Discrepancies between the NMR and x-ray structures of uncomplexed barstar: Analysis suggests that packing densities of protein structures determined by NMR are unreliable

Biochemistry

Volumn 37, Issue 19, 1998, Pages 6958-6966

  Ratnaparkhi, Girish S ^a   Ramachandran, S ^a   Udgaonkar, Jayant B ^a   Varadarajan, R ^a,b  

^a INDIAN INSTITUTE OF SCIENCE   (India)

^b JAWAHARLAL NEHRU CENTRE FOR ADVANCED SCIENTIFIC RESEARCH   (India)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL ENZYME; DIMER; MUTANT PROTEIN; RIBONUCLEASE;

ALGORITHM; ARTICLE; BACILLUS AMYLOLIQUEFACIENS; CRYSTAL STRUCTURE; ENZYME INHIBITOR COMPLEX; NONHUMAN; NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; PROTEIN STRUCTURE; SEQUENCE HOMOLOGY; X RAY CRYSTALLOGRAPHY;

ALANINE; AMINO ACID SUBSTITUTION; BACILLUS; BACTERIAL PROTEINS; CRYSTALLIZATION; CRYSTALLOGRAPHY, X-RAY; CYSTEINE; DIMERIZATION; MACROMOLECULAR SUBSTANCES; MODELS, MOLECULAR; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PROTEIN BINDING; PROTEIN FOLDING; RIBONUCLEASES; STRUCTURE-ACTIVITY RELATIONSHIP;

BACILLUS AMYLOLIQUEFACIENS; BACTERIA (MICROORGANISMS);

EID: 0032510813     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi972857n     Document Type: Article

References (50)

1. Hartley, R. W. (1989) Trends Biochem. Sci. 14, 450-454.
2. Hartley, R. W. (1997) in Ribonucleases, Structure and Function (D'Alessio, G., & Riordan, J. F., Eds.) pp 51-100, Academic Press, New York.
3. Hartley, R. W. (1993). Biochemistry 32, 5978-5984.
4. Blackburn, P., Wilson, G., and Moore, S. (1977) J. Biol. Chem. 252, 5904-5910.
5. Kobe, B., and Deisenhofer, J. (1993) Nature 366, 751-756.
6. Kobe, B., and Deisenhofer, J. (1995) Nature 374, 183-186.
7. Lubienski, M. J., Bycroft, M., Freund, S. M. V., and Fersht, A. R. (1994) Biochemistry 33, 8866-8877.
8. Buckle, A. M, Schreiber, G., and Fersht, A. R. (1994) Biochemistry 33, 8878-8889.
9. Guillet, V., Lapthorn, A., Hartley, R. W., and Mauguen, Y. (1993) Structure 1, 165-177.
10. Schreiber, G., and Fersht, A. R. (1993) Biochemistry 32, 5145-5150.
11. Jones, D. N., Bycroft, M., Lubienski, M. J., and Fersht, A. R. (1993) FEBS Lett. 331, 165-172.
12. Martinez, J. C., Filimnov, V. V., Mateo, P. L., Schreiber, G., and Fersht, A. R. (1995) Biochemistry 34, 5224-5233.
13. Agashe, V. R., Shastry, M. C. R., and Udgaonkar, J. B. (1995) Nature 377, 754-757.
14. Nath, U., and Udgaonkar, J. B. (1997) Biochemistry 36, 8602-8610.
15. Nath, U., Agashe, V. R., and Udgaonkar, J. B. (1996) Nat. Struct. Biol. 3, 920-923.
16. Zaidi, F. N., Nath, U., and Udgaonkar, J. B. (1997) Nat. Struct. Biol. 12, 1016-1024.
17. Nath, U., and Udgaonkar, J. B. (1995) Biochemistry 34, 1702-1713.
18. Ramachandran, S., and Udgaonkar, J. B. (1996) Biochemistry 35, 8776-8785.
19. Guillet, V., Lapthorn, A., Fourniat, J., Benoit, J.-P., Hartley, R. W., and Mauguen, Y. (1993) Proteins 17, 325-328.
20. Raghunanthan, V., Khurana, S., Gupta, V., Khurana, R., Udgaonkar, J. B., and Salunke, D. M. (1994) J. Mol. Biol. 243, 533-536.
21. Schoppe, A., Hinz, H.-J., Agashe, V. R., Ramachandran, S., and Udgaonkar, J. B. (1997) Protein Sci. 6, 2196-2202.
22. Wong, K., Fersht, A. R., and Freund, S. M. V. (1997) J. Mol. Biol. 268, 494-511.
23. McPherson, A. (1990) Eur. J. Biochem. 189, 1-23.
24. Khurana, R., and Udgaonkar, J. B. (1994) Biochemistry 33, 106-115.
25. Kabsch, W. (1993) J. Appl. Crystallogr. 26, 795-800.
26. Navaza, J. (1994) Acta Crystallogr. A50, 157-163.
27. Rice, L. M., and Brunger, A. T. (1994) Proteins 19, 277-290.
28. Braig, K., Adams, P. D., and Brunger, A. T. (1995) Nat. Struct. Biol. 2, 1083-1094.
29. Brunger, A. T. (1996) X-PLOR, version 3.851, Yale University, New Haven, CT.
30. Kleywegt, G. J., and Jones, T. A. (1998) Methods Enzymol. (in press).
31. Brunger, A. T. (1992) Nature 355, 472-474.
32. Kleywegt, G. J., and Brunger, A. T. (1996) Structure 4, 897-904.
33. Weis, W. I., Brunger, A. T., Skehel, J. J., and Wiley, D. C. (1990) J. Mol. Biol. 212, 737-761.
34. Read, R. J. (1986) Acta Crystallogr. A42, 140-149.
35. Jones, T. A. (1985) Methods Enzymol. 115, 157-171.
36. Connolly, M. L. (1983) Science 221, 709-713.
37. Pattabiraman, N., Ward, K. B., and Fleming, P. J. (1995) J. Mol. Recognit. 8, 334-344.
38. DeDecker, B. S., O'Brien, R., Fleming, P., Geiger, J. H., Jackson, S. P., and Sigler, P. B. (1996) J. Mol. Biol. 264, 1072-1084.
39. Collaborative Computational Project, Number 4 (1994) Acta Crystallogr. D50, 760-763.
40. Laskowski, R. A., MacArthur, M. W., Moss, D. S., and Thornton, J. M. (1993) J. Appl. Crystallogr. 26, 283-291.
41. Bernstein, F. C., Koetzle, K. F., Williams, G. J. B., Meyer, E. F., Jr., Brice, M. D., Rodgers, J. R., Kennard, O., Shimanouchi, T., and Tasumi, M. (1977) J. Mol. Biol. 112, 535-542.
42. Bhuyan, A. K., and Udgaonkar, J. U. (1998) Proteins 30, 295-308.
43. Lubienski, M. J., Bycroft, M., Jones, D. M., and Fersht, A. R. (1993) FEBS Lett. 332, 81-87.
44. Frisch, C., Schreiber, G., Johnson, C. M., and Fersht, A. R. (1997) J. Mol. Biol. 267, 696-706.
45. Sturtevant, J. M. (1977) Proc. Natl. Acad. Sci. U.S.A. 74, 2236-2240.
46. Wintrode, P. L., Griko, Y. U., and Privalov, P. L. (1995) Protein Sci. 4, 1528-1534.
47. Agashe, V. R., and Udgaonkar, J. B. (1995) Biochemistry 34, 3286-3299.
48. Privalov, P. L. (1979) Adv. Protein Chem. 33, 167.
49. Wutrich, K. (1995) Acta Crystallogr. D51, 249-270.
50. Wagner, G., Hyberts, S. G., and Havel, F. H. (1992) Annu. Rev. Biophys. Biomol. Struct. 21, 167-198.