Transient enzyme - Substrate recognition monitored by real-time NMR

Journal of the American Chemical Society

Volumn 133, Issue 29, 2011, Pages 11154-11162

  Haupt, Caroline ^a   Patzschke, Rica ^a   Weininger, Ulrich ^a,b   Gröger, Stefan ^a   Kovermann, Michael ^a   Balbach, Jochen ^a  

^a MARTIN LUTHER UNIVERSITY HALLE WITTENBERG   (Germany)

^b LUND UNIVERSITY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

ACTIVE SITE; ENZYME REACTION; ESCHERICHIA COLI (E. COLI); FOLDING INTERMEDIATES; FOLDING PROCESS; FUNCTIONAL DOMAINS; INTERACTION SITE; KINETIC FOLDING INTERMEDIATES; LIVING CELL; PROLYL BONDS; SPEED-UPS; STRUCTURAL CHARACTERIZATION; SUBSTRATE RECOGNITION; TIME-RESOLVED;

AMINO ACIDS; CATALYSIS; ESCHERICHIA COLI; KINETIC ENERGY; KINETICS; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PROTEIN FOLDING; PROTEINS;

ENZYMES;

ISOMERASE; PEPTIDYL CARRIER PROTEIN; PROLINE DERIVATIVE; RIBONUCLEASE T1;

ARTICLE; CATALYSIS; CHEMICAL BOND; ENZYME ACTIVE SITE; ENZYME SUBSTRATE; ENZYME SUBSTRATE COMPLEX; ESCHERICHIA COLI; HETERONUCLEAR SINGLE QUANTUM COHERENCE; ISOMERIZATION; MICHAELIS MENTEN KINETICS; NONHUMAN; PROTEIN AGGREGATION; PROTEIN FOLDING; PROTON NUCLEAR MAGNETIC RESONANCE;

BINDING SITES; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; MODELS, MOLECULAR; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PEPTIDYLPROLYL ISOMERASE; PROTEIN FOLDING; RIBONUCLEASE T1; SUBSTRATE SPECIFICITY;

EID: 79960616811     PISSN: 00027863     EISSN: 15205126     Source Type: Journal    
DOI: 10.1021/ja2010048     Document Type: Article

References (88)

1. Dobson, C. M. Trends Biochem. Sci. 1999, 24, 329
2. Kelly, S. M.; Price, N. C. Curr. Protoc. Protein Sci. 2006, Charper 20 Unit 20.10
3. Royer, C. A. Chem. Rev 2006, 106, 1769
4. Schuler, B.; Eaton, W. A. Curr. Opin. Struct. Biol. 2008, 18, 16
5. Balbach, J.; Steegborn, C.; Schindler, T.; Schmid, F. X. J. Mol. Biol. 1999, 285, 829
6. Dyson, H. J.; Wright, P. E. Nat. Rev. Mol. Cell Biol. 2005, 6, 197
7. Korzhnev, D. M.; Kay, L. E. Acc. Chem. Res. 2008, 41, 442
8. Bartlett, A.; Radford, S. E. Nat. Struct. Mol. Biol. 2009, 16, 582
9. Fersht, A. R. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 1525
10. Jackson, S. E. Folding Des. 1998, 3, R81
11. Schindler, T.; Herrler, M.; Marahiel, M. A.; Schmid, F. X. Nat. Struct. Biol. 1995, 2, 663
12. Eaton, W. A.; Munoz, V.; Hagen, S. J.; Jas, G. S.; Lapidus, L. J.; Henry, E. R.; Hofrichter, J. Annu. Rev. Biophys. Biomol. Struct. 2000, 29, 327
13. Ferguson, N.; Fersht, A. R. Curr. Opin. Struct. Biol. 2003, 13, 75
14. Jahn, T. R.; Radford, S. E. FEBS J. 2005, 272, 5962
15. Dobson, C. M. Nature 2003, 426, 884
16. Dobson, C. M. Semin. Cell Dev. Biol. 2004, 15, 3
17. Bukau, B.; Deuerling, E.; Pfund, C.; Craig, E. A. Cell 2000, 101, 119
18. Young, J. C.; Agashe, V. R.; Siegers, K.; Hartl, F. U. Nat. Rev. Mol. Cell Biol. 2004, 5, 781
19. Walter, S.; Buchner, J. Angew. Chem., Int. Ed. 2002, 41, 1098
20. Collet, J. F.; Riemer, J.; Bader, M. W.; Bardwell, J. C. J. Biol. Chem. 2002, 277, 26886
21. Fischer, G.; Wittmann-Liebold, B.; Lang, K.; Kiefhaber, T.; Schmid, F. X. Nature 1989, 337, 476
22. Rouviere, P. E.; Gross, C. A. Gene Dev. 1996, 10, 3170
23. Ramm, K.; Plückthun, A. J. Biol. Chem. 2000, 275, 17106
24. Ramm, K.; Plückthun, A. J. Mol. Biol. 2001, 310, 485
25. Saul, F. A.; Arie, J. P.; Vulliez-le Normand, B.; Kahn, R.; Betton, J. M.; Bentley, G. A. J. Mol. Biol. 2004, 335, 595
26. Scholz, C.; Stoller, G.; Zarnt, T.; Fischer, G.; Schmid, F. X. EMBO J. 1997, 16, 54
27. Hesterkamp, T.; Bukau, B. FEBS Lett. 1996, 389, 32
28. Stoller, G.; Rücknagel, K. P.; Nierhaus, K.; Schmid, F. X.; Fischer, G.; Rahfeld, J.-U. EMBO J. 1995, 14, 4939
29. Suzuki, R.; Nagata, K.; Yumoto, F.; Kawakami, M.; Nemoto, N.; Furutani, M.; Adachi, K.; Maruyama, T.; Tanokura, M. J. Mol. Biol. 2003, 328, 1149
30. Wülfing, C.; Lombardero, J.; Plückthun, A. J. Biol. Chem. 1994, 269, 2895
31. Roof, W. D.; Horne, S. M.; Young, K. D.; Young, R. J. Biol. Chem. 1994, 269, 2902
32. Roof, W. D.; Fang, H. Q.; Young, K. D.; Sun, J.; Young, R. Mol. Microbiol. 1997, 25, 1031
33. Scholz, C.; Eckert, B.; Hagn, F.; Schaarschmidt, P.; Balbach, J.; Schmid, F. X. Biochemistry 2006, 45, 20
34. Scholz, C.; Schaarschmidt, P.; Engel, A. M.; Andres, H.; Schmitt, U.; Faatz, E.; Balbach, J.; Schmid, F. X. J. Mol. Biol. 2005, 345, 1229
35. Weininger, U.; Haupt, C.; Schweimer, K.; Graubner, W.; Kovermann, M.; Brüser, T.; Scholz, C.; Schaarschmidt, P.; Zoldak, G.; Schmid, F. X.; Balbach, J. J. Mol. Biol. 2009, 387, 295
36. Martino, L.; He, Y.; Hands-Taylor, K. L.; Valentine, E. R.; Kelly, G.; Giancola, C.; Conte, M. R. FEBS J. 2009, 276, 4529
37. Hottenrott, S.; Schumann, T.; Plückthun, A.; Fischer, G.; Rahfeld, J. U. J. Biol. Chem. 1997, 272, 15697
38. Löw, C.; Neumann, P.; Tidow, H.; Weininger, U.; Haupt, C.; Friedrich-Epler, B.; Scholz, C.; Stubbs, M. T.; Balbach, J. J. Mol. Biol. 2010, 398, 375
39. Zhang, J. W.; Butland, G.; Greenblatt, J. F.; Emili, A.; Zamble, D. B. J. Biol. Chem. 2005, 280, 4360
40. Zhang, J. W.; Leach, M. R.; Zamble, D. B. J. Bacteriol. 2007, 189, 7942
41. Leach, M. R.; Zhang, J. W.; Zamble, D. B. J. Biol. Chem. 2007, 282, 16177
42. Graubner, W.; Schierhorn, A.; Brüser, T. J. Biol. Chem. 2007, 282, 7116
43. Kiefhaber, T.; Grunert, H.-P.; Hahn, U.; Schmid, F. X. Biochemistry 1990, 29, 6475
44. Kiefhaber, T.; Quaas, R.; Hahn, U.; Schmid, F. X. Biochemistry 1990, 29, 3061
45. Kiefhaber, T.; Quaas, R.; Hahn, U.; Schmid, F. X. Biochemistry 1990, 29, 3053
46. Kiefhaber, T.; Schmid, F. X.; Willaert, K.; Engelborghs, Y.; Chaffotte, A. Protein Sci. 1992, 1, 1162
47. Heinemann, U.; Hahn, U. Structural and functional studies of ribonuclease T1. In Protein-Nucleic Acid Interaction; Saenger, W.; Heinemann, U., Eds.; MacMillan: London, 1989; p 111.
48. Mücke, M.; Schmid, F. X. Biochemistry 1994, 33, 14608
49. Steegborn, C.; Schneider-Hassloff, H.; Zeeb, M.; Balbach, J. Biochemistry 2000, 39, 7910
50. Balbach, J.; Forge, V.; van Nuland, N. A. J.; Winder, S. L.; Hore, P. J.; Dobson, C. M. Nat. Struct. Biol. 1995, 2, 865
51. Schlepckow, K.; Wirmer, J.; Bachmann, A.; Kiefhaber, T.; Schwalbe, H. J. Mol. Biol. 2008, 378, 686
52. Hore, P. J.; Winder, S. L.; Roberts, C. H.; Dobson, C. M. J. Am. Chem. Soc. 1997, 119, 5049
53. Mok, K. H.; Hore, P. J. Methods 2004, 34, 75
54. Bhuyan, A. K.; Udgaonkar, J. B. Biochemistry 1999, 38, 9158
55. Killick, T. R.; Freund, S. M.; Fersht, A. R. Protein Sci. 1999, 8, 1286
56. Balbach, J.; Forge, V.; Lau, W. S.; van Nuland, N. A. J.; Brew, K.; Dobson, C. M. Science 1996, 274, 1161
57. Felli, I. C.; Brutscher, B. Chem. Phys. Chem. 2009, 10, 1356
58. Szyperski, T.; Atreya, H. S. Magn. Reson. Chem. 2006, 44, S51
59. Freeman, R.; Kupce, E. Concepts Magn. Reson., Part A 2004, 23A, 63
60. Szyperski, T.; Wider, G.; Bushweller, J. H.; Wuthrich, K. J. Biomol. NMR 1993, 3, 127
61. Kupce, E.; Freeman, R. J. Am. Chem. Soc. 2004, 126, 6429
62. Kupce, E.; Freeman, R. J. Biomol. NMR 2003, 25, 349
63. Brutscher J. Biomol. NMR 2004, 29, 57
64. Frydman, L.; Scherf, T.; Lupulescu, A. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 15858
65. Hyberts, S. G.; Takeuchi, K.; Wagner, G. J. Am. Chem. Soc. 2010, 132, 2145
66. Ernst, R. R.; Bodenhausen, G.; Wokaun, A. Principles of Nuclear Magnetic Resonance in One and Two Dimensions; Oxford University Press: Oxford, 1987; p 124.
67. Ross, A.; Salzman, M.; Senn, H. J. Biomol. NMR 1997, 10, 389
68. Lescop, E.; Schanda, P.; Brutscher, B. J. Magn. Reson. 2007, 187, 163
69. Pervushin, K.; Vögeli, B.; Eletsky, A. J. Am. Chem. Soc. 2002, 124, 12898
70. Schanda, P.; Brutscher, B. J. Am. Chem. Soc. 2005, 127, 8014
71. Schanda, P.; Forge, V.; Brutscher, B. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 11257
72. Schanda, P.; Kupce, E.; Brutscher, B. J. Biomol. NMR 2005, 33, 199
73. Schanda, P.; Van Melckebeke, H.; Brutscher, B. J. Am. Chem. Soc. 2006, 128, 9042
74. Corazza, A.; Rennella, E.; Schanda, P.; Mimmi, M. C.; Cutuil, T.; Raimondi, S.; Giorgetti, S.; Fogolari, F.; Viglino, P.; Frydman, L.; Gal, M.; Bellotti, V.; Brutscher, B.; Esposito, G. J. Biol. Chem. 2010, 285, 5827
75. Mücke, M.; Schmid, F. X. J. Mol. Biol. 1994, 239, 713
76. Löw, C.; Neumann, P.; Tidow, H.; Weininger, U.; Haupt, C.; Friedrich-Epler, B.; Scholz, C.; Stubbs, M. T.; Balbach, J. J. Mol. Biol. 2010, 398, 375-390
77. Haupt, C.; Weininger, U.; Kovermann, M.; Balbach, J. Biochemistry 2011, submitted for publication.
78. Delaglio, F.; Grzesiek, S.; Vuister, G. W.; Zhu, G.; Pfeifer, J.; Bax, A. J. Biomol. NMR 1995, 6, 277
79. Johnson, B. A. Methods Mol. Biol. 2004, 278, 313
80. Weininger, U.; Jakob, R. P.; Eckert, B.; Schweimer, K.; Schmid, F. X.; Balbach, J. Proc. Natl. Acad. Sci. U.S.A. 2009, 106, 12335
81. Neal, S.; Nip, A. M.; Zhang, H.; Wishart, D. S. J. Biomol. NMR 2003, 26, 215-240
82. Zeeb, M.; Balbach, J. Methods 2004, 34, 65
83. Aumüller, T.; Fischer, G. J. Mol. Biol. 2008, 376, 1478
84. Knappe, T. A.; Eckert, B.; Schaarschmidt, P.; Scholz, C.; Schmid, F. X. J. Mol. Biol. 2007, 368, 1458
85. Scholz, C.; Thirault, L.; Schaarschmidt, P.; Zarnt, T.; Faatz, E.; Engel, A. M.; Upmeier, B.; Bollhagen, R.; Eckert, B.; Schmid, F. X. Biochemistry 2008, 47, 4276
86. Benanti, E. L.; Chivers, P. T. J. Bacteriol. 2009, 191, 2405
87. Stingl, K.; Schauer, K.; Ecobichon, C.; Labigne, A.; Lenormand, P.; Rousselle, J. C.; Namane, A.; de Reuse, H. Mol. Cell Proteomics 2008, 7, 2429
88. Han, K. Y.; Song, J. A.; Ahn, K. Y.; Park, J. S.; Seo, H. S.; Lee, J. Protein Eng. Des. Sel. 2007, 20, 543