., Jackson, A.P., Howells, A.J. & Maxwell, A. (1993) The 43-kilodalton N-terminal fragment of DNA gyrase B protein hydrolyses ATP and binds coumarin drugs. Biochemistry 32, 2717-1714.
8. Maxwell, A. (1993) The interaction between coumarin drugs and DNA gyrase. Mol. Microbiol. 9, 681-686.
9. Maxwell, A. (1997) DNA gyrase as a drug target. Trends Microbiol. 5, 102-109.
10. Sugino, A., Higgins, N.P., Brown, P.O., Peebles, C.L. & Cozzarelli, N.R. (1978) Energy coupling in DNA gyrase and the mechanism of action of novobiocin. Proc. Natl Acad. Sci. U S A 75, 4838-4842.
11. Mizuuchi, K., O'Dea, M.H. & Gellert, M. (1978) DNA gyrase: subunit structure and ATPase activity of the purified enzyme. Proc. Natl Acad. Sci. U S A 75, 5960-5963.
12. Gilbert, E.J. & Maxwell, A. (1994) The 24 kDa N-terminal sub-domain of the DNA gyrase B protein binds coumarin drugs. Mol. Microbiol. 12, 365-373.
13. Gormley, N.A., Orphanides, G., Meyer, A., Cullis, P.M. & Maxwell A. (1996) The interaction of coumarin antibiotics with fragments of the DNA gyrase B protein. Biochemistry 35, 5083-5092.
14. 1. Proc. Natl Acad. Sci. USA 88, 8860-8864.
15. Contreras, A. & Maxwell, A. (1992) GyrB mutations which confer coumarin resistance also affect DNA supercoiling and ATP hydrolysis by Escherichia coli DNA gyrase. Mol. Microbiol. 6, 1617-1624.
16. Lewis, R.J., Singh, O.M.P., Smith, C.V., Skarzynski, T., Maxwell, A., Wonacott, A.J. & Wigley, D.B. (1996) The nature of inhibition of DNA gyrase by the coumarins and the cyclothialidines revealed by X-ray crystallography. EMBO J. 15, 1412-1420.
17. Tsai, F.T.F., Singh, O.M.P., Skarzynsky, T., Wonacott, A.J., Weston, S., Tucker, A., Pauptit, R.A., Breeze, A.L., Poyser, J.P., O'Brien, R., Ladbury, J.E. & Wigley, D.B. (1997) The high-resolution crystal structure of a 24-kDa gyrase B fragment from E. coli complexed with one of the most potent coumarin inhibitors, clorobiocin. Proteins 28, 41-51.
18. Holdgate, G.A., Tunnicliffe, A., Ward, W.H.J, Weston, S.A., Rosembrock, G., Barth, P.T., Taylor, I.W.F., Pauptit, R.A. & Timms, D. (1997) The entropy penalty of ordered water accounts for weaker binding of the antibiotic novobiocin to a resistant mutant of DNA gyrase: a thermodynamic and crystallographic study. Biochemistry 36, 9663-9673.
19. Laffite, D., Lamour, V., Tsvetkov, P.O., Makarov, A.A., Klich, M., Deprez, P., Moras, D., Briand, C. & Gilli, R. (2002) DNA gyrase interaction with coumarin-based inhibitors: the role of the hydroxybenzoate isopentenyl moiety and the 5′-methyl group of the noviose. Biochemistry 41, 7217-7123.
20. Scatigno, A.C., Garrido, S.S. & Marchetto, R. (2004) A 4.2 kDa synthetic peptide as potential probe to evaluate the antibacterial activity of coumarin drugs. J. Pept. Sci. 10, 566-577.
21. Marchetto, R., Nicolas, E., Castillo, N., Bacardit, J., Navia, M., Vila, J. & Giralt, E. (2001) Two short peptides including segments of subunit A of Escherichia coli DNA gyrase as potential probes to evaluate the antibacterial activity of quinolones. J. Pept. Sci. 7, 27-40.
22. Lacowicz, J.R. (ed.) (1987) Principles of Fluorescence Spectroscopy. Plenum Press, New York, USA, p. 496.
23. Fields, G.B. & Noble, R.L. (1990) Solid-phase peptide synthesis utilizing 9-fluorenyl-methoxycarbonyl amino acids. Int. J. Pept. Protein Res. 35, 161-214.
24. Borissevitch, I.E. (1999) More about the inner filter effect: corrections of Stern-Volmer fluorescence quenching constants are necessary at very low optical absorption of the quencher. J. Luminescence 81, 219-224.
25. Sekiguchi, J., Stivers, J.T., Mildvan, A.S. & Shuman, S. (1996) Mechanism of inhibition of vaccinia DNA topoisomerase by novobiocin and coumermycin. J. Biol. Chem. 271, 2313-2322.
26. Gellert, M., O'Dea, M.H., Itoh, T. & Tomizawa, J. (1976) Novobiocin and coumermycin inhibit DNA supercoiling catalysed by DNA gyrase. Proc. Natl Acad. Sci. U S A 73, 4474-4478.
27. Maxwell, A. (1999) DNA gyrase as a drug target. Biochem. Soc. Trans. 27, 48-53.
28. Maxwell, A. & Gellert M. (1984) The DNA dependence of the ATPase activity of DNA gyrase. J. Biol. Chem. 159, 14472-14480.
29. Noble, C.G. & Maxwell, A. (2002) The role of GyrB in the DNA cleavage-religation reaction of DNA gyrase: a proposed two metal-ion mechanism. J. Mol. Biol. 318, 361-371.
30. Tamura, J.K., Bates, A.D. & Gellert, M. (1992) Slow interaction of 5′-adenylyl-β,γ-imidodiphosphate with Escherichia coli DNA gyrase. J. Biol. Chem. 167, 9214-9222.
31. Sugino, A. & Cozzarelli, N.R. (1980) The intrinsic ATPase of DNA gyrase. J. Biol. Chem. 155, 6299-6306.
32. Kampranis, S.C., Gormley, N.A., Tranter, R., Orphanides, G. & Maxwell, A. (1999) Probing the binding of coumarins and cyclothialidines to DNA gyrase. Biochemistry 38, 1967-1976.
33. Guy, H.R. (1985) Amino acid side-chain partition energies and distribution of residues in soluble proteins. Biophys. J. 47, 61-70.
34. Abraham, D.J. & Leo, A.J. (1987) Extension of the fragment method to calculate amino acid zwitterion and side chain partition coefficients. Proteins 2, 130-152.
35. Roseman, M.A. (1988) Hydrophilicity of polar amino acid side-chains is markedly reduced by flanking peptide bonds. J. Mol. Biol. 100, 513-522.