The entropic 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

Volumn 36, Issue 32, 1997, Pages 9663-9673

  Holdgate, Geoffrey A ^a   Tunnicliffe, Alan ^a,b   Ward, Walter H J ^a   Weston, Simon A ^a   Rosenbrock, Gina ^a   Barth, Peter T ^a   Taylor, Ian W F ^a   Pauptit, Richard A ^a   Timms, David ^a  

^a ASTRAZENECA   (United Kingdom)

^b FRITZ LIPMANN INSTITUTE   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

DNA FRAGMENT; DNA TOPOISOMERASE (ATP HYDROLYSING); NOVOBIOCIN;

ANTIMICROBIAL ACTIVITY; ARTICLE; BINDING AFFINITY; CALORIMETRY; CRYSTALLOGRAPHY; DRUG BINDING; ENTHALPY; ENTROPY; GENE MUTATION; HYDROGEN BOND; PRIORITY JOURNAL; PROTEIN ANALYSIS;

BINDING SITES; CRYSTALLOGRAPHY, X-RAY; DNA TOPOISOMERASES, TYPE II; DRUG RESISTANCE, MICROBIAL; ENTROPY; ESCHERICHIA COLI; MACROMOLECULAR SUBSTANCES; MOLECULAR WEIGHT; MUTAGENESIS, SITE-DIRECTED; NOVOBIOCIN; PEPTIDE FRAGMENTS; PROTEIN STRUCTURE, TERTIARY; THERMODYNAMICS; WATER;

EID: 0030758672     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi970294+     Document Type: Article

References (61)

1. Ali, J. A., Jackson, A. P., Howells, A. J., & Maxwell, A. (1993) Biochemistry 32, 2717-2724.
2. Ali, J. A., Orphanides, G., & Maxwell, A. (1995) Biochemistry 34, 9801-9808.
3. Allen, F. H., & Kennard, O. (1993) Chem. Design Automation News 8, 31-37.
4. Bailey, D., Cooper, J. B., Veerapandian, B., Blundell, T. L., Atrash, B., Jones, D. M., & Szelke, M. (1993) Biochem. J. 289, 363-371.
5. Becker, J. W., Rotonda, J., McKeever, B. M., Chan, H. K., Marcy, A. I., Wiederrecht, G., Hermes, J. D., & Springer, J. P. (1993) J. Biol. Chem. 268, 11335-11339.
6. Berger, J. M., Gamblin, S. J., Harrison, S. C., & Wang, J. C. (1996) Nature 379, 225-232.
7. Bernstein, F. C., Koetzle, T. F., Williams, G. J. B., Meyer, E. F., Jr., Brice, M. D., Rodgers, J. R., Kennard, O., Shimanouchi, T., & Tasumi, M. (1977) J. Mol. Biol. 112, 535-542.
8. Bhat, T. N., Bentley, G. A., Boulot, G., Greene, M. I., Tello, D., Dall'Acqua, W., Souchon, H., Schwarz, F. P., Mariuzza, R. A., & Poljak, R. J. (1994) Proc. Natl. Acad. Sci. U.S.A. 91, 1089-1093.
9. Blundell, T. L., Jenkins, J. A., Sewell, B. T., Pearl, L. H., Cooper, J. B., Tickle, I. J., Veerapandian, B., & Wood, S. P. (1990) J. Mol. Biol. 211, 919-941.
10. Boles, M. O., & Taylor, D. J. (1975) Acta Crystallogr. B 31, 1400.
11. Brand, J. G., & Toribara, T. Y. (1972) Mol. Pharmacol. 8, 751-758.
12. Brünger, A. T., Kuriyan, J., & Karplus, M. (1987) Science 235, 458-460.
13. Bundle, D. R., & Sigurskjold, B. W. (1995) Methods Enzymol. 247, 288-305.
14. CCP4 (1994) Acta Crystallogr. D 50, 760-763.
15. Chervenak, M. C., & Toone, E. J. (1994) J. Am. Chem. Soc. 116, 10533-10539.
16. Connelly, P. R., Thomson, J. A., Fitzgibbon, M. J., & Bruzzese, F. J. (1993) Biochemistry 32, 5583-5590.
17. Contreras, A., & Maxwell, A. (1992) Mol. Microbiol. 6, 1617-1624.
18. Dunitz, J. D. (1995) Chem. Biol. 2, 709-712.
19. Fersht, A. R., Jackson, S. E., & Serrano, L. (1993) Philos. Trans. R. Soc. London, Ser. A 345, 141-151.
20. Freire, E. (1994) Methods Enzymol. 240, 502-530.
21. Frisch, C., Schreiber, G., Johnson, C. M., & Fersht, A. R. (1997) J. Mol. Biol. 267, 696-706.
22. Gilbert, E. J., & Maxwell, A. (1994) Mol. Microbiol. 12, 365-373.
23. Gomez, J., & Freire, E. (1995) J. Mol. Biol. 252, 337-350.
24. Gormley, N. A., Orphanides, G., Meyer, A., Cullis, P. M., & Maxwell, A. (1996) Biochemistry 35, 5083-5092.
25. Grunwald, E., & Steel, C. (1995) J. Am. Chem. Soc. 117, 5687-5692.
26. Guinto, E. R., & Di Cera, E. (1996) Biochemistry 35, 8800-8804.
27. Haberman, S. M., & Murphy, K. P. (1996) Protein Sci. 5, 1229-1239.
28. Hallet, P., Grimshaw, A. J., Wigley, D. B., & Maxwell, A. (1990) Gene 93, 139-142.
29. Hilser, V. J., Gomez, J., & Freire, E. (1996) Proteins: Struct., Funct., Genet. 26, 123-133.
30. Hu, D. D., & Eftink, M. R. (1994) Biophys. Chem. 49, 233-239.
31. Jones, T. A., Cowan, S., Zou, J.-Y., & Kyeldgaard, M. (1991) Acta Crystallogr. A 47, 110-119.
32. Ladbury, J. E., & Chowdhry, B. Z. (1996) Chem. Biol. 3, 791-801.
33. Ladbury, J. E., Wright, J. G., Sturtevant, J. M., & Sigler, P. B. (1994) J. Mol. Biol. 238, 669-681.
34. Lam, P. Y. S., Jadhav, P. K., Evermann, C. J., Hodge, C. N., Ru, Y., Bacheler, L. T., Meek, J. L., Otto, M. J., Rayner, M. L., Wong, N. Y., Chang, C. H., Weber, P. C., Jackson, D. A., Sharpe, T. R., & Erickson-Viitanen, S. (1994) Science 263, 380-383.
35. Laskowski, R. A., MacArthur, M. W., Moss, D. S., & Thornton, J. M. (1993) J. Appl. Crystallogr. 26, 283-291.
36. Lawson, C. L., Zhang, R.-G., Schevitz, R. W., Otinowski, Z., Joachimak, A., & Sigler, P. B. (1988) Proteins: Struct., Funct., Genet. 3, 18-31.
37. Lee, B., & Richards, F. M. (1971) J. Mol. Biol. 55, 379-400.
38. Lewis, R. J., Singh, O. M. P., Smith, C. V., Skarzynski, T., Maxwell, A., Wonacott, A. J., & Wigley, D. B. (1996a) EMBO J. 15, 1412-1420.
39. Lewis, R. J., Tsai, F. T. F., & Wigley, D. B. (1996b) BioEssays 18, 661-671.
40. Lisgarten, J. N., Gupta, V., Maes, D., Wyns, L., Zegers, I., Palmer, R. A., Delawis, C. G., Aguilar, C. F., & Hemmings, A. M. (1993) Acta Crystallogr. D 49, 541-547.
41. Liu, Y., & Sturtevant, J. M. (1995) Protein Sci. 4, 2559-2561.
42. Mannervik, B. (1982) Methods Enzymol. 87, 370-390.
43. Maxwell, A. (1992) J. Antimicrob. Chemother. 30, 409-416.
44. Maxwell, A. (1993) Mol. Microbiol. 9, 681-686.
45. Mikol, V., Papageorgiou, C., & Borer, X. (1995) J. Med. Chem. 38, 3361-3367.
46. Morton, C. J., & Ladbury, J. E. (1996) Protein Sci. 5, 2115-2118.
47. Naismith, J. H., Emmerich, C., Habash, J., Harrop, S. J., Helliwell, J. R., Hunter, W. N., Raftery, J., Kalb(Gilboa), A. J., & Yariv, J. (1994) Acta Crystallogr. D 50, 847-858.
48. Pauptit, R. A., Weston, S. A., Breeze, A. L., Derbyshire, D. J., Tucker, A. D., Hales, N., Hollinshead, D., & Timms, D. (1997) in Experimental and Computational Approaches to Structure-Based Drug Design (Codding, P. W., Ed.) Kluwer Academic Publishers, Dordrecht, The Netherlands, (in press).
49. Pearlman, R. S. (1982) QCPE. 413.
50. Reece, R. J., & Maxwell, A. (1991) Nucleic Acids Res. 19, 1399-1405.
51. Schwarz, F. P., Tello, D., Goldbaum, F. A., Mariuzza, R. A., & Poljak, R. J. (1995) Eur. J. Biochem. 228, 388-394.
52. Spolar, R. S., Ha, J.-H., & Record, M. T., Jr. (1989) Proc. Natl. Acad. Sci. U.S.A. 86, 8382-8385.
53. Sturtevant, J. M. (1977) Proc. Natl. Acad. Sci. U.S.A. 74, 2236-2240.
54. Sugino, A., Higgins, N. P., Brown, P. O., Peebles, C. L., & Cozzarelli, N. R. (1978) Proc. Natl. Acad. Sci. U.S.A. 75, 4838-4842.
55. Tronrud, D. E., Ten Eyck, L. F., & Matthews, B. W. (1987) Acta Crystallogr. A 43, 489-501.
56. Tsai, F. T. F., Singh, O. M. P., Skarzynski, 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) Proteins: Struct., Funct., Genet. 28, 41-52.
57. Van Duyne, G. D., Standaert, R. F., Schreiber, S. L.. & Clardy, J. (1991) J. Am. Chem. Soc. 113, 7433-7434.
58. Vijayalakshmi, J., Padmanabhan, K. P., Mann, K. G., & Tulinsky, A. (1994) Protein Sci. 3, 2254-2271.
59. Wigley, D. B. (1996) Structure 4, 117-120.
60. Wigley, D. B., Davies, G. J., Dodson, E. J., Maxwell, A., & Dodson, G. 0991) Nature 351, 624-629.
61. Wiseman, T., Williston, S., Brandts, J. F., & Lin, L. N. (1989) Anal. Biochem. 179, 131-137.