Probing the dimeric structure of porcine aminoacylase 1 by mass spectrometric and modeling procedures

Biochemistry

Volumn 42, Issue 15, 2003, Pages 4430-4443

  D'Ambrosio, Chiara ^a   Talamo, Fabio ^a   Vitale, Rosa Maria ^b   Amodeo, Pietro ^a   Tell, Gianluca ^c   Ferrara, Lino ^a   Scaloni, Andrea ^a  

^a CNR   (Italy)

^b SECOND UNIVERSITY OF NAPLES   (Italy)

^c UNIVERSITY OF TRIESTE   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; CATALYST ACTIVITY; CHEMICAL MODIFICATION; CROSSLINKING; DIMERS; HYDROLYSIS; INTERFACES (MATERIALS); MASS SPECTROMETRY; MONOMERS; POLYPEPTIDES; PROTEINS; ZINC;

CHEMICAL REAGENTS;

BIOCHEMISTRY;

AMINOACYLASE; LYSINE; MONOMER; PROTEINASE; REAGENT;

ACETYLATION; ALPHA HELIX; AMINO ACID ANALYSIS; AMINO ACID SEQUENCE; ARTICLE; BETA SHEET; CHEMICAL MODIFICATION; CHEMICAL REACTION; CONTROLLED STUDY; CROSS LINKING; DATA ANALYSIS; DIMERIZATION; DISCRIMINANT ANALYSIS; ENZYME PURIFICATION; ENZYME STRUCTURE; HUMAN; HYDROLYSIS; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; MOLECULAR DYNAMICS; MOLECULAR MODEL; MOLECULAR WEIGHT; NITRATION; OLIGOMERIZATION; OXIDATION REDUCTION REACTION; PEPTIDE MAPPING; POLYACRYLAMIDE GEL ELECTROPHORESIS; PRIORITY JOURNAL; PROTEIN DEGRADATION; PROTEIN DOMAIN; SEQUENCE ALIGNMENT; STANDARD; STRUCTURE ANALYSIS; SWINE;

AMIDOHYDROLASES; AMINO ACID SEQUENCE; ANIMALS; DIMERIZATION; ELECTROPHORESIS, POLYACRYLAMIDE GEL; ENDOPEPTIDASES; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; OXIDATION-REDUCTION; PROTEIN STRUCTURE, TERTIARY; SEQUENCE ALIGNMENT; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION; SWINE;

SUIDAE; SUS SCROFA;

EID: 0037461355     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi0206715     Document Type: Article

References (63)

1. Gade, W., and Brown, J. L. (1981) Biochim. Biophys. Acta 662, 86-93.
2. Heese, D., Loffler, H., and Rohm, K. H. (1990) Biol. Chem. Hoppe-Seyler 369, 559-566.
3. Jones, W., Scaloni, A., and Manning, J. M. (1994) Methods Enzymol. 244, 227-231.
4. Scaloni, A., Jones, W. M., Barra, D., Pospischil, M., Sassa, S., Popowicz, A., Manning, L., Schneewind, O., and Manning, J. M. (1992) J. Biol. Chem. 267, 3811-3818.
5. Jones, W. M., Manning, L. R., and Manning, J. M. (1986) Biochem. Biophys. Res. Commun. 139, 244-250.
6. Chongcharoen, K., and Sharma, K. K. (1998) Biochem. Biophys. Res. Commun. 247, 136-141.
7. Cook, R. M., Burke, B. J., Buchhagen, D. L., Minna, J. D., and Miller, Y. E. (1993) J. Biol. Chem. 268, 17010-17017.
8. Mitta, M., Ohnogi, H., Yamamoto, A., Kato, I., Sakiyama, F., and Tsunasawa, S. (1992) J. Biochem. 112, 737-742.
9. Miyagi, M., Sakiyama, F., Kato, I., and Tsunasawa, S. (1995) J. Biochem. 118, 771-779.
10. Erlandsson, R., Boldog, F., Persson, B., Zabarovsky, E. R., Allikmets, R. L., Sumegi, J., Klein, G., and Jomvall, H. (1991) Oncogene 6, 1293-1295.
11. Jones, W., Scaloni, A., Bossa, F., Popowicz, A., Schneewind, O., and Manning, J. M. (1991) Proc. Natl. Acad. Sci. U.S.A. 88, 2194-2198.
12. Ginzinger, D. G., Shridhar, V., Baldini, A., Taggart, R. T., Miller, O. J., and Smith, D. I. (1992) Am. J. Hum. Genet. 50, 826-833.
13. Miller, Y. E., Minna, J. D., and Gazdar, A. F. (1989) J. Clin. Invest. 83, 2120-2124.
14. Balabanov, S., Zimmermann, U., Protzel, C., Scharf, C., Klebingat, K. J., and Walther, R. (2001) Eur. J. Biochem. 268, 5977-5980.
15. Scaloni, A., Jones, W. M., Pospischil, M., Schneewind, O., Popowicz, A., Bossa, F., Graziano, S., and Manning, J. M. (1992) J. Lab. Clin. Med. 120, 546-552.
16. Naylor, S. L., Johnson, B. E., Minna, J. D., and Sakaguchi, A. Y. (1987) Nature 329, 451-454.
17. McNail-Killary, A., Wolf, M. E., Giambernardi, T. A., and Naylor, S. L. (1992) Proc. Natl. Acad. Sci. U.S.A. 89, 10877-10881.
18. Fulop, V., Bocskei, Z., and Polgar, L. (1998) Cell 94, 161-170.
19. Feese, M., Scaloni, A., Jones, W. M., Manning, J. M., and Remington, S. (1993) J. Mol. Biol. 233, 546-549.
20. Rowsell, S., Pauptit, R. A., Tucker, A. D., Melton, R., Blow, D. M., and Brick, P. (1997) Structure 5, 337-347.
21. Biagini, A., and Puigserver, A. (2001) Comp. Biochem. Physiol., Part B 128, 469-481.
22. Giardina, T., Perrier, J., and Puigserver, A. (2000) Eur. J. Biochem. 267, 6249-6255.
23. Spormann, D. O., Heim, J., and Wolf, D. H. (1991) Eur. J. Biochem. 197, 399-405.
24. Palm, G. J., and Rohm, K. H. (1995) J. Protein Chem. 14, 233-240.
25. Zappacosta, F., Pessi, A., Bianchi, E., Venturini, S., Sollazzo, M., Tramontano, A., Marino, G., and Pucci, P. (1996) Protein Sci. 5, 802-813.
26. Fontana, A., Polverino de Laureto, P., De Filippis, V., Scaramella, E., and Zambonin, M. (1997) Folding Des. 266, 223-230.
27. Suckau, D., Kohl, J., Karwath, G., Schneider, K., Casaretto, M., Bitter-Suermann, D., and Przybylski, M. (1990) Proc. Natl. Acad. Sci. U.S.A. 87, 9848-9852.
28. Zhao, Y., Muir, T., Kent, S. B., Tischer, E., Scardina, J. M., and Chait, B. T. (1996) Proc. Natl. Acad. Sci. U.S.A. 93, 4020-4024.
29. Cohen, S. L., Ferrè-D'amare, A. R., Burley, S. K., and Chait, B. T. (1995) Protein Sci. 4, 1088-1099.
30. Scaloni, A., Miraglia, N., Orrù, S., Amodeo, P., Motta, A., Marino, G., and Pucci, P. (1998) J. Mol. Biol. 277, 945-958.
31. Scaloni, A., Monti, M., Acquaviva, R., Tell, G., Damante, G., Formisano, S., and Pucci, P. (1999) Biochemistry, 38, 64-72.
32. Suckau, D., Mak, M., and Przybylski, M. (1992) Proc. Natl. Acad. Sci. U.S.A. 89, 5630-5634.
33. Glocker, M. O., Borchers, C., Fiedler, W., Suckau, D., and Przybylski, M. (1994) Bioconjugate Chem. 5, 583-590.
34. Zappacosta, F., Ingallinella, P., Scaloni, A., Pessi, A., Bianchi, E., Sollazzo, M., Tramontano, A., Marino, G., and Pucci, P. (1997) Protein Sci. 6, 1901-1909.
35. Leite, J. F., and Cascio, M. (2002) Biochemistry 41, 6140-6148.
36. Ploug, M., Rahbek-Nielsen, H., Ellis, V., Roepstorff, P., and Dano, K. (1995) Biochemistry 34, 12524-12534.
37. Bennett, K. L., Kussmann, M., Bjork, P., Godzwon, M., Mikkelsen, M., Sorensen, P., and Roepstorff, P. (2000) Protein Sci. 9, 1503-1518.
38. McLafferty, F. W., Fridriksson, E., Horn, D., Lewis, M. A., and Zubarev, R. A. (1999) Science 284, 1289-1290.
39. Vilardo, P. G., Scaloni, A., Amodeo, P., Barsotti, C., Cecconi, I., Cappiello, M., Lopez Mendez, B., Rullo, R., Dal Monte, M., Del Corso, A., and Mura, U. (2001) Biochemistry 40, 11985-11994.
40. Allegrini, S., Scaloni, A., Ferrara, L., Pesi, R., Pinna, P., Camici, M., Eriksson, S., and Tozzi, M. G. (2001) J. Biol. Chem. 276, 33526-33532.
41. Peitsch, M. C. (1996) Biochem. Soc. Trans. 24, 274-279.
42. Sali, A., and Blundell, T. L. (1993) J. Mol. Biol. 234, 779-815.
43. Rowsell, S., Pauptit, R. A., Tucker, A., Melton, R. G., Blow, D. M., and Brick, P. (1997) Structure 5, 337-347.
44. Higgins, D., Thompson, J., Gibson, T., Thompson, J. D., Higgins, D. G., and Gibson, T. J. (1994) Nucleic Acids Res. 22, 4673-4680.
45. Kabsch, W., and Sander, C. (1983) Biopolymers 22, 2577-2637.
46. Laskowski, R. A., MacArthur, M. W., Moss, D. S., and Thornton, J. M. (1993) J. Appl. Crystallogr. 26, 283-291.
47. Case, D. A., Pearlman, D. A., Caldwell, J. W., Cheatham, T. E., III, Ross, W. S., Simmerling, C. L., Darden, T. A., Merz, K. M., Stanton, R. V., Cheng, A. L., Vincent, J. J., Crowley, M., Tsui, V., Radmer, R. J., Duan, Y., Pitera, J., Massova, I., Seibel, G. L., Singh, U. C., Weiner, P. K., and Kollman, P. A. (1999) AMBER 6, University of California, San Francisco.
48. Weiner, S. J., Kollman, P. A., Case, D. A., Chandra Singh, U., Ghio, C., Alagona, G., Profeta, S., and Weiner, P. K. (1984) J. Am. Chem. Soc. 106, 765-784.
49. Weiner, S. J., Kollman, P. A., Nguyen, D. T., and Case, D. A. (1986) J. Comput. Chem. 7, 230-252.
50. Sippl, M. J. (1993) Proteins 17, 355-362.
51. Lee, B., and Richard, F. M. (1971) J. Mol. Biol. 55, 379-400.
52. Koradi, R., Billeter, M., and Wüthrich, K. (1996) J. Mol. Graphics 14, 51-55.
53. Petersson, A. S., Steen, H., Kalume, D. E., Caidahl, K., and Roepstorff, P. (2001) J. Mass Spectrom. 36, 616-625.
54. Ji, T. H. (1983) Methods Enzymol. 91, 580-609.
55. Hermanson, G. T. (1996) Bioconjugate techniques, Academic Press, San Diego.
56. Young, M., Tang, N., Hempel, J., Oshiro, C., Taylor, E., Kuntz, I., Gibson, B., and Dollinger, G. (2000) Proc. Natl. Acad. Sci. U.S.A. 97, 5802-5806.
57. Heese, D., Berger, S., and Rohm, K. H. (1990) Eur. J. Biochem. 188, 175-180.
58. Moult, J., Hubbard, T., Bryant, S. H., Fidelis, K., and Pedersen, J. T. (1999) Proteins S1, 2-6.
59. Heese, D., and Rohm, K. H. (1989) Biol. Chem. Hoppe-Seyler 370, 607-612.
60. Castagnetto, J. M., Hennessy, S. W., Roberts, V. A., Getzoff, E. D., Tainer, J. A., and Pique, M. E. (2002) Nucleic Acids Res. 30, 379-382.
61. Greenblatt, H. M., Almog, O., Maras, B., Spungin-Bialik, A., Barra, D., Blumberg, S., and Shoham, G. (1997) J. Mol. Biol. 265, 620-636.
62. Chevrier, B., Schalk, C., D'Orchymont, H., Rondeau, J. M., Moras, D., and Tarnus, C. (1994) Structure 2, 283-291.
63. Saqi, M. A., Bates, P. A., and Sternberg, M. J. (1992) Protein Eng. 5, 305-311.