Identifying ligand-binding hot spots in proteins using brominated fragments

Acta Crystallographica Section F: Structural Biology and Crystallization Communications

Volumn 69, Issue 9, 2013, Pages 1060-1065

  Grøftehauge, Morten K ^a   Therkelsen, Martin Ø ^b   Taaning, Rolf ^c   Skrydstrup, Troels ^c   Morth, J Preben ^d   Nissen, Poul ^b  

^a DURHAM UNIVERSITY   (United Kingdom)

^b AARHUS UNIVERSITY   (Denmark)

^c AARHUS UNIVERSITY   (Denmark)

^d UNIVERSITY OF OSLO   (Norway)

Author keywords

brominated fragments; EF Tu; ligand binding

Indexed keywords

BACTERIAL PROTEIN; CYCLOPEPTIDE; ELONGATION FACTOR TU; GE 2270A; GUANOSINE TRIPHOSPHATE; LIGAND; RECOMBINANT PROTEIN; THIAZOLE DERIVATIVE; TRANSFER RNA;

ARTICLE; BINDING SITE; BROMINATED FRAGMENTS; CHEMISTRY; EF-TU; ESCHERICHIA COLI; GENE EXPRESSION; GENETICS; HALOGENATION; ISOLATION AND PURIFICATION; LIGAND BINDING; MASS SPECTROMETRY; METABOLISM; MOLECULAR DOCKING; MOLECULAR LIBRARY; PEPTIDE MAPPING; PROTEIN BINDING; PROTEIN SECONDARY STRUCTURE; THERMUS THERMOPHILUS; X RAY CRYSTALLOGRAPHY;

BROMINATED FRAGMENTS; EF-TU; LIGAND BINDING;

BACTERIAL PROTEINS; BINDING SITES; CRYSTALLOGRAPHY, X-RAY; ESCHERICHIA COLI; GENE EXPRESSION; GUANOSINE TRIPHOSPHATE; HALOGENATION; LIGANDS; MASS SPECTROMETRY; MOLECULAR DOCKING SIMULATION; PEPTIDE ELONGATION FACTOR TU; PEPTIDE MAPPING; PEPTIDES, CYCLIC; PROTEIN BINDING; PROTEIN STRUCTURE, SECONDARY; RECOMBINANT PROTEINS; RNA, TRANSFER; SMALL MOLECULE LIBRARIES; THERMUS THERMOPHILUS; THIAZOLES;

EID: 84883381367     PISSN: None     EISSN: 17443091     Source Type: Journal    
DOI: 10.1107/S1744309113018551     Document Type: Article

References (44)

1. Adams, P. D. et al. (2010). Acta Cryst. D66, 213-221.
2. Altschul, S. F., Madden, T. L., Scha ffer, A. A., Zhang, J., Zhang, Z., Miller, W. & Lipman, D. J. (1997). Nucleic Acids Res. 25, 3389-3402.
3. Antonysamy, S., Hirst, G., Park, F., Sprengeler, P., Stappenbeck, F., Steensma, R., Wilson, M. & Wong, M. (2009). Bioorg. Med. Chem. Lett. 19, 279-282.
4. Baell, J. B. & Holloway, G. A. (2010). J. Med. Chem. 53, 2719-2740.
5. Barelier, S., Pons, J., Gehring, K., Lancelin, J.-M. & Krimm, I. (2010). J. Med. Chem. 53, 5256-5266.
6. Berchtold, H., Reshetnikova, L., Reiser, C. O., Schirmer, N. K., Sprinzl, M. &Hilgenfeld, R. (1993). Nature (London), 365, 126-132.
7. Blank, J., Grillenbeck, N. W., Kreutzer, R. & Sprinzl, M. (1995). Protein Expr. Purif. 6, 637-645.
8. Blomberg, N., Cosgrove, D. A., Kenny, P. W. & Kolmodin, K. (2009). J. Comput. Aided Mol. Des. 23, 513-525.
9. Brenke, R., Kozakov, D., Chuang, G.-Y., Beglov, D., Hall, D., Landon, M. R., Mattos, C. & Vajda, S. (2009). Bioinformatics, 25, 621-627.
10. Brennfu hrer, A., Neumann, H. & Beller, M. (2009). Angew. Chem. Int. Ed. Engl. 48, 4114-4133.
11. Chessari, G. & Woodhead, A. J. (2009). Drug Discov. Today, 14, 668-675.
12. Chilingaryan, Z., Yin, Z. & Oakley, A. J. (2012). Int. J. Mol. Sci. 13, 12857-12879.
13. Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. (2010). Acta Cryst. D66, 486-501.
14. Evans, P. R. & Murshudov, G. N. (2013). Acta Cryst. D69, 1204-1214.
15. Gull, S. & Daniell, G. (1978). Nature (London), 272, 686-690.
16. Hajduk, P. J. & Greer, J. (2007). Nature Rev. Drug Discov. 6, 211-219.
17. Heck, R. F. & Nolley, J. P. (1972). J. Org. Chem. 37, 2320-2322.
18. Hermange, P., Lindhardt, A. T., Taaning, R. H., Bjerglund, K., Lupp, D. & Skrydstrup, T. (2011). J. Am. Chem. Soc. 133, 6061-6071.
19. Jurnak, F., McPherson, A., Wang, A. H.-J. & Rich, A. (1980). J. Biol. Chem. 255, 6751-6757.
20. Kabsch, W. (2010). Acta Cryst. D66, 125-132.
21. Kawashima, T., Berthet-Colominas, C., Wulff, M., Cusack, S. & Leberman, R. (1996). Nature (London), 379, 511-518.
22. Kjeldgaard, M., Nissen, P., Thirup, S. & Nyborg, J. (1993). Structure, 1, 35-50.
23. Kjeldgaard, M. & Nyborg, J. (1992). J. Mol. Biol. 223, 721-742.
24. Landon, M. R., Lieberman, R. L., Hoang, Q. Q., Ju, S., Caaveiro, J. M. M., Orwig, S. D., Kozakov, D., Brenke, R., Chuang, G.-Y., Beglov, D., Vajda, S., Petsko, G. A. & Ringe, D. (2009). J. Comput. Aided Mol. Des. 23, 491-500.
25. Mattos, C., Bellamacina, C. R., Peisach, E., Pereira, A., Vitkup, D., Petsko, G. A. & Ringe, D. (2006). J. Mol. Biol. 357, 1471-1482.
26. McCoy, A. J., Grosse-Kunstleve, R. W., Adams, P. D., Winn, M. D., Storoni, L. C. & Read, R. J. (2007). J. Appl. Cryst. 40, 658-674.
27. Miyaura, N. & Suzuki, A. (1995). Chem. Rev. 95, 2457-2483.
28. Mizoroki, T., Mori, K. & Ozaki, A. (1971). Bull. Chem. Soc. Jpn, 44, 581.
29. Morikawa, K., la Cour, T. F., Nyborg, J., Rasmussen, K. M., Miller, D. L. &Clark, B. F. (1978). J. Mol. Biol. 125, 325-338.
30. Murray, C. W. & Blundell, T. L. (2010). Curr. Opin. Struct. Biol. 20, 497-507.
31. Murray, C.W., Verdonk, M. L. & Rees, D. C. (2012). Trends Pharmacol. Sci. 33, 224-232.
32. Nilsson, J. & Nissen, P. (2005). Curr. Opin. Struct. Biol. 15, 349-354.
33. Nissen, P., Kjeldgaard, M., Thirup, S., Polekhina, G., Reshetnikova, L., Clark, B. F. & Nyborg, J. (1995). Science, 270, 1464-1472.
34. Parmeggiani, A., Krab, I.M., Okamura, S., Nielsen, R. C., Nyborg, J. & Nissen, P. (2006). Biochemistry, 45, 6846-6857.
35. Parmeggiani, A., Krab, I. M., Watanabe, T., Nielsen, R. C., Dahlberg, C., Nyborg, J. & Nissen, P. (2006). J. Biol. Chem. 281, 2893-2900.
36. Parmeggiani, A. & Nissen, P. (2006). FEBS Lett. 580, 4576-4581.
37. Rees, D. C., Congreve, M., Murray, C. W. & Carr, R. (2004). Nature Rev. DrugDiscov. 3, 660-672.
38. Schmeing, T. M., Voorhees, R. M., Kelley, A. C., Gao, Y.-G., Murphy, F. V., Weir, J. R. & Ramakrishnan, V. (2009). Science, 326, 688-694.
39. Scott, D. E., Coyne, A. G., Hudson, S. A. & Abell, C. (2012). Biochemistry, 45, 6846-6857.
40. Sonogashira, K., Tohda, Y. & Hagihara, N. (1975). Tetrahedron Lett. 16, 4467-4470.
41. Vogeley, L., Palm, G. J., Mesters, J. R. & Hilgenfeld, R. (2001). J. Biol. Chem. 276, 17149-17155.
42. Warr, W. A. (2009). J. Comput. Aided Mol. Des. 23, 453-458.
43. Wilcken, R., Zimmermann, M. O., Lange, A., Joerger, A. C. & Boeckler, F. M. (2013). J. Med. Chem. 56, 1363-1388.
44. Winter, G. (2010). J. Appl. Cryst. 43, 186-190.