Computational design of catalytic dyads and oxyanion holes for ester hydrolysis

Journal of the American Chemical Society

Volumn 134, Issue 39, 2012, Pages 16197-16206

  Richter, Florian ^a,b   Blomberg, Rebecca ^c,i   Khare, Sagar D ^a   Kiss, Gert ^d,j   Kuzin, Alexandre P ^e   Smith, Adam J T ^d,k   Gallaher, Jasmine ^a   Pianowski, Zbigniew ^c   Helgeson, Roger C ^d   Grjasnow, Alexej ^h   Xiao, Rong ^f   Seetharaman, Jayaraman ^e   Su, Min ^e   Vorobiev, Sergey ^e   Lew, Scott ^e   Forouhar, Farhad ^e   Kornhaber, Gregory J ^f   Hunt, John F ^e   Montelione, Gaetano T ^f,g   Tong, Liang ^e   Houk, K N ^d   Hilvert, Donald ^c   Baker, David ^a,b   more..

^a UNIVERSITY OF WASHINGTON SCHOOL OF MEDICINE   (United States)

^b UNIVERSITY OF WASHINGTON   (United States)

^c ETH ZURICH   (Switzerland)

^d UNIVERSITY OF CALIFORNIA   (United States)

^e Howard Hughes Medical Institute   (United States)

^f RUTGERS UNIVERSITY   (United States)

^g RUTGERS ROBERT WOOD JOHNSON MEDICAL SCHOOL   (United States)

^h UNIVERSITY OF MUNICH   (Germany)

ⁱ Email:   (Switzerland)

^j STANFORD UNIVERSITY   (United States)

^k UNIVERSITY OF KENTUCKY   (United States)

more..

Author keywords

[No Author keywords available]

Indexed keywords

ACTIVE SITE; AMIDE HYDROLYSIS; CATALYTIC EFFICIENCIES; COMPUTATIONAL DESIGN; ESTER HYDROLYSIS; ESTERASE ACTIVITIES; KINETIC EXPERIMENT; NH GROUPS; NUCLEOPHILIC CATALYSIS; OXYANION HOLE; SIDE-CHAINS; SUBSTRATE ACTIVATION; WATER MOLECULE;

AMIDES; AMINO ACIDS; ENZYMES; ESTERIFICATION; ESTERS; HYDROLYSIS; POSITIVE IONS; SCAFFOLDS;

DESIGN;

ANION; CYSTEINE; ENZYME; ESTERASE; HISTIDINE; OXYANION; THEOZYME; UNCLASSIFIED DRUG;

ARTICLE; CATALYSIS; ENZYME ACTIVITY; ENZYME STRUCTURE;

BIOCATALYSIS; CATALYTIC DOMAIN; DRUG DESIGN; ESTERASES; ESTERS; HYDROGEN BONDING; HYDROLYSIS; KINETICS; MODELS, MOLECULAR;

EID: 84867053249     PISSN: 00027863     EISSN: 15205126     Source Type: Journal    
DOI: 10.1021/ja3037367     Document Type: Article

References (56)

1. Clark, J. D.; Schievella, A. R.; Nalefski, E. A.; Lin, L. L. J. Lipid Mediat. Cell. Signal. 1995, 12, 83-117
2. Mignatti, P.; Rifkin, D. B. Enzyme Protein 1996, 49, 117-137
3. DeClerck, Y. A.; Imren, S.; Montgomery, A. M.; Mueller, B. M.; Reisfeld, R. A.; Laug, W. E. Adv. Exp. Med. Biol. 1997, 425, 89-97
4. MacDonald, T.; DeClerck, Y.; Laug, W. Thromb. Haemostasis 1997, S1541-S1541
5. Gorrell, M. D. Clin. Sci. (Lond) 2005, 108, 277-292
6. Panke, S.; Held, M.; Wubbolts, M. Curr. Opin. Biotechnol. 2004, 15, 272-279
7. Sio, C. F.; Quax, W. J. Curr. Opin. Biotechnol. 2004, 15, 349-355
8. Riva, S.; Koskinen, A. M. P.; Klibanov, A. M. Enzymatic Reactions in Organic Media; Springer: Berlin, 1995; p 140.
9. Patel, R. N. Annu. Rev. Microbiol. 1998, 52, 361-395
10. Breslow, R.; Dong, S. D. Chem. Rev. 1998, 98, 1997-2012
11. Murakami, Y. Top. Curr. Chem. 1983, 115, 107-155
12. Cram, D. J. Angew. Chem. Int. Ed. Engl. 1988, 27, 1009-1020
13. Tanaka, F. Chem. Rev. 2002, 102, 4885-4906
14. MacBeath, G.; Hilvert, D. Chem. Biol. 1996, 3, 433-445
15. Janda, K. D.; Schloeder, D.; Benkovic, S. J.; Lerner, R. A. Science 1988, 241, 1188-1191
16. Stewart, J. D.; Krebs, J. F.; Siuzdak, G.; Berdis, A. J.; Smithrud, D. B.; Benkovic, S. J. Proc. Natl. Acad. Sci. U.S.A. 1994, 91, 7404-7409
17. Bolon, D N; Mayo, S. L. Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 14274-14279
18. Smith, A. J. T.; Muller, R.; Toscano, M. D.; Kast, P.; Hellinga, H. W.; Hilvert, D; Houk, K. N. J. Am. Chem. Soc. 2008, 130, 15361-15373
19. Simón, L; Goodman, J. M. J. Org. Chem. 2010, 75 (6) 1831-1840
20. Kamerlin, S. C. L.; Zhen, T. C.; Warshel, A. J. Org. Chem. 2010, 75, 6391-6401
21. Röthlisberger, D.; Khersonsky, O.; Wollacott, A. M.; Jiang, L.; DeChancie, J.; Betker, J.; Gallaher, J. L.; Althoff, E. A.; Zanghellini, A.; Dym, O.; Albeck, S.; Houk, K. N.; Tawfik, D. S.; Baker, D. Nature 2008, 453, 190-195
22. Jiang, L.; Althoff, E. A.; Clemente, F. R.; Doyle, L.; Röthlisberger, D.; Zanghellini, A.; Gallaher, J. L.; Betker, J. L.; Tanaka, F.; Barbas, C. F., III; Hilvert, D.; Houk, K. N.; Stoddard, B. L.; Baker, D. Science 2008, 319, 1387-1391
23. Siegel, J. B.; Zanghellini, A.; Lovick, H. M.; Kiss, G.; Lambert, A. R.; St Clair, J. L.; Gallaher, J. L.; Hilvert, D.; Gelb, M. H.; Stoddard, B. L.; Houk, K. N.; Michael, F. E.; Baker, D. Science 2010, 329, 309-313
24. Leaver-Fay, A.; Tyka, M.; Lewis, S. M.; Lange, O. F.; Thompson, J.; Jacak, R.; Kaufman, K.; Renfrew, P. D.; Smith, C. A.; Sheffler, W.; Davis, I. W.; Cooper, S.; Treuille, A.; Mandell, D. J.; Richter, F.; Ban, Y. E.; Fleishman, S. J.; Corn, J. E.; Kim, D. E.; Lyskov, S.; Berrondo, M.; Mentzer, S.; Popovic, Z.; Havranek, J. J.; Karanicolas, J.; Das, R.; Meiler, J.; Kortemme, T.; Gray, J. J.; Kuhlman, B.; Baker, D.; Bradley, P. Methods Enzymol. 2011, 487, 545-574
25. Richter, F.; Leaver-Fay, A.; Khare, S. D.; Bjelic, S.; Baker, D. PLoS ONE 2011, 6 (5) e19230
26. Hedstrom, L. Chem. Rev. 2002, 102, 4501-4523
27. Otto, H. H.; Schirmeister, T. Chem. Rev. 1997, 97, 133-171
28. Ma, S.; Devi-Kesavan, L. S.; Gao, J. J. Am. Chem. Soc. 2007, 129, 13633-13645
29. Kast, P.; Asif-Ullah, M.; Jiang, N.; Hilvert, D. Proc. Natl. Acad. Sci. U.S.A. 1996, 93, 5043-5048
30. Zanghellini, A.; Jiang, L.; Wollacott, A. M.; Cheng, G.; Meiler, J.; Althoff, E. A.; Rothlisberger, D.; Baker, D. Protein Sci. 2006, 15, 2785-2794
31. Vernet, T.; Tessier, D. C.; Chatellier, J.; Plouffe, C.; Lee, T. S.; Thomas, D. Y.; Storer, A. C.; Menard, R. J. Biol. Chem. 1995, 270, 16645-16652
32. Tantillo, D. J.; Chen, J. G.; Houk, K. N. Curr. Opin. Chem. Biol. 1998, 2, 743-750
33. Zhang, X.; DeChancie, J.; Gunaydin, H.; Chowdry, A. B.; Clemente, F. R.; Smith, A. J. T.; Handel, T. M.; Houk, K. N. J. Org. Chem. 2008, 73, 889-899
34. Abbott, D. W.; Boraston, A. B. J. Mol. Biol. 2007, 369, 759-770
35. Kiss, G.; Rothlisberger, D.; Baker, D.; Houk, K. N. Protein Sci. 2010, 19, 1760-1773
36. Kellogg, E. H.; Leaver-Fay, A.; Baker, D. Proteins 2011, 79, 830-838
37. Lowe, G.; Williams, A. Biochem. J. 1965, 96, 199
38. Cheng, Y.; Prusoff, W. H. Biochem. Pharmacol. 1973, 22, 3099-3108
39. Carter, P.; Abrahmsen, L.; Wells, J. A. Biochemistry 1991, 30, 6142-6148
40. Chu, S. H.; Mautner, H. G. J. Org. Chem. 1966, 31, 308-&
41. Weerapana, E.; Wang, C.; Simon, G. M.; Richter, F.; Khare, S.; Dillon, M. B. D.; Bachovchin, D. A.; Mowen, K.; Baker, D.; Cravatt, B. F. Nature 2010, 468, 790
42. Retailleau, P.; Huang, X.; Yin, Y.; Hu, M.; Weinreb, V.; Vachette, P.; Vonrhein, C.; Bricogne, G.; Roversi, P.; Ilyin, V.; Carter, C. W., Jr. J. Mol. Biol. 2003, 325, 39-63
43. Bryan, P.; Pantoliano, M. W.; Quill, S. G.; Hsiao, H. Y.; Poulos, T. Proc. Natl. Acad. Sci. U.S.A. 1986, 83, 3743-3745
44. Hinkle, P. M.; Kirsch, J. F. Biochemistry 1971, 10, 2717
45. Brocklehurst, K.; Malthouse, J. P. Biochem. J. 1981, 193, 819-823
46. Patai, S., Ed. The Chemistry of the Thiol Group; John Wiley & Sons, Ltd: New York, 1974; Chapter 8
47. Craik, C. S.; Roczniak, S.; Largman, C.; Rutter, W. J. Science 1987, 237, 909-913
48. Carter, P.; Wells, J. A. Nature 1988, 332, 564-568
49. Bostrom, J.; Greenwood, J. R.; Gottfries, J. J. Mol. Graph. Model. 2003, 21, 449-462
50. Sheffler, W.; Baker, D. Protein Sci. 2009, 18, 229-239
51. Vigers, G. P. A.; Rizzi, J. P. J. Med. Chem. 2004, 47, 80-89
52. Davis, I. W.; Baker, D. J. Mol. Biol. 2009, 385, 381-392
53. Charbonnier, J. B.; Carpenter, E.; Gigant, B.; Golinelli-Pimpaneau, B.; Eshhar, Z.; Green, B. S.; Knossow, M. Proc. Natl. Acad. Sci. U.S.A. 1995, 92, 11721-11725
54. Lesley, S. A.; Patten, P. A.; Schultz, P. G. Proc. Natl. Acad. Sci. U.S.A. 1993, 90, 1160-1165
55. Guo, J.; Huang, W.; Scanlan, T. S. J. Am. Chem. Soc. 1994, 116, 6062-6069
56. Stewart, J. D.; Roberts, V. A.; Thomas, N. R.; Getzoff, E. D.; Benkovic, S. J. Biochemistry 1994, 33, 1994-2003