Functional and mechanistic analyses of biomimetic aminoacyl transfer reactions in de novo designed coiled coil peptides via rational active site engineering

Journal of the American Chemical Society

Volumn 129, Issue 10, 2007, Pages 2959-2966

  Leman, Luke J ^a   Weinberger, Dana A ^a   Huang, Zheng Zheng ^a   Wilcoxen, Keith M ^a   Ghadiri, M Reza ^a  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; BIOMIMETIC MATERIALS; BIOSYNTHESIS; CATALYSIS; ENZYME KINETICS; NUCLEAR MAGNETIC RESONANCE; PROTEINS;

AMINOACYL TRANSFER; COILED-COIL ASSEMBLIES; RATIONAL ACTIVE SITE ENGINEERING;

PEPTIDES;

AMINE; AMINO ACID; CYSTEINE; LYSINE; PEPTIDE; PEPTIDE SYNTHASE;

AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; ARTICLE; CATALYSIS; ENZYME ACTIVE SITE; ENZYME KINETICS; ESTERIFICATION; GEOMETRY; NITROGEN NUCLEAR MAGNETIC RESONANCE; PEPTIDE SYNTHESIS; PKA; PROTEIN ENGINEERING; REACTION ANALYSIS; RIBOSOME;

AMINO ACID SEQUENCE; AMINO ACIDS; BINDING SITES; BIOMIMETIC MATERIALS; PEPTIDE SYNTHASES; PEPTIDES; PROTEIN ENGINEERING; PROTEIN STRUCTURE, SECONDARY;

EID: 33947266363     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja068052x     Document Type: Article

References (82)

1. (a) Jencks, W. P. Catalysis in Chemistry and Enzymology, McGraw-Hill Series in Advanced Chemistry; McGraw-Hill Book Company: New York, 1969.
2. (b) Fersht, A. Structure and Mechanism in Protein Science; W. H. Freeman and Company: U.S.A., 1999.
3. (c) Wolfenden, R.; Snider, M. J. Acc. Chem. Res. 2001, 34, 938-45.
4. (d) Bruice, T. C. Acc. Chem. Res. 2002, 35, 139-48.
5. (e) Menger, F. M. Pure Appl. Chem. 2005, 77, 1873-86.
6. Corey, M. J.; Corey, E. Proc. Natl. Acad. Sci. U.S.A. 1996, 93, 11428-34.
7. Johnsson, K.; Allemann, R. K.; Widmer, H.; Benner, S. A. Nature 1993, 365, 530-2.
8. (a) Broo, K.; Brive, L.; Lundh, A. C.; Ahlberg, P.; Baltzer, L. J. Am. Chem. Soc. 1996, 118, 8172-3.
9. (b) Broo, K.; Allert, M.; Andersson, L.; Erlandsson, P.; Stenhagen, G.; Wigstrom, J.; Ahlberg, P.; Baltzer, L. J. Chem. Soc., Perkin Trans. 2 1997, 2, 397-8.
10. (c) Broo, K. S.; Brive, L.; Ahlberg, P.; Baltzer, L. J. Am. Chem. Soc. 1997, 119, 11362-72.
11. (d) Broo, K. S.; Nilsson, H.; Nilsson, J.; Baltzer, L. J. Am. Chem. Soc. 1998, 120, 10287-95.
12. (e) Jarvo, E. R.; Copeland, G. T.; Papaioannou, N.; Bonitatebus, P. J., Jr.; Miller, S. J. J. Am. Chem. Soc. 1999, 121, 11638-43.
13. (f) Baltzer, L.; Nilsson, H.; Nilsson, J. Chem. Rev. 2001, 101, 3153-63.
14. (g) Miller, S. J. Acc. Chem. Res. 2004, 37, 601-10.
15. (h) Nicoll, A. J.; Allemann, R. K. Org. Biomol. Chem. 2004, 2, 2175-80.
16. (i) Blank, J. T.; Miller, S. J. Biopolymers 2006, 84, 38-47.
17. (a) Allert, M.; Baltzer, L. Chem.-Eur. J. 2002, 8, 2549-60.
18. (b) Andersson, L. K.; Caspersson, M.; Baltzer, L. Chem.-Eur. J. 2002, 8, 3687-97.
19. (a) Lee, D. H.; Granja, J. R.; Martinez, J. A.; Severin, K.; Ghadiri, M. R. Nature 1996, 382, 525-8.
20. (b) Severin, K.; Lee, D. H.; Martinez, J. A.; Ghadiri, M. R. Chem.-Eur. J. 1997, 3, 1017-24.
21. (c) Severin, K.; Lee, D. H.; Kennan, A. J.; Ghadiri, M. R. Nature 1997, 389, 706-9.
22. (d) Yao, S.; Ghosh, I.; Zutshi, R.; Chmielewski, J. J. Am. Chem. Soc. 1997, 119, 10559-60.
23. (e) Yao, S.; Ghosh, I.; Zutshi, R.; Chmielewski, J. Nature 1998, 396, 447-50.
24. (f) Kennan, A. J.; Haridas, V.; Severin, K.; Lee, D. H.; Ghadiri, M. R. J. Am. Chem. Soc. 2001, 123, 1797-803.
25. (g) Matsumura, S.; Takahashi, T.; Ueno, A.; Mihara, H. Chem.-Eur. J. 2003, 9, 4829-37.
26. (a) Sasaki, T.; Kaiser, E. T. J. Am. Chem. Soc. 1989, 111, 380-1.
27. (b) Mihara, H.; Tomizaki, K. Y.; Nishino, N.; Fujimoto, T. Chem. Lett. 1993, 1533-6.
28. (c) Choma, C. T.; Lear, J. D.; Nelson, M. J.; Dutton, P. L.; Robertson, D. E.; DeGrado, W. F. J. Am. Chem. Soc. 1994, 116, 856-65.
29. (d) Geier, G. R.; Sasaki, T. Peptides: Chemistry, Structure and Biology, Proceeding of the American Peptide Symposium, 14th, Columbus, Ohio, June 18-23, 1995 1996, 591-2.
30. (e) Roy, R. S.; Imperiali, B. Protein Eng. 1997, 10, 691-8.
31. (f) Sakamoto, S.; Ueno, A.; Mihara, H. J. Chem. Soc., Perkin Trans. 2 1998, 2395-404.
32. (g) Baltzer, L. Curr. Opin. Struct. Biol. 1998, 8, 466-70.
33. (h) Shogren-Knaak, M. A.; Imperiali, B. Bioorg. Med. Chem. 1999, 7, 1993-2002.
34. (i) Geier, G. R., III; Sasaki, T. Tetrahedron 1999, 55, 1859-70.
35. (j) Tomizaki, K.; Tsunekawa, Y.; Akisada, H.; Mihara, H.; Nishino, N. J. Chem. Soc., Perk. Trans. 2 2000, 4, 813-22.
36. (k) Lombardi, A.; Nastri, F.; Pavone, V. Chem. Rev. 2001, 101, 3165-89.
37. (l) Rosenblatt, M. M.; Wang, J.; Suslick, K. S. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 13140-5.
38. (m) Kaplan, J.; DeGrado, W. F. Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 11566-70.
39. (n) Sakamoto, S.; Ito, A.; Kudo, K.; Yoshikawa, S. Chem.-Eur. J. 2004, 10, 3717-26.
40. (o) Butterfield, S. M.; Goodman, C. M.; Rotello, V. M.; Waters, M. L. Angew. Chem., Int. Ed. 2004, 43, 724-7.
41. (p) Huang, S. S.; Koder, R. L.; Lewis, M.; Wand, A. J.; Dutton, P. L. Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 5536-41.
42. (q) Ishida, M.; Dohmae, N.; Shiro, Y.; Oku, T.; Iizuka, T.; Isogai, Y. Biochemistry 2004, 43, 9823-33.
43. (r) Zhuang, J.; Amoroso, J. H.; Kinloch, R.; Dawson, J. H.; Baldwin, M. J.; Gibney, B. R. Inorg. Chem. 2004, 43, 8218-20.
44. (s) Rossi, P.; Tecilla, P.; Baltzer, L.; Scrimin, P. Chem.-Eur. J. 2004, 10, 4163-70.
45. (t) Nanda, V.; Rosenblatt, M. M.; Osyczka, A.; Kono, H.; Getahun, Z.; Dutton, P. L.; Saven, J. G.; DeGrado, W. F. J. Am. Chem. Soc. 2005, 127, 5804-5.
46. (u) Cochran, F. V.; Wu, S. P.; Wang, W.; Nanda, V.; Saven, J. G.; Therien, M. J.; DeGrado, W. F. J. Am. Chem. Soc. 2005, 127, 1346-7.
47. (v) Fukushima, H.; Sakamoto, S.; Kudo, K. Pept. Sci. 2006, 42, 419-22.
48. (a) Cane, D. E.; Walsh, C. T. Chem. Biol. 1999, 6, R319-R25.
49. (b) Khosla, C.; Harbury, P. B. Nature 2001, 409, 247-52.
50. (c) Sieber, S. A.; Marahiel, M. A. Chem. Rev. 2005, 105, 715-38.
51. (d) Fischbach, M. A.; Walsh, C. T. Chem. Rev. 2006, 106, 3468-96.
52. Wilcoxen, K. M.; Leman, L. J.; Weinberger, D. A.; Huang, Z.-Z.; Ghadiri, M. R. J. Am. Chem. Soc. 2007, 129, 748-9.
53. (a) Wieland, T.; Bokelmann, E.; Bauer, L.; Lang, H. U.; Lau, H.; Schafer, W. Justus Liebigs Ann. Chem. 1953, 583, 129-49.
54. (b) Brenner, M. Pept. Proc. Eur. Pept. Symp., 8th 1967, 1-7.
55. (c) Neumann, H.; Shashoua, V. E.; Sheehan, J. C.; Rich, A. Proc. Natl. Acad. Sci. U.S.A. 1968, 61, 1207-14.
56. (d) Kemp, D. S. Biopolymers 1981, 20, 1793-804.
57. (e) Sasaki, S.; Shionoya, M.; Koga, K. J. Am. Chem. Soc. 1985, 107, 3371-2.
58. (f) Dawson, P. E.; Muir, T. W.; Clark-Lewis, I.; Kent, S. B. H. Science 1994, 266, 776-9.
59. (g) Tamura, K.; Schimmel, P. Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 1393-7.
60. (h) Offer, J.; Boddy, C. N. C.; Dawson, P. E. J. Am. Chem. Soc. 2002, 124, 4642-6.
61. (i) Leleu, S.; Penhoat, M.; Bouet, A.; Dupas, G.; Papamicaeel, C.; Marsais, F.; Levacher, V. J. Am. Chem. Soc. 2005, 127, 15668-9.
62. (j) Snyder, T. M.; Liu, D. R. Angew. Chem., Int. Ed. 2005, 44, 7379-82.
63. (k) Chen, G.; Warren, J. D.; Chen, J.; Wu, B.; Wan, Q.; Danishefsky, S. J. J. Am. Chem. Soc. 2006, 128, 7460-2.
64. Harbury, P. B.; Zhang, T.; Kim, P. S.; Alber, T. Science 1993, 262, 1401-7.
65. Yadav, M. K.; Redman, J. E.; Leman, L. J.; Alvarez-Gutierrez, J. M.; Zhang, Y.; Stout, C. D.; Ghadiri, M. R. Biochemistry 2005, 44, 9723-32.
66. Yadav, M. K.; Leman, L. J.; Price, D. J.; Brooks, C. L.; Stout, C. D.; Ghadiri, M. R. Biochemistry 2006, 45, 4463-73.
67. (a) Lodi, P. J.; Knowles, J. R. Biochemistry 1993, 32, 4338-43.
68. (b) Zhu, L.; Kemple, M. D.; Yuan, P.; Prendergast, F. G. Biochemistry 1995, 34, 13196-202.
69. (c) Tsilikounas, E.; Rao, T.; Gutheil, W. G.; Bachovchin, W. W. Biochemistry 1996, 35, 2437-44.
70. (d) Zhou, Z.; Macosko, J. C.; Hughes, D. W.; Sayer, B. G.; Hawes, J.; Epand, R. M. Biophys. J. 2000, 78, 2418-25.
71. (a) Bundi, A.; Wuethrich, K. Biopolymers 1979, 18, 285-97.
72. (b) Matthew, J. B.; Gurd, F. R. N.; Garcia-Moreno, B.; Flanagan, M. A.; March, K. L.; Shire, S. J. Crit. Rev. Biochem. 1985, 18, 91-197.
73. (c) Song, J.; Laskowski, M., Jr.; Qasim, M. A.; Markley, J. L. Biochemistry 2003, 42, 2847-56.
74. (a) Spera, S.; Bax, A. J. Am. Chem. Soc. 1991, 113, 5490-2.
75. (b) Holtzer, M. E.; Lovett, E. G.; D'Avignon, D. A.; Holtzer, A. Biophys. J. 1997, 73, 1031-41.
76. (a) Wishart, D. S.; Sykes, B. D.; Richards, F. M. J. Mol. Biol. 1991, 222, 311-33.
77. (b) Wishart, D. S.; Sykes, B. D. Methods Enzymol. 1994, 239, 363-92.
78. Ashkenasy, G.; Jagasia, R.; Yadav, M.; Ghadiri, M. R. Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 10872-7.
79. (a) O'Shea, E. K.; Klemm, J. D.; Kim, P. S.; Alber, T. Science 1991, 254, 539-44.
80. (b) Harbury, P. B.; Kimm P. S.; Alber, T. Nature 1994, 371, 80-3.
81. DeLano, W. L. The PyMOL Molecular Graphics System: 2002; http:// www.pymol.org.
82. Sievers, D.; von Kiedrowski, G. Chem.-Eur. J. 1998, 4, 629-41.