Dynamics of ribonuclease H: Temperature dependence of motions on multiple time scales

Biochemistry

Volumn 35, Issue 50, 1996, Pages 16009-16023

  Mandel, Arthur M ^a   Akke, Mikael ^a   Palmer III, Arthur G ^a  

^a Columbia University ^*  (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RIBONUCLEASE H;

ARTICLE; CARBOXY TERMINAL SEQUENCE; ENTHALPY; ENZYME CONFORMATION; ENZYME PURIFICATION; ESCHERICHIA COLI; MOLECULAR DYNAMICS; NONHUMAN; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; NUCLEAR OVERHAUSER EFFECT; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE; TEMPERATURE DEPENDENCE; TIME;

AMINO ACID SEQUENCE; COMPUTER SIMULATION; ESCHERICHIA COLI; KINETICS; MAGNETIC RESONANCE SPECTROSCOPY; MODELS, CHEMICAL; MODELS, STRUCTURAL; PROTEIN STRUCTURE, SECONDARY; RECOMBINANT PROTEINS; RIBONUCLEASE H, CALF THYMUS; THERMODYNAMICS;

EID: 0030445011     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi962089k     Document Type: Article

References (105)

1. Abragam, A. (1961) Principles of Nuclear Magnetism, pp 1-599, Clarendon Press, Oxford.
2. Akke, M., & Palmer, A. G. (1996) J. Am. Chem. Soc. 118, 911-912.
3. Akke, M., Brüschweiler, R., & Palmer, A. G. (1993) J. Am. Chem. Soc. 115, 9832-9833.
4. Akke, M., Carr, P. A., & Palmer, A. G. (1994) J. Magn. Reson. Ser. B 104, 298-302.
5. Allerhand, A., & Gutowsky, H. S. (1965) J. Chem. Phys. 42, 1587-1599.
6. Barkhuijsen, H., de Beer, R., & van Ormondt. D. (1987) J. Magn. Reson. 73, 553-557.
7. Bloom, M., Reeves, L. W., & Wells, E. J. (1965) J. Chem. Phys. 42, 1615-1624.
8. Boyd, J., Hommel, U., & Campbell, I. D. (1990) Chem. Phys. Lett. 175, 477-482.
9. Brink, D. M., & Satchler, G. R. (1993) Angular Momentum. pp 1-170, Clarendon Press, Oxford.
10. Brüschweiler, R., & Wright, P. E. (1994) J. Am. Chem. Soc. 116, 8426-8427.
11. Brüschweiler, R., Liao, X., & Wright, P. E. (1995) Science 268, 886-889.
12. Cantor, R. C., & Schimmel, P. R. (1980) Biophysical Chemistry. pp 1-1371, W. H. Freeman, San Francisco.
13. Carr, H. Y., & Purcell, E. M. (1954) Phys. Rev. 94, 630-638.
14. Chamberlain, A. K., Handel, T. M., & Marqusee, S. (1996) Nat. Struct. Biol. 3, 782-787.
15. Champoux, J. J., Gilboa, E., & Baltimore, D. (1984) J. Virol. 49, 686-691.
16. Clore, G. M., Driscoll, P. C., Wingfield, P. T., & Gronenborn, A. M. (1990a) Biochemistry 29, 7387-7401.
17. Clore, G. M., Szabo, A., Bax, A., Kay, L. E., Driscoll, P. C., & Gronenborn, A. M. (1990b) J. Am. Chem. Soc. 112, 4989-4991.
18. Crouch, R. J. (1990) New Biol. 2, 771-777.
19. Crouch, R. J., & Dirksen, M.-L. (1982) in Nuclease, pp 211-241, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY.
20. Dabora, J. M., & Marqusee, S. (1994) Protein Sci. 3, 1401-1408.
21. Davies, J. F., II, Hostomska, Z., Hostomsky, Z., Jordan, S. R., & Matthews, D. A. (1991) Science 252, 88-95.
22. Davis, D. G., Perlman, M. E., & London, R. E. (1994) J. Magn. Reson., Ser. B 104, 266-275.
23. de Massy, B., Fayet, O., & Kogoma, T. (1984) J. Mol. Biol. 178, 227-236.
24. Denisov, V. P., Peters, J., Hörlein, H. D., & Halle, B. (1996) Nat. Struct. Biol. 3, 505-509.
25. Doolittle, R. F., Feng, D. F., Johnson, M. S., & McClure, M. A. (1989) Q. Rev. Biol. 64, 1-30.
26. Farrow, N. A., Zhang, O., Szabo, A., Torchia, D. A., & Kay, L. E. (1995) J. Biomol. NMR 6, 153-162.
27. Frauenfelder, H., Parak, F., & Young, R. D. (1988) Annu. Rev. Biophys. Biophys. Chem. 17, 451-479.
28. Frauenfelder, H., Sugar, S. G., & Wolynes, P. G. (1991) Science 254, 1598-1603.
29. Furfine, E. S., & Reardon, J. E. (1991) Biochemistry 30, 7041-7046.
30. Garcia de la Torre, J., & Bloomfield, V. A. (1981) Q. Rev. Biophys. 14, 81-139.
31. Gilboa, E., Mitra, S. W., Goff, S., & Baltimore, D. (1979) Cell 18, 93-100.
32. Gurd, F. R. N., & Rothgeb, T. M. (1979) Adv. Protein Chem. 33, 73-165.
33. Hendrickson, W. A., Horton, J. R., & LeMaster, D. M. (1990) EMBO J. 9, 1665-1672.
34. Henry, E. R., & Szabo, A. (1985) J. Chem. Phys. 82, 4753-4761.
35. Hiyama, Y., Niu, C.-H., Silverton, J. V., Bavoso, A., & Torchia, D. A. (1988) J. Am. Chem. Soc. 110, 2378-2383.
36. Horiuchi, T., Maki, H., & Sekiguchi, M. (1984) Mol. Gen. Genet. 195, 17-22.
37. Huber, H. E., & Richardson, C. C. (1990) J. Biol. Chem. 265, 10565-10573.
38. Ishikawa, K., Nakamura, H., Morikawa, K., & Kanaya, S. (1993a) Biochemistry 32, 6171-6178.
39. Ishikawa, K., Nakamura, H., Morikawa, K., Kimura, S., & Kanaya, S. (1993b) Biochemistry 32, 7136-7142.
40. Ishikawa, K., Okumura, M., Katayanagi, K., Kimura, S., Kanaya, S., Nakamura, H., & Morikawa, K. (1993c) J. Mol. Biol. 230, 529-542.
41. Ishima, R., & Nagayama, K. (1995) J. Magn. Reson., Ser. B 108, 73-76.
42. Jen, J. (1978) J. Magn. Reson. 30, 111-128.
43. Kanaya, S., Kohara, A., Miura, Y., Sekiguchi, A., Iwai, S., Inoue, H., Ohtsuka, E., & Ikehara, M. (1990) J. Biol. Chem. 265, 4615-4621.
44. Katayanagi, K., Miyagawa, M., Matsusbima, M., Ishikawa, S., Kanaya, S., Ikehara, M., Matsuzaki, T., & Morikawa, K. (1990) Nature 347, 306-309.
45. Katayanagi, K., Miyagawa, M., Matsushima, M., Ishikawa, M., Kanaya, S., Nakamura, H., Ikehara, M., Matsuzaki, T., & Morikawa, K. (1992) J. Mol. Biol. 223, 1029-1052.
46. Katayanagi, K., Ishikawa, M., Okumura, M., Ariyoshi, M., Kanaya, S., Kawano, Y., Suzuki, M., Tanaka, I., & Morikawa, K. (1993) J. Biol. Chem. 268, 22092-22099.
47. Kay, L. E., Nicholson, L. K., Delagio, F., Bax, A., & Torchia, D. A. (1992) J. Magn. Reson. 97, 359-375.
48. Kimura, S., Kanaya, S., & Nakamura, H. (1992a) J. Biol. Chem. 267, 22014-22017.
49. Kimura, S., Nakamura, H., Hashimoto, T., Oobatake, M., & Kanaya, S. (1992b) J. Biol. Chem. 267, 21535-21542.
50. Kitani, T., Yoda, K., Ogawa, T., & Okazaki, T. (1985) J. Mol. Biol. 184, 45-52.
51. Kördel, J., Skelton, N. J., Akke, M., Palmer, A. G., & Chazin, W. J. (1992) Biochemistry 31, 4856-4866.
52. Kowalewski, J. (1989) Annu. Rep. NMR Spectrosc. 22, 307-414.
53. Kowalewski, J. (1991) Annu. Rep. NMR Spectrosc. 23, 289-374.
54. Kraulis, P. J. (1991) J. Appl. Crystallogr. 24, 946-950.
55. Lee, L. K., Rance, M., Chazin, W. J., & Palmer, A. G. (1996) J. Biomol. NMR (in press).
56. Li, Y.-C., & Montelione, G. T. (1994) J. Magn. Reson., Ser. B 105, 45-51.
57. Lipari, G., & Szabo, A. (1982a) J. Am. Chem. Soc. 104, 4546-4559.
58. Lipari, G., & Szabo, A. (1982b) J. Am. Chem. Soc. 104, 4559-4570.
59. Luz, Z., & Meiboom, S. (1963) J. Chem. Phys. 39, 366-370.
60. Mandel, A. M., Akke, M., & Palmer, A. G. (1995) J. Mol. Biol. 246, 144-163.
61. Marion, D., Ikura, M., & Bax, A. (1989a) J. Magn. Reson. 84, 425-430.
62. Marion, D., Ikura, M., Tschudin, R., & Bax, A. (1989b) J. Magn. Reson. 85, 393-399.
63. Meiboom, S., & Gill, D. (1958) Rev. Sci. Instrum. 29, 688-691.
64. Messerle, B. A., Wider, G., Otting, G., Weber, C., & Wüthrich, K. (1989) J. Magn. Reson. 85, 608-613.
65. Mispelter, J., Lefevre, C., Adjadj, E., Quiniou, E., & Favaudon, V. (1995) J. Biomol. NMR 5, 233-244.
66. Mölling, K., Bolognesi, D. P., Bauer, H., Büsen, W., Plassmann, H. W., & Hausen, P. (1971) Nat. New Biol. 234, 240-243.
67. Muhandiram, D. R., Yamazaki, T., Sykes, B. D., & Kay, L. E. (1995) J. Am. Chem. Soc. 117, 11536-11544.
68. Nakamura, H., Oda, Y., Iwai, S., Inoue, H., Ohtsuka, E., Kanaya, S., Kimura, S., Katsuda, C., Katayanagi, K., Morikawa, K., Miyashiro, H., & Ikehara, M. (1991) Proc. Natl. Acad. Sci. U.S.A. 88, 11535-11539.
69. Nicholls, A., Sharp, K., & Honig, B. (1991) Proteins: Struct., Funct., Genet. 11, 281-296.
70. Nicholson, L. K., Kay, L. E., Baldisseri, D. M., Arango, J., Young, P. E., & Torchia, D. A. (1992) Biochemistry 31, 5253-5263.
71. Noggle, J. H., & Shirmer, R. E. (1971) The Nuclear Overhauser Effect: Chemical Applications, pp 1-259, Academic Press, New York.
72. Oda, Y., Nakamura, H., Kanaya, S., & Ikehara, M. (1991) J. Biomol. NMR 1, 247-255.
73. Oda, Y., Iwai, S., Ohtsuka, E., Ishikawa, M., Ikehara, M., & Nakamura, H. (1993a) Nucleic Acids Res. 21, 4690-4695.
74. Oda, Y., Yoshida, M., & Kanaya, S. (1993b) J. Biol. Chem. 268, 88-92.
75. Orner, C. A., & Faras, A. J. (1982) Cell 30, 797-805.
76. Palmer, A. G. (1993) Curr. Opin. Biotechnol. 4, 385-391.
77. Palmer, A. G., Rance, M., & Wright, P. E. (1991) J. Am. Chem. Soc. 113, 4371-4380.
78. Palmer, A. G., Skelton, N. J., Chazin, W. J., Wright, P. E., & Rance, M. (1992) Mol. Phys. 75, 699-711.
79. Palmer, A. G., Williams, J., & McDermott, A. (1996) J. Phys. Chem. 100, 13293-13310.
80. Peng, J. W., & Wagner, G. (1992) J. Magn. Reson. 98, 308-332.
81. Philippopoulos, M., & Lim, C. (1995) J. Mol. Biol. 254, 771-792.
82. Philippopoulos, M., Mandel, A. M., Palmer, A. G., & Lim, C. (1996) Proteins: Struct., Funct., Genet. (submitted for publication).
83. Shaka, A. J., Barker, P. B., & Freeman, R. (1985) J. Magn. Reson. 64, 547-552.
84. Skelton, N. J., Palmer, A. G., Akke, M., Kordel, J., Rance, M., & Chazin, W. J. (1993) J. Magn. Reson., Ser. B 102, 253-264.
85. Smith, J. S., & Roth, M. J. (1992) J. Biol. Chem. 267, 15071-15079.
86. Stein, H., & Hausen, P. (1969) Science 166, 393-395.
87. Steinbach, P. J., Ansari, A., Berendzen, J., Brauenstein, D., Chu, K., Cowen, B. R., Ehrenstein, D., Frauenfelder, H., Johnson, J. B., Lamb, D. C., Luck, S., Mourant, J. R., Nienhaus, G. U., Ormos, P., Philipp, R., Xie, A., & Young, R. D. (1991) Biochemistry 30, 3988-4001.
88. Studier, F. W., & Moffat, B. A. (1986) J. Mol. Biol. 189, 113-130.
89. Szyperski, T., Luginbühl, P., Otting, G., Güntert, P., & Wüthrich, K. (1993) J. Biomol. NMR 3, 151-164.
90. Tilton, R. F., Dewan, J. C., & Petsko, G. A. (1992) Biochemistry 31, 2469-2481.
91. Tjandra, N., Feller, S. E., Pastor, R. W., & Bax, A. (1995) J. Am. Chem. Soc. 117, 12562-12566.
92. Void, R. L., Waugh, J. S., Klein, M. P., & Phelps, D. E. (1968) J. Chem. Phys. 48, 3831-3832.
93. Wagner, G. (1983) Q. Rev. Biophys. 16, 1-57.
94. Wagner, G. (1993) Curr. Opin. Struct. Biol. 3, 748-753.
95. Wand, A. J., Urbauer, J. L., McEvoy, R. P., & Bieber, R. J. (1996) Biochemistry 35, 6116-6125.
96. Wennerström, H. (1972) Mol. Phys. 24, 69-80.
97. Wintersberger, U. (1990) Pharmacol. Ther. 48, 259-280.
98. Yamazaki, T., Yoshida, M., & Nagayama, K. (1993) Biochemistry 32, 5656-5669.
99. Yamasaki, K., Ogasahara, K., Yutani, K., Oobatake, M., & Kanaya, S. (1995a) Biochemistry 34, 16552-16562.
100. Yamasaki, K., Saito, M., Oobatake, M., & Kanaya, S. (1995b) Biochemistry 34, 6587-6601.
101. Yang, D., & Kay, L. E. (1996) J. Mol. Biol. 263, 369-382.
102. Yang, W., Hendrickson, W. A., Crouch, R. J., & Satow, Y. (1990a) Science 249, 1398-1405.
103. Yang, W., Hendrickson, W. A., Kalman, E. T., & Crouch, R. J. (1990b) J. Biol. Chem. 265, 13553-13559.
104. Zheng, Z., Czaplicki, J., & Jardetzky, O. (1995) Biochemistry 34, 5212-5223.
105. Zhu, G., Torchia, D. A., & Bax, A. (1993) J. Magn. Reson., Ser. A 105, 219-222.