Deamidation of asparagine residues: Direct hydrolysis versus succinimide-mediated deamidation mechanisms

Journal of Physical Chemistry A

Volumn 113, Issue 6, 2009, Pages 1111-1120

  Catak, Saron ^a,b   Monard, Gérald ^a   Aviyente, Viktorya ^b   Ruiz López, Manuel F ^a  

^a NANCY UNIVERSITÉ   (France)

^b BOGAZICI UNIVERSITY   (Turkey)

Author keywords

[No Author keywords available]

Indexed keywords

AMIDES; AMINES; ORGANIC ACIDS; PROTEINS; QUANTUM CHEMISTRY;

ASPARAGINE RESIDUES; ASPARTIC ACIDS; BASE CATALYSIS; CATALYTIC EFFECTS; DEAMIDATION; DENSITY-FUNCTIONAL LEVELS; DIRECT HYDROLYSIS; ENERGY PROFILES; PLAUSIBLE MECHANISMS; QUANTUM CHEMICAL CALCULATIONS; RATE-DETERMINING STEPS; REACTION MECHANISMS; REACTION PRODUCTS; REACTION STEPS; SUCCINIMIDE; TAUTOMERIZATION;

HYDROLYSIS;

AMIDE; ASPARAGINE; ASPARTIC ACID; SUCCINIMIDE; SUCCINIMIDE DERIVATIVE; WATER;

ARTICLE; CATALYSIS; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION; FEASIBILITY STUDY; HYDROLYSIS; QUANTUM THEORY;

AMIDES; ASPARAGINE; ASPARTIC ACID; CATALYSIS; FEASIBILITY STUDIES; HYDROLYSIS; MODELS, CHEMICAL; MODELS, MOLECULAR; MOLECULAR CONFORMATION; QUANTUM THEORY; SUCCINIMIDES; WATER;

EID: 61649094568     PISSN: 10895639     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp808597v     Document Type: Article

References (40)

1. Robinson, A. B.; Rudd, C. Curr. Top. Cell Regul. 1974, 8, 247-295.
2. Robinson, A. B.; Scothler, J. W.; McKerrow, J. H. J. Am. Chem. Soc. 1973, 95, 8156-8159.
3. Bornstein, P.; Balian, G. J. Biol. Chem. 1970, 245, 4854-4856.
4. Geiger, T.; Clarke, S. J. Biol. Chem. 1987, 262, 785-794.
5. Meinwald, C. Y.; Stimson, E. R.; Scheraga, H. A. Int. J. Pept. Protein Res. 1986, 28, 79-84.
6. Gupta, R.; Srivastava, O. P. J. Biol. Chem. 2004, 279, 44258-44269.
7. Solstad, T.; Carvalho, R. N.; Anderson, O. A.; Waidelich, D.; Flatmark, T. Eur. J. Biochem. 2003, 270, 929-938.
8. Kim, E.; Lowenson, J. D.; MacLaren, D. C.; Clarke, S.; Young, S. G. Proc. Natl. Acad. Sci. U.S.A. 1997, 94, 6132-6137.
9. Robinson, N. E.; Robinson, A. B. Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 12409-12413.
10. Weintraub, S. J.; Manson, S. R. Mech. Age. Dev. 2004, 125, 255-257.
11. Robinson, N. E.; Robinson, A. B. Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 944-949.
12. Capasso, S.; Mazzarella, L.; Sica, F.; Zagari, A.; Salvadori, S. J. Chem. Soc., Perkin Trans. 2 1993, 679-682.
13. Capasso, S.; Mazzarella, L.; Sica, F.; Zagon, A. J. Peptide Res. 1989, 2, 195-197.
14. Capasso, S.; Salvadori, S. J. Peptide Res. 1999, 54, 377-382.
15. Tam, J. P.; Riemen, M. W.; Merrifield, R. B. Peptide Res. 1988, 1, 6-18.
16. Robinson, N. E.; Robinson, A. B. J. Peptide Res. 2004, 63, 437-448.
17. Robinson, N. E.; Robinson, Z. W.; Robinson, B. R.; Robinson, A. L.; Robinson, M. R.; Robinson, A. B. J. Peptide Res. 2004, 63, 426-436.
18. Robinson, N. E.; Robinson, A. B. Molecular Clocks: Deamidation of Asparaginyl and Glutaminyl Residues in Peptides and Proteins; Althouse Press: Cave Junction, OR, 2004.
19. Robinson, N. E.; Robinson, A. B. Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 4367-4372.
20. Konuklar, F. A.; Aviyente, V.; Sen, T. Z.; Bahar, I. J. Mol. Model. 2001, 7, 147-160.
21. Konuklar, F. A.; Aviyente, V. Org. Biomol.Chem. 2003, 1, 2290-2297.
22. Konuklar, F. A.; Aviyente, V.; Ruiz-Lopez, M. F. J. Phys. Chem. A 2002, 106, 11205-11214.
23. Radkiewicz, J. L.; Zipse, H.; Clarke, S.; Houk, K. N. J. Am. Chem. Soc. 1996, 118, 9148-9155.
24. Radkiewicz, J. L.; Zipse, H.; Clarke, S.; Houk, K. N. J. Am. Chem. Soc. 2001, 123, 3499-3506.
25. Peters, B.; Trout, B. L. Biochemistry 2006, 45, 5384-5392.
26. (a) Catak, S.; Monard, G.; Aviyente, V.; Ruiz-López, M. F. J. Phys. Chem. A 2006, 110, 8354-8365.
27. (b) Catak, S.; Monard, G.; Aviyente, V.; Ruiz-López, M. F. J. Phys. Chem. A 2008, 112, 8752-8761.
28. Stewart, J. J. P. J. Comput. Chem. 1989, 10, 221-264.
29. Parr, R. G., Yang, W. Density-Functional Theory of Atoms and Molecules; Oxford University Press: Oxford, 1989.
30. Hohenberg, P.; Kohn, W. Phys. Rev. B 1964, 136, 864.
31. Kohn, W.; Sham, L. J. Phys. Rev. A 1965, 140, 1133.
32. Becke, A. D. J. Chem. Phys. 1993, 98, 5648-5652.
33. Lee, C.; Yang, W.; Parr, R. G. Phys. Rev. B 1988, 37, 785.
34. Madura, J.; Jorgensen, W. L. J. Am. Chem. Soc. 1986, 108, 2517-2527.
35. Gonzalez, C.; Schlegel, H. B. J. Chem. Phys. 1989, 90, 2154-2161.
36. Gonzalez, C.; Schlegel, H. B. J. Phys. Chem. 1990, 94, 5523-5527.
37. Gorb, L.; Asensio, A.; Tunon, I.; Ruiz-Lopez, M. F. Chem.-Eur. J. 2005, 11, 6743-6753.
38. Gaussian 03, Revision B.05, Frisch, M. J. et al. Gaussian, Inc.: Wallingford CT, 2004.
39. Robinson, N. E.; Robinson, A. B. Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 4367-4372.
40. Pries, F.; Kingma, J.; Janssen, D. B. FEBS Lett. 1995, 358, 171-174.