Ionic interactions in crystalline bovine pancreatic ribonuclease A

Biochemistry

Volumn 35, Issue 50, 1996, Pages 15962-15979

  Fedorov, Alexander A ^a   Joseph McCarthy, Diane ^b   Fedorov, Elena ^a   Sirakova, Dora ^a   Graf, Isaac ^a,c   Almo, Steven C ^a  

^a ALBERT EINSTEIN COLLEGE OF MEDICINE   (United States)

^b HARVARD MEDICAL SCHOOL   (United States)

^c USA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HYBRID PROTEIN; PANCREATIC RIBONUCLEASE; RECOMBINANT ENZYME;

ARTICLE; CATTLE; CHEMICAL BOND; CRYSTAL STRUCTURE; CRYSTALLIZATION; ENZYME CONFORMATION; ENZYME PURIFICATION; ENZYME STRUCTURE; ESCHERICHIA COLI; IONIC STRENGTH; NONHUMAN; PRIORITY JOURNAL; PROTEIN EXPRESSION; STEREOCHEMISTRY;

EID: 0030481340     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi961533g     Document Type: Article

References (87)

1. Aguilar, C. F., Thomas, P. J., Moss, D. S., Mills, A., & Palmer, R. A. (1991) Biochim. Biophys. Acta 1118, 6-20.
2. Aguilar, C. F., Thomas, P. J., Moss, D. S., & Palmer, R. A. (1992) J. Mol. Biol. 224, 265-267.
3. Alber, T. W., Gilbert, W. A., Ponzi, D. R., & Petsko, G. A. (1973) Ciba Found. Symp. 93, 4-24.
4. Allen, K. N., Bellamacina, C. R., Ding, X., Jeffery, C. J., Mattos, C., Petsko, G. A., & Ringe, D. (1996) J. Phys. Chem. 100, 2605-2611.
5. Ball, J. A., Wilson, K. P., Zhang, X.-J., Farber, H. R., Nicholsoin, H., & Matthews, B. W. (1991) Proteins: Struct., Fund., Genet. 10, 10-21.
6. Baudet-Nessler, S., Jullien, M., Crosiom M. P., & Janin, J. (1993) Biochemistry 32, 8457-8464.
7. Bernstein, F. C., Koetzle, T. F., Williams, G. J. B., Meyer, E. F., Brice, M. D., Rogers, J. R., Kennard, O., Shimanouchi, T., & Tasumi, M. (1977) J. Mol. Biol. 112, 535-542.
8. Bientema, J. J., Schuller, C., Irie, M., & Carsana, A. (1988) Prog. Biophys. Mol. Biol. 51, 165-192.
9. Blackburn, P., & Moore, S. (1982) Enzymes 15, 317-433.
10. Bode, W., & Huber, R. (1978) FEBS Lett. 90, 265-269.
11. Bolen, D. W., Flogel, M., & Biltonen, R. (1971) Biochemistry 10, 4136-4140.
12. Borah, B., Chen, C. W., Egan, W., Miller, M., Wlodawer, A., & Cohen, J. S. (1985) Biochemistry 24, 2058-2067.
13. Borkakoti, N. (1983) Eur. J. Biochem. 132, 89-94.
14. Borkakoti, N., Moss, D. S., & Palmer, R. A. (1992) Acta Crystallogr. B38, 2210-2217.
15. Brooks, B. R., Bruccoleri, R. E., Olafson, B. D., States, D. J., Swaminathan, S. & Karplus, M. (1983) J. Comput. Chem. 4,187-217.
16. Brünger, A. T. (1992) X-PLOR Version 3.0 Manual: a System for Crystallography and NMR, Yale University, New Haven, CT.
17. Brünger, A. T., Kuriyan, J., & Karplus, M. (1987) Science 223, 458-460.
18. Campbell, R. L., & Petsko, G. A. (1987) Biochemistry 26, 8579-8584.
19. Chakrabarti, P. (1990a) Biochemistry 29, 651-658.
20. Chakrabarti, P. (1990b) Protein Eng. 4, 49-56.
21. Chakrabarti, P. (1993) J. Mol. Biol. 234, 463-482.
22. Clore, G. M., Bax, A., Wingfield, P. T., & Gronenborn, A. M. (1990) Biochemistry 29, 5671-5676.
23. Crosio, M. P., Janin, J., & Jullien, M. (1994) J. Mol. Biol. 228, 243-245.
24. delCarayre, S. B., & Raines, R. T. (1994) Biochemistry 33, 6031-6037.
25. de Llorens, R., Arus, C., Pares, X., & Cuchillo, C. M. (1989) Protein Eng. 2, 417-429.
26. deMel, V. R., Martin, P. D., Doscher, M. S., & Edwards, B. F. P. (1992) J. Biol. Chem. 267, 247-256.
27. deMel, V. R., Doscher, M. S., Glinn, M. A., Martin, P. D., Ram, M. L., & Edwards, B. F. P. (1994) Protein Sci. 3, 39-50.
28. Dewan, J. C., Mikami, B., Hirose, M., & Sacchettini, J. C. (1993) Biochemistry 32, 11963-11968.
29. Finzel, B. C. (1987) J. Appl. Crystallogr. 20, 53-55.
30. Fitzpatrick, P. A., Steinmetz, A. C. U., Ringe, D., & Klibanov, A. M. (1993) Proc. Natl. Acad. Sci. U.S.A. 90, 8653-8657.
31. Fitzpatrick, P. A., Ringe, D., & Klibanov, A. M. (1994) Biochem. Biophys. Res. Commun. 198, 675-681.
32. Gallagher, W. H., & Croker, K. M. (1994) Protein Sci. 3, 1602-1604.
33. Gorenstein, D. G., & Wyrwicz, A. M. (1974) Biochemistry 13, 3828-3836.
34. Haffner, P. H., & Wang, J. H. (1973) Biochemistry 12, 1608-1618.
35. Hemmings, A. M. (1993) Acta Crystallogr. D49, 541-547.
36. Hendrickson, W. A. (1985) Methods Enzymol. 115, 252-270.
37. Irie, M. (1965) J. Biochem. 57, 355-362.
38. Irie, M., Watanabe, H., Ohgi, K., Tobe, M., Matsumura, G., Arata, Y., Hirose, T. & Inayama, S. (1984a) J. Biochem. 95, 751-759.
39. Irie, M., Mikami, F., Monma, K., Ohgi, K., Wtaabe, H., Yamaguchi, R., & Nagase, H. (1984b) J. Biochem. 96, 89-96.
40. Iwahashi, K., Nakamura, K., Mitsui, Y., Ohgi, K., & Irie, M. (1981) J. Biochem. 90, 1685-1690.
41. Jones, J. A. (1985) Methods Enzymol. 115, 157-171.
42. Joseph-McCarthy, D., Fedorov, A. A., & Almo, S. C. (1996) Protein Eng. 9, 773-780.
43. Kabsch, W. (1988) J. Appl. Crystallogr. 21, 916-924.
44. Kartha, G., Bello, J., & Harker, D. (1967) Nature (London) 213, 862-865.
45. Katoh, H., Yoshinaga, M., Yanagita, T., Ohgi, K., Irie, M., Beintema, J. J., & Meinsma, D. (1986) Biochim. Biophys. Acta 873, 367-371.
46. Kim, E. E., Varadarajan, R., Wyckoff, H. W., & Richards, F. M. (1992) Biochemistry 31, 12304-12314.
47. Kurachi, K., Davie, E. W., Strydom, D. J., Riordan, J. F., & Vallee, B. L. (1985) Biochemistry 24, 5494-5499.
48. Laity, J. H., Shimotakahara, S., & Scheraga, H. A. (1993) Proc. Natl. Acad. Sci. U.S.A. 90, 615-619.
49. Lee, F. S., & Vallee, B. L. (1989) Biochem. Biophys. Res. Commun. 161, 121-126.
50. Li, J. R. T., & Walz, G. F. (1974) Arch. Biochem. Biophys. 161, 227-233.
51. Lisgrarten, J. N., Gupta, V., Maes, D., Wyns, L., Zegers, I., Palmer, R. A., Dealwis, L. G., Aguilar, C. F., Matthew, J. B., & Richards, I. M. (1982) Biochemistry 21, 4989-4999.
52. Luzzati, V. (1952) Acta Crystallogr. 5, 802-810.
53. Martin, P. D., Doscher, M. S., & Edwards, B. F. P. (1987) J. Biol. Chem. 262, 15930-15938.
54. Mazzarella, L., Capasso, S., Demasi, D., Di Lorenzo, G., Mattia, C. A., & Zagari, A. (1993) Acta Crystallogr. D49, 389-402.
55. Meadows, G. H., Roberts, G. C. K., & Jardetsky, O. (1969) J. Mol. Biol. 45, 491.
56. Miranker, A., & Karplus, M. (1991) Proteins 11, 29-34.
57. Mitsui, Y., Urata, Y., Torii, K., & Irie, M. (1978) Biochim. Biophys. Acta 535, 299-308.
58. Moroianu, J., & Riordan, J. F. (1994) Biochem. Biophvs. Res. Commun. 203, 1765-1772.
59. Moult, J., Yaonath, A., Traub, W., Smilansky, A., Podajrny, A., Rabinovich, D., & Saya, A. (1976) J. Mol. Biol. 100, 179-195.
60. Nachman, J., Miller, M., Gilliland, G. L., Carty, R. P., Pincus, M., & Wlodawer, A. (1990) Biochemistry 29, 928-937.
61. Nicholls, A., Sharp, K A., & Honig, B. H. (1991) Proteins 11, 281-296.
62. Pares, X., de Lorens, R., Arus, C., & Cuchillo, C. M. (1980) Eur. J. Biochem. 105, 571-579.
63. Pavlosky, A. G., Borisova, S. N., Borisov, V. V., Antonov, I. V., & Karpeisky, M. Y. (1978) FEBS Lett. 92, 258-262.
64. Potts, J. T., Berger, A., Cooke, J., & Anfinsen, C. B. (1962) J. Biol. Chem. 237, 1851-1855.
65. Richards, F. M., & Wyckoff, H. W. (1971) Enzymes (3rd Ed.) 4, 647-806.
66. Richardson, R. M., Pares, X., & Cuchillo, C. M. (1990) Biochem. J. 267, 593-599.
67. Rossmann, M. G., & Argos, P. (1975) J. Biol. Chem. 250, 7525.
68. Roussel, A., & Cambillau, C. (1989) in Silicon Graphics Geometry Partner Directory (Silicon Graphics, Ed.) pp 77-78, Silicon Graphics, Mountain View, CA.
69. Ruterjans, H., & Witzel, H. (1969) Eur. J. Biochem. 9, 118-127.
70. Sanishvilli, R., Volz, K. W., Westbrook, E. M., & Margoliash, E. (1995) Structure 3, 707-716.
71. Sawada, F., & Irie, M. (1969) J. Biochem. 66, 415-418.
72. Sheriff, S. (1987) J. Appl. Crystallogr. 20, 55-57.
73. Smyth, D. G., Stein, W. H., & Moore, S. (1963) J. Biol. Chem. 238, 277-234.
74. Strydom, D. J., Fett, J. W., Lobb, R. R., Alderman, E. M., Bethune, J. L., Riordan, J. F., & Vallee, B. L. (1985) Biochemistry 24, 5486-5494.
75. Tarragona-Fiol, A., Eggelte, H. J., Harbron, S., Sanchez, C. J., Ward, J. M., & Rabin, B. R. (1993) Protein Eng. 6, 901-906.
76. Usher, D. A., Richardson, D. I., & Eckstein, F. (1970) Nature (London) 288, 663.
77. Usher, D. A., Erenrich, E. S., & Eckstein, F. (1972) Proc. Natl. Acad. Sci. U.S.A. 69, 115.
78. Varadarajan, R., & Richards, F. M. (1992) Biochemistry 31, 315-327.
79. Williams, R. L., Greene, S. M., & McPherson, A. (1987) J. Biol. Chem. 262, 16020-16030.
80. Witzel, H. (1963) Prog. Nucleic Acid Res. 2, 221-251.
81. Wlodawer, A. (1985) in Biological Micromolecules and Assemblies, Vol. 2, pp 393-439, John Willey and Sons, New York.
82. Wlodawer, A., & Hodgson, K. O. (1975) Proc. Natl. Acad. Sci. U.S.A. 72, 398-399.
83. Wlodawer, A., Deisenhofer, J., & Huber, R. (1987a) J. Mol. Biol. 193, 145-156.
84. Wlodawer, A., Nachman, J., Gilliland, G. L., Gallagher, W., & Woodward, C. (1987b) J. Mol. Biol. 198, 469-480.
85. Wlodawer, A., Svensson, L. A., Sjolin, L., & Gilliland, G. (1988) Biochemistry 27, 2705-2717.
86. Wodak, S. Y., Lin, M. Y., & Wyckoff, H. W. (1977) J. Mol. Biol. 116, 855-875.
87. Wyckoff, H. W., Carlson, W., & Wodak, S. (1977) in Nucleic Acid-Protein Recognition (Vogel, N. J., Ed.) pp 569-500, Academic Press, New York.