Temperature dependence of the backbone dynamics of ribonuclease A in the ground state and bound to the inhibitor 5′-phosphothymidine (3′-5′)pyrophosphate adenosine 3′-phosphate

Biochemistry

Volumn 42, Issue 18, 2003, Pages 5279-5291

  Kovrigin, Evgenii L ^a   Cole, Roger ^a   Loria, J Patrick ^a  

^a YALE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

LIGAND BINDING;

CALORIMETRY; DISSOCIATION; ENZYMES; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; THERMAL EFFECTS;

BIOCHEMISTRY;

5' PHOSPHOTHYMIDINE[3',5']PYROPHOSPHATE ADENOSINE 3' PHOSPHATE; PHOSPHATE; RIBONUCLEASE A; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ARTICLE; BINDING AFFINITY; CALORIMETRY; CONTROLLED STUDY; CORRELATION ANALYSIS; DISSOCIATION CONSTANT; ENTROPY; ENZYME ACTIVITY; ENZYME BINDING; LIGAND BINDING; NONHUMAN; PHYSICAL CHEMISTRY; PRIORITY JOURNAL; PROTON NUCLEAR MAGNETIC RESONANCE; STRUCTURE ANALYSIS; TEMPERATURE DEPENDENCE;

ADENOSINE MONOPHOSPHATE; ANIMALS; CATTLE; DIPHOSPHATES; ENTROPY; ENZYME INHIBITORS; MAGNETIC RESONANCE SPECTROSCOPY; MODELS, CHEMICAL; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN FOLDING; RECOMBINANT PROTEINS; RIBONUCLEASE, PANCREATIC; TEMPERATURE; THERMODYNAMICS; THYMIDINE;

BOVINAE;

EID: 0038219675     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi034027h     Document Type: Article

References (97)

1. delCardayre, S. B., and Raines, R. T. (1994) Biochemistry 33, 6031-6037.
2. Riordan, J. F. (1997) in Ribonucleases: Structures and Functions (D'Alessio, G., and Riordan, J. F., Eds.) pp 445-489, Academic Press, New York.
3. D'Alessio, G., Di Donato, A., Mazzarella, L., and Piccoli, R. (1997) in Ribonucleases: Structures and Functions (D'Alessio, G., and Riordan, J. F., Eds.) pp 383-423, Academic Press, New York.
4. Youle, R. J., and D'Alessio, G. (1997) in Ribonucleases: Structures and Functions (D'Alessio, G., and Riordan, J. F., Eds.) pp 491-514, Academic Press, New York.
5. Anfinsen, C. B. (1973) Science 181, 223-230.
6. Moore, S., and Stein, W. H. (1973) Science 180, 458-464.
7. Merrifield, B. (1986) Science 232, 341-347.
8. Kartha, G., Bello, J., and Harker, D. (1967) Nature 213, 862-865.
9. Rasmussen, B. F., Stock, A. M., Ringe, D., and Petsko, G. A. (1992) Nature 357, 423-424.
10. Raines, R. T. (1998) Chem. Rev. 98, 1045-1066.
11. Thompson, J. E., Kutateladze, M. C., Venegas, F. D., Messmore, J. M., and Raines, R. T. (1995) Bioorg. Chem. 23, 471-481.
12. Erman, J. E., and Hammes, G. G. (1966) J. Am. Chem. Soc. 88, 5607-5614.
13. Cathou, R. E., and Hammes, G. G. (1965) J. Am. Chem. Soc. 86, 3240-3245.
14. Hammes, G. G. (2002) Biochemistry 41, 8221-8228.
15. Cole, R., and Loria, J. P. (2002) Biochemistry 41, 6072-6081.
16. Pauling, L. (1948) Nature 161, 707-709.
17. Bruice, T. C., and Benkovic, S. J. (2000) Biochemistry, 39, 6267-6274.
18. Young, L., and Post, C. B. (1996) Biochemistry 35, 15129-15133.
19. Cameron, C. E., and Benkovic, S. J. (1997) Biochemistry 36, 15792-15800.
20. Fushman, D., Weisemann, R., Thüring, H., and Rüterjans, H. (1994) J. Biomol. NMR 4, 61-78.
21. Mandel, A. M., Akke, M., and Palmer, A. G. (1995) J. Mol. Biol. 246, 144-163.
22. Shapiro, Y. E., Sinev, M. A., Sineva, E. V., Tugarinov, V., and Meirovitch, E. (2000) Biochemistry 39, 6634-6644.
23. Wang, L., Pang, Y., Holder, T., Brender, J. R., Kurochkin, A. V., and Zuiderweg, E. R. (2001) Proc. Natl. Acad. Sci. U.S.A. 98, 7684-7689.
24. Deng, H., Zhadin, N., and Callender, R. (2001) Biochemistry 40, 3767-3773.
25. Rader, S. D., and Agard, D. A. (1997) Protein Sci. 6, 1375-1386.
26. Tilton, R. F., Dewan, J. C., and Petsko, G. A. (1992) Biochemistry 31, 2469-2481.
27. Kohen, A., and Klinman, J. P. (2000) J. Am. Chem. Soc. 122, 10738-10739.
28. Antoniou, D., and Schwartz, S. D. (2001) J. Phys. Chem. B. 105, 5553-5558.
29. Radkiewicz, J. L., and Brooks, C. L. I. (2000) J. Am. Chem. Soc. 122, 225-231.
30. Villa, J., and Warshel, A. (2001) J. Phys. Chem. B 105, 7887-7907.
31. Ota, N., and Agard, D. A. (2001) Protein Sci. 10, 1403-1414.
32. Broos, J., Visser, A. J. W. G., Engbersen, J. F. J., Verboom, W., van Hoek, A., and Reinhoudt, D. N. (1995) J. Am. Chem. Soc. 117, 12657-12663.
33. Akerud, T., Thulin, E., Van Etten, R. L., and Akke, M. (2002) J. Mol. Biol. 322, 137-152.
34. Eisenmesser, E. Z., Bosco, D. A., Akke, M., and Kem, D. (2002) Science 295, 1520-1523.
35. Rozovsky, S., Jogl, G., Tong, L., and McDermott, A. E. (2001) J. Mol. Biol. 310, 271-280.
36. Williams, J. C., and McDermott, A. E. (1995) Biochemistry 34, 8309-8319.
37. Akke, M., Brüschweiler, R., and Palmer, A. G. (1993) J. Am. Chem. Soc. 115, 9832-9833.
38. Li, Z., Raychaudhuri, S., and Wand, A. J. (1996) Protein Sci. 5, 2647-2650.
39. Yang, D., and Kay, L. E. (1996) J. Mol. Biol. 263, 369-382.
40. Bracken, C., Carr, P. A., Cavanagh, J., and Palmer, A. G. (1999) J. Mol. Biol. 285, 2133-2146.
41. Seewald, M. J., Pichumani, K., Stowell, C., Tibbals, B. V., Regan, L., and Stone, M. J. (2000) Protein Sci. 9, 1177-1193.
42. Yang, D., Mok, Y. K., Forman-Kay, J. D., Farrow, N. A., and Kay, L. E. (1997) J. Mol. Biol. 272, 790-804.
43. Lee, A. L., and Wand, A. J. (2001) Nature 411, 501-504.
44. Lee, A. L., Sharp, K. A., Kranz, J. K., Song, X.-J., and Wand, A. J. (2002) Biochemistry 41, 13814-13825.
45. Mandel, A. M., Akke, M., and Palmer, A. G. (1996) Biochemistry 35, 16009-16023.
46. delCardayre, S. B., Ribo, M., Yokel, E. M., Quirk, D. J., Rutter, W. J., and Raines, R. T. (1995) Protein Eng. 8, 261-273.
47. Anderson, D. G., Hammes, G. G., and Walz, F. G., Jr. (1968) Biochemistry 7, 1637-1645.
48. Moffat, J. G., and Khorana, H. G. (1961) J. Am. Chem. Soc. 83, 663-675.
49. Russo, N., and Shapiro, R. (1999) J. Biol. Chem. 274, 14902-14908.
50. Son, T. D., and Chachaty, C. (1977) Biochim. Biophys. Acta 500, 405-418.
51. Jelesarov, I., and Bosshard, H. R. (1999) J. Mol. Recognit. 12, 3-18.
52. Spolar, R. S., Livingstone, J. R., and Record, M. T., Jr. (1992) Biochemistry 31, 3947-3955.
53. Murphy, K. P., and Freire, E. (1992) Adv. Protein Chem. 43, 313-361.
54. Hubbard, S. J., and Thornton, J. M. (1993) Department of Biochemistry and Molecular Biology, University College, London.
55. Wlodawer, A., Svensson, L. A., Sjolin, L., and Gilliland, G. L. (1988) Biochemistry 27, 2705-2717.
56. Leonidas, D. D., Shapiro, R., Irons, L. I., Russo, N., and Acharya, K. R. (1999) Biochemistry 38, 10287-10297.
57. Kordel, J., Skelton, N. J., Akke, M., Plamer, A. G., and Chazin, W. J. (1992) Biochemistry 31, 4856-4866.
58. Skelton, N. J., Palmer, A. G., Akke, M., Kördel, J., Rance, M., and Chazin, W. J. (1993) J. Magn. Reson., Ser. B 102, 253-264.
59. Kay, L. E., Keifer, P., and Saarinen, T. (1992) J. Am. Chem. Soc. 114, 10663-10665.
60. Kempf, J. G., and Loria, J. P. (2003) in Protein NMR Techniques (Downing, A. K., Ed.) Humana Press, Totowa, NJ (in press).
61. Kroenke, C. D., Loria, J. P., Lee, L. K., Rance, M., and Palmer, A. G. (1998) J. Am. Chem. Soc. 120, 7905-7915.
62. Tjandra, N., Szabo, A., and Bax, A. (1996) J. Am. Chem. Soc. 118, 6986-6991.
63. Delaglio, F., Grzesiak, S., Vuister, G., Zhu, G., Pfeifer, J., and Bax, A. (1995) J. Biomol. NMR 6, 277-293.
64. Goddard, T., and Kneller, D. G. SPARKY 3, University of California, San Francisco.
65. Lipari, G., and Szabo, A. (1982) J. Am. Chem. Soc. 104, 4546-4559.
66. Lipari, G., and Szabo, A. (1982) J. Am. Chem. Soc. 104, 4559-4570.
67. Cole, R., and Loria, J. P. (2003) J. Biomol. NMR (in press).
68. Palmer, A. G., Rance, M., and Wright, P. E. (1991) J. Am. Chem. Soc. 113, 4371-4380.
69. Tjandra, N., Feller, S. E., Pastor, R. W., and Bax, A. (1995) J. Am. Chem. Soc. 117, 12562-12566.
70. Hiyama, Y., Niu, C.-H., Silverton, J. V., Bavoso, A., and Torchia, D. A. (1988) J. Am. Chem. Soc. 110, 2378-2383.
71. Fairbrother, W. J., Liu, J., Pisacane, P. I., Sliwkowski, Sliwkowski, M. X., and Palmer, A. G. (1998) J. Mol. Biol. 279, 1149-1161.
72. Fushman, D., Tjandra, N., and Cowbum, D. (1998) J. Am. Chem. Soc. 120, 10947-10952.
73. Evenas, J., Forsen, S., Malmendal, A., and Akke, M. (1999) J. Mol. Biol. 289, 603-617.
74. Fisher, H. F., and Singh, N. (1995) Methods Enzymol. 259, 194-221.
75. Eftink, M. R., Anusiem, A. C., and Biltonen, R. L. (1983) Biochemistry, 22, 3884-3896.
76. Horn, J. R., Russell, D., Lewis, E. A., and Murphy, K. P. (2001) Biochemistry 40, 1774-8.
77. Marion, D., Driscoll, P. C., Kay, L. E., Wingfield, P. T., Bax, A., Gronenborn, A. M., and Clore, G. M. (1989) Biochemistry 28, 6150-6156.
78. Marion, D., Kay, L. E., Sparks, S. W., Torchia, D. A., and Bax, A. (1989) J. Am. Chem. Soc. 111, 1515-1517.
79. Zuiderweg, E., and Fesik, S. (1989) Biochemistry 28, 2387-2391.
80. Russo, N., Shapiro, R., and Vallee, B. L. (1997) Biochem. Biophys. Res. Commun. 231, 671-674.
81. Leon-Lai, C. H., Gresser, M. J., and Tracey, A. S. (1996) Can. J. Chem. 74, 38-48.
82. Messmore, J. M., and Raines, R. T. (2000) J. Am. Chem. Soc. 122, 9911-9916.
83. Dwek, R. A. (1973) NMR in Biochemistry: Applications to Enzyme Systems, Clarendon Press, Oxford.
84. Millet, O. M., Loria, J. P., Kroenke, C. D., Pons, M., and Palmer, A. G. (2000) J. Am. Chem. Soc. 122, 2867-2877.
85. Loria, J. P., Rance, M., and Palmer, A. G. (1999) J. Am. Chem. Soc. 121, 2331-2332.
86. Borah, B., Chen, C., Egan, W., Miller, M., Wlodawer, A., and Cohen, J. S. (1985) Biochemistry 24, 2058-2067.
87. Palmer, A. G. (1993) Curr. Opin. Biotechnol. 4, 385-391.
88. Stivers, J. T., Abeygunawardana, C., and Mildvan, A. S. (1996) Biochemistry 35, 16036-16047.
89. Spolar, R. S., and Record, M. T. (1994) Science 263, 777-784.
90. Devore, J. (2000) Probability and Statistics for Engineering and the Sciences, Brooks/Cole Publishing Company, Monterey.
91. Dubins, D. N., Filfil, R., Macgregor, R. B., and Chalikian, T. V. (2000) J. Phys. Chem. B 104, 390-401.
92. Makhatadze, G. I., and Privalov, P. L. (1995) Adv. Protein Chem. 47, 307-425.
93. Privalov, P. L., and Makhatadze, G. I. (1993) J. Mol. Biol. 232, 660-679.
94. Pickett, S. D., and Sternberg, M. J. E. (1993) J. Mol. Biol. 231, 825-839.
95. Creamer, T. P., and Rose, G. D. (1992) Proc. Natl. Acad. Sci. U.S.A. 89, 5937-5941.
96. Prompers, J. J., and Bruschweiler, R. (2000) J. Phys. Chem. 104, 11416-11424.
97. Grzesiek, S., Stahl, S. J., Wingfield, P. T., and Bax, A. (1996) Biochemistry 35, 10256-10261.