Ligation-state hydrogen exchange: Coupled binding and folding equilibria in ribonuclease P protein

Journal of the American Chemical Society

Volumn 128, Issue 24, 2006, Pages 7772-7781

  Henkels, Christopher H ^a,b   Oas, Terrence G ^a  

^a DUKE UNIVERSITY MEDICAL CENTER   (United States)

^b UNIVERSITY OF VIRGINIA HEALTH SYSTEM   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DATA REDUCTION; HYDROGEN; ION EXCHANGE; IONIC STRENGTH; MATHEMATICAL MODELS; PHASE EQUILIBRIA;

CONFORMATIONAL PROPERTIES; GLOBAL OPENING REACTIONS; RIBONUCLEASE P PROTEIN;

PROTEINS;

AMIDE; ANION; BACTERIAL ENZYME; HYDROGEN; LIGAND; RIBONUCLEASE P; SULFATE;

ARTICLE; BACILLUS SUBTILIS; CALCULATION; CHEMICAL REACTION KINETICS; CONCENTRATION RESPONSE; ENERGY; FREE ENERGY; IONIC STRENGTH; LIGATION; LIGATION STATE HYDROGEN EXCHANGE; NUCLEAR MAGNETIC RESONANCE; PH; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN INTERACTION; PROTON TRANSPORT;

ALGORITHMS; BACILLUS SUBTILIS; DEUTERIUM EXCHANGE MEASUREMENT; HYDROGEN; HYDROGEN-ION CONCENTRATION; KINETICS; LIGANDS; MAGNETIC RESONANCE SPECTROSCOPY; OSMOLAR CONCENTRATION; PROTEIN CONFORMATION; PROTEIN FOLDING; RIBONUCLEASE P; SULFATES; THERMODYNAMICS;

EID: 33745428137     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja057279+     Document Type: Article

References (61)

1. Lindorff-Larsen, K.; Best, R. B.; Depristo, M. A.; Dobson, C. M.; Vendruseolo, M. Nature 2005, 433 (7022), 128-32.
2. Volkman, B. F.; Lipson, D.; Wemmer, D. E.; Kern, D. Science 2001, 291 (5512), 2429-33.
3. Koshland, D. E. Proc. Natl. Acad. Sci. U.S.A. 1958, 44 (2), 98-104.
4. Mulder, F. A.; Mittermaier, A.; Hon, B.; Dahlquist, F. W.; Kay, L. E. Nat. Struct. Biol. 2001, 8 (11), 932-5.
5. Clarke, J.; Itzhaki, L. S. Curr. Opin. Struct. Biol. 1998, 8 (1), 112-8.
6. Raschke, T. M.; Marqusee, S. Curr. Opin. Biotechnol. 1998, 9 (1), 80-6.
7. Englander, S. W. Annu. Rev. Biophys. Biomol. Struct. 2000, 29, 213-38.
8. Chakshusmathi, G.; Ratnaparkhi, G. S.; Madhu, P. K.; Varadarajan, R. Proc. Natl. Acad. Sci. U.S.A. 1999, 96 (14), 7899-904.
9. Wildes, D.; Marqusee, S. Protein Sci. 2005, 14 (1), 81-8.
10. Hsieh, J.; Andrews, A. J.; Fierke, C. A. Biopolymers 2004, 73 (1), 79-89.
11. Altman, S.; Kirsebom, L. In The RNA World. 2nd ed.; Gesteland, R. F., Cech, T. R., Atkins, J. F., Eds.; CSH Press: Cold Spring Harbor, NY, 1999; pp 351-80.
12. Frank, D. N.; Pace, N. R. Annu. Rev. Biochem. 1998, 67, 153-80.
13. Henkels, C. H.; Kurz, J. C.; Fierke, C. A.; Oas, T. G. Biochemistry 2001, 40 (9), 2777-89.
14. Tompa, P. TRENDS in Biochemical Sciences 2002, 27 (10), 527-533.
15. Dunker, A. K.; et al. J. Mol. Graphics Modell. 2001, 19 (1), 26-59.
16. Stams, T.; Niranjanakutnari, S.; Fierke, C. A.; Christianson, D. W. Science 1998, 280 (5364), 752-5.
17. Spitzfaden, C.; Nicholson, N.; Jones, J. J.; Guth, S.; Lehr, R.; Prescott, C. D.; Hegg, L. A.; Eggleston, D. S. J. Mol. Biol. 2000, 295 (1), 105-15.
18. Kazantsev, A. V.; Krivenko, A. A.; Harrington, D. J.; Carter, R. J.; Holbrook, S. R.; Adams, P. D.; Pace, N. R. Proc. Natl. Acad. Sci. U.S.A. 2003, 100 (13), 7497-502.
19. Henkels, C. H.; Oas, T. G. Biochemistry 2005, 44 (39), 13014-26.
20. Englander, S. W.; Mayne, L.; Bai, Y.; Sosnick, T. R. Protein Sci. 1997, 6 (5), 1101-9.
21. Schmid, F. X. In Protein structure: a practical approach, ed.; Creighton, T. E., Ed.; IRL Press: Oxford, 1989; pp 251-285.
22. Edelhoch, H. Biochemistry 1967, 6, 1948-1954.
23. Pace, C. N. Methods Emymol. 1986, 131, 266-80.
24. Santoro, M. M.; Bolen, D. W. Biochemistry 1988, 27 (21), 8063-8.
25. Delaglio, F.; Grzesiek, S.; Vuister, G. W.; Zhu, G.; Pfeifer, J.; Bax, A. J. Biomol. NMR 1995, 6 (3), 277-93.
26. Johnson, B. A. Methods Mol. Biol. 2004, 278, 313-52.
27. Bai, Y.; Milne, J. S.; Mayne, L.; Englander, S. W. Proteins 1993, 17 (1), 75-86.
28. Milne, J. S.; Mayne, L.; Roder, H.; Wand, A. J.; Englander, S. W. Protein Sci. 1998, 7 (3), 739-45.
29. Tuchsen, E.; Woodward, C. J. Mol. Biol. 1985, 185 (2), 405-19.
30. Englander, S. W.; Kallenbach, N. R. Q. Rev. Biophys. 1983, 16 (4), 521-655.
31. Woodward, C.; Simon, I.; Tuchsen, E. Mol. Cell Biochem. 1982, 48 (3), 135-60.
32. Hvidt, A.; Nielsen, S. O. Adv. Protein Chem. 1966, 21, 287-386.
33. Li, R.; Woodward, C. Protein Sci. 1999, 8 (8), 1571-90.
34. Bai, Y.; Sosnick, T. R.; Mayne, L.; Englander, S. W. Science 1995, 269 (5221), 192-7.
35. Baldwin, R. L. Biophys. J. 1996, 71 (4), 2056-63.
36. Ferreon, J. C.; Volk, D. E.; Luxon, B. A.; Gorenstein, D. G.; Hilser, V. J. Biochemistry 2003, 42 (19), 5582-91.
37. Paterson, Y.; Englander, S. W.; Roder, H. Science 1990, 249 (4970), 755-9.
38. Mayne, L.; Paterson, Y.; Cerasoli, D.; Englander, S. W. Biochemistry 1992, 31 (44), 10678-85.
39. Werner, M. H.; Wemmer, D. E. J. Mol. Biol. 1992, 225 (3), 873-89.
40. Benjamin, D. C.; Williams, D. C., Jr.; Smith-Gill, S. J.; Rule, G. S. Biochemistry 1992, 31 (40), 9539-45.
41. Orban, J.; Alexander, P.; Bryan, P. Biochemistry 1994, 33 (19), 5702-10.
42. Yi, Q.; Erman, J. E.; Satterlee, J. D. Biochemistry 1994, 33 (40), 12032-41.
43. Williams, D. C., Jr.; Benjamin, D. C.; Poljak, R. J.; Rule, G. S. J. Mol. Biol. 1996, 257 (4), 866-76.
44. Williams, D. C., Jr.; Rule, G. S.; Poljak, R. J.; Benjamin, D. C. J. Mol. Biol. 1997, 270 (5), 751-62.
45. Wang, C.; Pawley, N. H.; Nicholson, L. K. J. Mol. Biol. 2001, 313 (4), 873-87.
46. Massiah, M. A.; Saraswat, V.; Azurmendi, H. F.; Mildvan, A. S. Biochemistry 2003, 42 (34), 10140-54.
47. Emerson, S. D.; Palermo, R.; Liu, C. M.; Tilley, J. W.; Chen, L.; Danho, W.; Madison, V. S.; Greeley, D. N.; Ju, G.; Fry, D. C. Protein Sci. 2003, 12 (4), 811-22.
48. Marcus, Y. Biophys. Chem. 1994, 51 (2-3), 111-127.
49. Dong, A.; Hyslop, R. M.; Pringle, D. L. Arch Biochem. Biophys. 1996, 333 (1), 275-81.
50. Cordier, F.; Wang, C.; Grzesiek, S.; Nicholson, L. K. J. Mol. Biol. 2000, 304 (4), 497-505.
51. Chamberlain, A. K.; Handel, T. M.; Marqusee, S. Nat. Struct. Biol. 1996, 3 (9), 782-7.
52. Raschke, T. M.; Marqusee, S. Nat. Struct. Biol. 1997, 4 (4), 298-304.
53. Krishna, M. M.; Lin, Y.; Mayne, L.; Englander, S. W. J. Mol. Biol. 2003, 334 (3), 501-13.
54. Lu, J.; Dahlquist, F. W. Biochemistry 1992, 31 (20), 4749-56.
55. Jennings, P. A.; Wright, P. E. Science 1993, 262 (5135), 892-6.
56. Fersht, A. R. Structure and Mechanism In Protein Structure: a guide to enzyme catalysis and protein folding, 2nd ed.; W. H. Freeman and Company: New York, 1999; p 631.
57. Mandell, J. G.; Falick, A. M.; Komives, E. A. Proc. Natl. Acad. Sci. U.S.A. 1998, 95 (25), 14705-10.
58. Engen, J. R.; Gmeiner, W. H.; Smithgall, T. E.; Smith, D. L. Biochemistry 1999, 38 (28), 8926-35.
59. Andersen, M. D.; Shaffer, J.; Jennings, P. A.; Adams, J. A. J. Biol. Chem. 2001, 276 (17), 14204-11.
60. Hamuro, Y.; Wong, L.; Shaffer, J.; Kim, J. S.; Stranz, D. D.; Jennings, P. A.; Woods, V. L., Jr.; Adams, J. A. J. Mol. Biol. 2002, 323 (5), 871-81.
61. Hoofnagle, A. N.; Resing, K. A.; Ahn, N. G. Annu. Rev. Biophys. Biomol. Struct. 2003, 32, 1-25.