Population Shift vs Induced Fit: The Case of Bovine Seminal Ribonuclease Swapping Dimer

Biopolymers

Volumn 73, Issue 6, 2004, Pages 689-695

  Merlino, Antonello ^a,b   Vitagliano, Luigi ^c   Sica, Filomena ^a,c   Zagari, Adriana ^a,c   Mazzarella, Lelio ^a,c  

^a UNIVERSITY OF NAPLES FEDERICO II   (Italy)

^b UNIVERSITY OF SALERNO   (Italy)

^c CNR   (Italy)

Author keywords

Ligand binding; Population shift; Protein dynamics; Protein structure function; Ribonucleases; Three dimensional domain swapping; X ray diffraction

Indexed keywords

COMPLEXATION; CONFORMATIONS; CRYSTAL STRUCTURE; ENZYME KINETICS; ISOMERS; MOLECULAR STRUCTURE;

LIGANDS; POPULATION SHIFT;

BIOPOLYMERS;

2' DEOXYCITIDYLYL (3',5') 2 DEOXYADENOSINE; BOVINE SEMINAL RIBONUCLEASE; DEOXYADENOSINE; DIMER; RIBONUCLEASE; SULFATE; UNCLASSIFIED DRUG;

ARTICLE; CATTLE; CHEMICAL BINDING; CONFORMATIONAL TRANSITION; CRYSTAL STRUCTURE; DISULFIDE BOND; ENZYME STRUCTURE; ISOMER; LIGAND BINDING;

ANIMALS; BINDING SITES; CATTLE; CRYSTALLOGRAPHY, X-RAY; DIMERIZATION; ENDORIBONUCLEASES; MODELS, MOLECULAR; PROTEIN STRUCTURE, QUATERNARY;

BOVINAE;

EID: 1942499483     PISSN: 00063525     EISSN: None     Source Type: Journal    
DOI: 10.1002/bip.20016     Document Type: Article

References (52)

1. Bennet, A. M.; Choe, S.; Eisenberg, D. Proc Natl Acad Sci USA 1994, 91, 3127-3131.
2. Bennet, M. J.; Schlunegger, M. P.; Eisenberg, D. Protein Sci 1995, 4, 2455-2468.
3. Schlunegger, M. P.; Bennet, M. J.; Eisenberg, D. In Advances in Protein Chemistry; Richards, F. M., Eisenberg, D. S., Kim, P. S., Eds.; Academic Press: New York, 1997; pp 61-122.
4. Newcomer, M. E. Nat Struct Biol 2001, 8, 282-284.
5. Newcomer, M. E. Curr Opin Struct Biol 2002, 12, 48-53.
6. Liu, Y.; Eisenberg, D. Protein Sci 2002, 11, 1285-1299.
7. Capasso, S.; Giordano, F.; Mattia, C. A.; Mazzarella, L.; Zagari, A. Biopolymers 1983, 22, 327-332.
8. Mazzarella, L.; Capasso, S.; Demasi, D.; Di Lorenzo, G.; Mattia, C.A.; Zagari, A. Acta Cryst D 1993, 49, 389-402.
9. Di Donato, A.; Piccoli, R.; D'Alessio G. Biochem J 1987, 241, 435-440.
10. Piccoli, R.; Di Donato, A.; D'Alessio, G. Biochem J 1988, 253, 329-336.
11. Piccoli, R.; Tamburini, M.; Piccialli, G.; Di Donato, A.; Parente, A.; D'Alessio, G. Proc Natl Acad Sci USA 1992, 89, 1870-1874.
12. Berisio, R.; Sica, F.; Di Lorenzo, C.; Di Fiore, A.; Piccoli, R.; Mazzarella, L. FEBS Lett 2003, 554, 105-110.
13. Di Donato, A.; Cafaro, V.; Romeo, I.; D'Alessio, G. Protein Sci 1995, 4, 1470-1477.
14. Ciglic, M. I.; Jackson, P. J.; Raillard, S. A.; Haugg, M.; Jermann, T. M.; Opitz, J. G.; Trabesinger-Ruf, N.; Benner, S. A. Biochemistry 1998, 37, 4008-4022.
15. Opitz, J. G.; Ciglic, M. I.; Haugg, M.; Trautwein-Fritz, K.; Raillard, S. A.; Jerman, T. M.; Benner, S. A. Biochemistry 1998, 37, 4023-4033.
16. Crestfield, A. M.; Stein, W. H.; Moore, S. Arch Biochem Biophys 1962, Suppl 1, 221-222.
17. Liu, Y.; Hart, P. J.; Schlunegger, M. P.; Eisenberg, D. Proc Natl Acad Sci USA 1998, 95, 3437-3442.
18. Liu, Y.; Gotte, G.; Libonati, M.; Eisenberg, D. Nat Struct Biol 2001, 8, 211-214.
19. D'Alessio, G. Nat Struct Biol 1995, 2, 11-13.
20. Vitagliano, L.; Adinolfi, S.; Sica, F.; Merlino, A.; Zagari, A.; Mazzarella, L. J Mol Biol 1999, 293, 569-577.
21. Vitagliano, L.; Adinolfi, S.; Riccio, A.; Sica, F.; Zagari, A.; Mazzarella, L. Protein Sci 1998, 7, 1691-1699.
22. Kumar, S. M.; Buyong, M.; Tsai, C. J.; Sinha, N.; Nussinov, R. Protein Sci 2000, 9, 10-19.
23. Ma, B.; Kumar, S. M.; Tsai, C. J.; Nussinov, R. Protein Eng 1999, 12, 713-720.
24. Koshland, D. E. Proc Natl Acad Sci USA 1958, 44, 98-123.
25. Monod, J.; Wyman, J.; Cahngeux, J. P. J Mol Biol 1965, 12, 80-118.
26. Sica, F.; Adinolfi, A.; Berisio, R.; De Lorenzo, C.; Mazzarella, L.; Piccoli, R.; Vitagliano, L.; Zagari, A. J Cryst Growth 1999, 196, 305-312.
27. Sica, F.; Adinolfi, A.; Vitagliano, L.; Zagari, A.; Capasso, S.; Mazzarella, L. J Cryst Growth 1996, 168, 192-197.
28. Otwinowsky, Z.; Minor, W. Methods Enzymol 1997, 276, 307-326.
29. Brunger, A. T. X-PLOR version 3.1: A System for X-Ray Crystallography and NMR; Yale University Press, New Haven, CT, 1992.
30. Jones, T. A.; Zou, J. Y.; Cowan, S. W.; Kjeldgaard, M. Acta Cryst A 1991, 47, 110-119.
31. Laskowski, R. A.; MacArthur, M. W.; Moss, M. D.; Thornton, J. M. J Appl Crystallogr 1993, 26, 283-291.
32. Hooft, R. W.; Vriend, G.; Sander, C.; Abola, E. E. Nature 1996, 381, 272.
33. Campbell, R. L.; Petsko G. A. Biochemistry 1987, 26, 8579-8584.
34. Wlodawer, A.; Svenson, L. A.; Sjolin, L.; Gilliland, G. L. Biochemistry 1988, 27, 2705-2717.
35. Leonidas, D. D.; Shapiro, R.; Irons, L. I.; Russo, N.; Acharya, K. R. Biochemistry 1997, 36, 5578-5588.
36. Vitagliano, L.; Merlino, A.; Zagari, A.; Mazzarella, L. Protein Sci 2000, 9, 1217-1225.
37. Berisio, R.; Lamzin, V. S.; Sica, F., Wilson, K. S.; Zagari, A.; Mazzarella, L. J Mol Biol 1999, 292, 845-854.
38. Berisio, R.; Lamzin, S.; Sica, F.; Wilson, K. S.; Zagari, A.; Mazzarella, L. Acta Cryst. D 2002, 58, 445-454.
39. Esposito, L.; Vitagliano, L.; Sica, F.; Sorrentino, G.; Zagari, A.; Mazzarella, L. J Mol Biol 2000, 297, 713-732.
40. Borkakoti, N.; Moss, D. S.; Palmer, R. A. Acta Cryst B 1982, 38, 2210-2217.
41. Gilliland, G. In Ribonucleases: Structures and Functions; Riordan, J. F., D'Alessio, G., Eds.; Academic Press: New York, 1997, pp 306-341.
42. Sica, F.; Di Fiore, A.; Zagari, A.; Mazzarella, L. Proteins 2003, 52, 263-271.
43. Zegers, I.; Maes, D.; Dao-Thi, M. H.; Poortmans, F.; Palmer, R.; Wyns, L. Protein Sci 1994, 3, 2322-2339.
44. Radha Kishan, K. V.; Chandra, N. R.; Sudarsanakumar, C.; Suguna, K.; Vijayan, M. Acta Cryst D 1995, 51, 703-710.
45. Sadasivan, C.; Nagendra, H. G.; Vijayan, M. Acta Cryst D 1998, 54, 1343-1352.
46. Vitagliano, L.; Merlino, A.; Zagari, A.; Mazzarella, L. Proteins 2002, 46, 97-104.
47. Merlino, A.; Vitagliano, L.; Ceruso, M. A.; Di Nola, A.; Mazzarella, L. Biopolymers 2002, 65, 274-283.
48. Merlino, A.; Vitagliano, L.; Ceruso, M. A.; Mazzarella, L. Proteins 2003, 53, 101-110.
49. Volkman, B. F.; Lipson, D.; Wemmer, D. E. Science 2001, 291, 2429-2433.
50. Stock, A. Nature 1999, 400, 221-222.
51. Feher, V. A.; Cavanagh, J. Nature 1999, 400, 289-290.
52. Nevo, R.; Stroth, C.; Kienberger, F.; Kaftan, D.; Brumfeld, V.; Elbaum, M.; Reich, Z.; Hinterdorfer, P. Nature Struct Biol 2003, 10, 553-557.