Reaction mechanism of deamidation of Asparaginyl residues in pep tides: Effect of solvent molecules

Journal of Physical Chemistry A

Volumn 110, Issue 27, 2006, Pages 8354-8365

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

^a BOGAZICI UNIVERSITY   (Turkey)

^b NANCY UNIVERSITÉ   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ACTIVATION ENERGY; AMINO ACIDS; MATHEMATICAL MODELS; PHYSIOLOGY; PROTEINS; SOLVENTS;

ASPARAGINYL RESIDUES; CYCLIZATION; DEAMIDATION; NEUTRAL MEDIA;

REACTION KINETICS;

AMIDE; ASPARAGINE; PEPTIDE; WATER;

AMINO ACID SEQUENCE; ARTICLE; BIOLOGY; CHEMICAL STRUCTURE; CHEMISTRY; ENERGY TRANSFER; MOLECULAR GENETICS; PROTEIN CONFORMATION; STRUCTURE ACTIVITY RELATION;

AMIDES; AMINO ACID SEQUENCE; ASPARAGINE; COMPUTATIONAL BIOLOGY; ENERGY TRANSFER; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MOLECULAR STRUCTURE; PEPTIDES; PROTEIN CONFORMATION; STRUCTURE-ACTIVITY RELATIONSHIP; WATER;

EID: 33746344019     PISSN: 10895639     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp056991q     Document Type: Article

References (36)

1. Robinson, A. B.; Rudd C. Curr. Top. Cell Regul. 1974, 5, 247-295.
2. Robinson, A. B.; Scothler, J. W.; McKerrow, J. H. J. Am. Chem. Soc. 1973, 95, 8156-8159.
3. Robinson, N. E.; Robinson, A. B. Molecular Clocks: Deamidation of Asparaginyl and Glutaminyl Residues in Peptides and Proteins; Althouse Press: Cave Junction, OR, 2004.
4. Gupta, R.; Srivastava, O. P. J. Biol. Chem. 2004, 279, 44258-44269.
5. Solstad, T.; Carvalho, R. N.; Anderson, O. A.; Waidelich, D.; Flatmark, T. 2003, Eur. J. Biochem. 270, 929-938.
6. Kim, E.; Lowenson, J. D.; MacLaren, D. C.; Clarke, S.; Young, S. G. Proc. Natl. Acad. Sci. U.S.A. 1997, 94, 6132-6137.
7. Robinson, N. E.; Robinson, A. B. Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 12409-12413.
8. Weintraub, S. J.; Manson, S. R. Mech. Age. Dev. 2004, 125, 255-257.
9. Robinson, N. E.; Robinson, A. B. Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 944-949.
10. Capasso, S.; Mazzarella, L.; Sica, P.; Zagari, A.; Salvadori, S. J. Chem. Soc. Chem. Commun. 1992, 919-921.
11. Capasso, S.; Mazzarella, L.; Sica, F.; Zagari, A.; Salvadori, S. J. Chem. Soc., Perkin Trans. 2 1993, 679-682.
12. Capasso, S., Salvadori, S. J. Peptide Res. 1999, 54, 377-382.
13. Capasso, S.; Mazzarella, L.; Sica, P.; Zagon, A. J. Peptide Res. 1989, 2, 195-197.
14. Konuklar, F. A.; Aviyente, V.; Sen, T. Z.; Bahar, I. J. Mol. Model. 2001, 7, 147-160.
15. Konuklar, F. A.; Aviyente, V. Org. Biomol. Chem. 2003, 1, 2290-2297.
16. Konuklar, F. A.; Aviyente, V.; Ruiz-Lopez, M. F. J. Phys. Chem. A 2002, 106, 11205-11214.
17. Robinson, N. E.; Robinson, A. B. J. Peptide Res. 2004, 63, 437-448.
18. Stewart, J. J. P. J. Comput. Chem. 1989, 10, 221-264.
19. Parr, R. G.; Yang, W. Density-functional theory of atoms and molecules; Oxford University Press: Oxford, U.K., 1989.
20. Hohenberg, P.; Kohn, W. Phys. Rev. 1964, 136, B 864.
21. Kohn, W.; Sham, L. J. Phys. Rev. 1965, A 1133.
22. Becke, A. D. J. Chem. Phys. 1993, 98, 5648-5652.
23. Lee, C.; Yang, W.; Parr, R. G. Phys. Rev. 1988, B37, 785.
24. Madura, J.; Jorgensen, W. L. J. Am. Chem. Soc. 1986, 108, 2517-2527.
25. Gonzalez, C.; Schlegel, H. B. J. Chem. Phys. 1989, 90, 2154-2161.
26. Gonzalez, C.; Schlegel, H. B. J. Phys. Chem. 1990, 94, 5523-5527.
27. Tomasi, J.; Mennucci, B.; Cancès, E. J. Mol. Struct. (THEOCHEM) 1999, 464, 211-226.
28. Cancès, M. T.; Mennucci, B.; Tomasi, J. J. Chem. Phys. 1997, 107, 3032-3041.
29. Mennucci, B.; Tomasi, J. J. Chem. Phys. 1997, 106, 5151-5158.
30. Mennucci, B.; Cancès, E.; Tomasi, J. J. Phys. Chem. B 1997, 101, 10506-10517.
31. Bondi, A. J. Phys. Chem. 1964, 68, 441-451.
32. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Montgomery, J. A., Jr.; Vreven, T.; Kudin, K. N.; Burant, J. C.; Millam, J. M.; Iyengar, S. S.; Tomasi, J.; Barone, V.; Mennucci, B.; Cossi, M.; Scalmani, G.; Rega, N.; Petersson, G. A.; Nakatsuji, H.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Klene, M.; Li, X.; Knox, J. E.; Hratchian, H. P.; Cross, J. B.; Bakken, V.; Adamo, C.; Jaramillo, J.; Gomperts, R.; Stratmann, R. E.; Yazyev, O.; Austin, A. J.; Cammi, R.; Pomelli, C.; Ochterski, J. W.; Ayala, P. Y.; Morokuma, K.; Voth, G. A.; Salvador, P.; Dannenberg, J. J.; Zakrzewski, V. G.; Dapprich, S.; Daniels, A. D.; Strain, M. C.; Farkas, O.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman, J. B.; Ortiz, J. V.; Cui, Q.; Baboul, A. G.; Clifford, S.; Cioslowski, J.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Martin, R. L.; Fox, D. J.; Keith, T.; Al-Laham, M. A.; Peng, C. Y.; Nanayakkara, A.; Challacombe, M.; Gill, P. M. W.; Johnson, B.; Chen, W.; Wong, M. W.; Gonzalez, C.; Pople, J. A. Gaussian 03, revision B.05; Gaussian, Inc.: Wallingford CT, 2004.
33. Liang, W.; Li, H.; Hu, X.; Han, S. J. Phys. Chem. A 2004, 108, 10219-10224.
34. Hazra, M. K.; Chakraborty, T. J. Phys. Chem. A 2005, 109, 7621-7625.
35. Du, D.; Fu. A.; Zhou, Z. Int. J. Quantum Chem. 2004, 99, 1-10.
36. Robinson, N. E.; Robinson, A. B. Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 4367-4372.