Predicting substrates by docking high-energy intermediates to enzyme structures

Journal of the American Chemical Society

Volumn 128, Issue 49, 2006, Pages 15882-15891

  Hermann, Johannes C ^a   Ghanem, Eman ^b   Li, Yingchun ^b   Raushel, Frank M ^b   Irwin, John J ^a   Shoichet, Brian K ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b TEXAS A AND M UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ENZYMES; GEOMETRY; ISOMERS; METABOLITES; MOLECULAR STRUCTURE;

AMIDOHYDROLASE; ENZYME STRUCTURES; HIGH ENERGY TRANSITION STATE ANALOGUES; KEGG METABOLITES;

SUBSTRATES;

ADENOSINE DEAMINASE; AMIDASE; CYTOSINE DEAMINASE; DIHYDROOROTASE; DIHYDROPYRIMIDINASE; ISOASPARTYL DIPEPTIDASE; N ACETYLGLUCOSAMINE 6 PHOSPHATE DEACETYLASE; PHOSPHOTRIESTERASE;

ARTICLE; CATALYSIS; DATA BASE; ENANTIOSELECTIVITY; ENZYME ACTIVITY; ENZYME STRUCTURE; ENZYME SUBSTRATE; ENZYME SUBSTRATE COMPLEX; MUTANT; STEREOCHEMISTRY; WILD TYPE;

ALGORITHMS; AMIDOHYDROLASES; BINDING SITES; COMPUTER SIMULATION; CRYSTALLOGRAPHY, X-RAY; DATABASES, PROTEIN; MODELS, CHEMICAL; PHOSPHORIC TRIESTER HYDROLASES; STEREOISOMERISM; SUBSTRATE SPECIFICITY;

EID: 33845458652     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja065860f     Document Type: Article

References (46)

1. Gerlt, J. A.; Babbitt, P. C. Genome Biol. 2000, 1, REVIEWS0005.
2. Levy, E. D.; Ouzounis, C. A.; Gilks, W. R.; Audit, B. BMC Bioinformatics 2005, 6, 302.
3. Devos, P.; Valencia, A. Trends Genet. 2001, 17, 429-431.
4. Pieper, U.; Eswar, N.; Davis, F. P.; Braberg, H.; Madhusudhan, M. S.; Rossi, A.; Marti-Renom, M.; Karchin, R.; Webb, B. M.; Eramian, D.; Shen, M. Y.; Kelly, L.; Melo, F.; Sali, A. Nucleic Acids Res. 2006, 34, D291-295.
5. Specker, E.; Bottcher, J.; Heine, A.; Sotriffer, C. A.; Lilie, H.; Schoop, A.; Muller, G.; Griebenow, N.; Klebe, G. J. Med. Chem. 2005, 48, 6607-6619.
6. Schapira, M.; Abagyan, R.; Totrov, M. J. Med. Chem. 2003, 46, 3045-3059.
7. Rao, M. S.; Olson, A. J. Proteins 1999, 34, 173-183.
8. Jorgensen, W. L. Science. 2004, 303, 1813-1818.
9. Li, C.; Xu, L.; Wolan, D. W.; Wilson, I. A.; Olson, A. J. J. Med. Chem. 2004, 47, 6681-6690.
10. Schnecke, V.; Kuhn, L. A. Perspect. Drug Discovery Des. 2000, 20, 171-190.
11. Fernandes, M. X.; Kairys, V.; Gilson, M. K. J. Chem. Inf. Comput. Sci. 2004, 44, 1961-1970.
12. Warshel, A.; Florian, J. Proc. Natl. Acad. Sci. U.S.A. 1998, 95, 5950-5955.
13. Macchiarulo, A.; Nobeli, I.; Thornton, J. M. Nat. Biotechnol. 2004, 22, 1039-1045.
14. Kalyanaraman, C.; Bernacki, K.; Jacobson, M. P. Biochemistry 2005, 44, 2059-2071.
15. Holm, L.; Sander, C. Proteins 1997, 28, 72-82.
16. Seibert, C. M.; Raushel, F. M. Biochemistry 2005, 44, 6383-6391.
17. Kanehisa, M.; Goto, S. Nucleic Acids Res. 2000, 28, 27-30.
18. Lopez, X.; Mujika, J. I.; Blackburn, G. M.; Karplus, M. J. Phys. Chem. A 2003, 107, 2304-2315.
19. Hermann, J. C.; Ridder, L.; Holtje, H. D.; Mulholland, A. J. Org. Biomol. Chem. 2006, 4, 206-210.
20. Lorber, D. M.; Shoichet, B. K. Curr. Top. Med. Chem. 2005, 5, 739-749.
21. Sadowski, J.; Schwab, C. H.; Gasteiger, J. In Computational Medicinal Chemistry and Drug Discovery; Bultinck, P., De Winter, H., Langenaeker, W., Tollenaere, J. P., Eds.; Dekker Inc.: New York, 2003; pp 151-212.
22. Sadowski, J. J. Comput.-Aided Mol. Des. 1997, 11, 53-60.
23. Bostrom, J.; Greenwood, J. R.; Gottfries, J. J. Mol. Graphics Modell. 2003, 21, 449-462.
24. Chambers, C. C.; Hawkins, G. D.; Cramer, C. J.; Truhlar, D. G. J. Phys. Chem. 1996, 100, 16385-16398.
25. Li, J. B.; Zhu, T. H.; Cramer, C. J.; Truhlar, D. G. J. Phys. Chem. A 1998, 102, 1820-1831.
26. Shoichet, B. K.; Leach, A. R.; Kuntz, I. D. Proteins 1999, 34, 4-16.
27. Brenk, R.; Vetter, S. W.; Boyce, S. E.; Goodin, D. B.; Shoichet, B. K. J. Mol. Biol. 2006, 357, 1449-1470.
28. Irwin, J. J.; Raushel, F. M.; Shoichet, B. K. Biochemistry 2005, 44, 12316-12328.
29. Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Kollman, P. A. J. Am. Chem. Soc. 1993, 115, 9620-9631.
30. Meng, E. C.; Shoichet, B.; Kuntz, I. D. J. Comput. Chem. 1992, 13, 505-524.
31. Gilson, M. K.; Honig, B. H. Nature 1987, 330, 84-86.
32. Kuntz, I. D.; Blaney, J. M.; Oatley, S. J.; Langridge, R.; Ferrin, T. E. J. Mol. Biol. 1982, 161, 269-288.
33. Hill, C. M.; Li, W. S.; Thoden, J. B.; Holden, H. M.; Raushel, F. M. J. Am. Chem. Soc. 2003, 125, 8990-8991.
34. Gschwend, D. A.; Kuntz, I. D. J. Comput.-Aided Mol. Des. 1996, 10, 123-132.
35. Marti-Arbona, R.; Fresquet, V.; Thoden, J. B.; Davis, M. L.; Holden, H. M.; Raushel, F. M. Biochemistry 2005, 44, 7115-7124.
36. Chen-Goodspeed, M.; Sogorb, M. A.; Wu, F.; Raushel, F. M. Biochemistry 2001, 40, 1332-1339.
37. Claeyssens, F.; Ranaghan, K. E.; Manby, F. R.; Harvey, J. N.; Mulholland, A. J. Chem. Commun. (Cambridge) 2005, 5068-5070.
38. Field, M. J.; Bash, P. A.; Karplus. M. J. Comput. Chem. 1990, 11, 700-733.
39. Thoden, J. B.; Phillips, G. N., Jr.; Neal, T. M.; Raushel, F. M.; Holden, H. M. Biochemistry 2001, 40, 6989-6997.
40. Abendroth, J.; Niefind, K.; Schomburg, D. J. Mol. Biol. 2002, 320, 143-156.
41. Vincent, F.; Yates, D.; Garman, E.; Davies, G. J.; Brannigan, J. A. J. Biol. Chem. 2004, 279, 2809-2816.
42. Thoden, J. B.; Marti-Arbona, R.; Raushel, F. M.; Holden, H. M. Biochemistry 2003, 42, 4874-4882.
43. Benning, M. M.; Shim, H.; Raushel, F. M.; Holden, H. M. Biochemistry 2001, 40, 2712-2722.
44. Ireton, G. C.; McDermott, G.; Black, M. E.; Stoddard, B. L. J. Mol. Biol. 2002, 315, 687-697.
45. Wang, Z.; Quiocho, F. A. Biochemistry 1998, 37, 8314-8324.
46. Nowlan, C.; Li, Y.; Hermann, J. C.; Evans, T.; Carpenter, J.; Ghanem, E.; Shoichet, B. K.; Raushel, F. M. J. Am. Chem. Soc. 2006, 128, 15892-15902.