Two-water-assisted racemization of the succinimide intermediate formed in proteins. A computational model study


Racemization of aspartic acid (Asp) residues in proteins plays an important role in the molecular biology of aging. In the widely accepted mechanism of the Asp racemization, a succinimide (SI) intermediate is the species which actually undergo the direct racemization. In the present study, a two-water-assisted mechanism of the SI racemization was computationally investigated using a model compound in which an aminosuccinyl (Asu) residue is capped with acetyl and NMe groups on the N-and C-termini, respectively. The two water molecules catalyze the enolization of the Hα-Cα-C=O portion in the Asu residue by mediating proton relay from the α-carbon atom to the carboxyl oxygen atom. After the enolization, migration of the water molecules and conformational change lead to the mirror image of the initially formed enol two-water complex, and the racemization is completed by the following ketonization. The overall activation barrier (28.2 kcal·mol-1) corresponds to the enolization and ketonization steps, and falls within the available experimental activation energies (21.4-29.0 kcal·mol-1). Therefore, the two-water-assisted mechanism investigated here is plausible for the in vivo and in vitro racemization reactions of the SI intermediates formed in peptides and proteins.

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Takahashi, O. (2013) Two-water-assisted racemization of the succinimide intermediate formed in proteins. A computational model study. Health, 5, 2018-2021. doi: 10.4236/health.2013.512273.

Conflicts of Interest

The authors declare no conflicts of interest.


[1] Geiger, T. and Clarke, S. (1987) Deamidation, isomerization, and racemization at asparaginyl and aspartyl residues in peptides. Succinimide-linked reactions that contribute to protein degradation. Journal of Biological Chemistry, 262, 785-794.
[2] Stephenson, R.C. and Clarke, S. (1989) Succinimide formation from aspartyl and asparaginyl peptides as a model for the spontaneous degradation of proteins. Journal of Biological Chemistry, 264, 6164-6170.
[3] Ritz-Timme, S. and Collins, M.J. (2002) Racemization of aspartic acid in human proteins. Ageing Research Reviews, 1, 43-59.
[4] Fujii, N. (2005) D-Amino acid in elderly tissues. Biological & Pharmaceutical Bulletin, 28, 1585-1589.
[5] Motoie, R., Fujii, N., Tsunoda, S., Nagata, K., Shimo-oka, T., Kinouchi, T., Fujii, N., Saito, T. and Ono, K. (2009) Localization of D-β-aspartyl residue-containing proteins in various tissues. International Journal of Molecular Sciences, 10, 1999-2009.
[6] Radkiewicz, J.L., Zipse, H., Clarke, S. and Houk, K.N. (1996) Accelerated racemization of aspartic acid and asparagine residues via succinimide intermediates: An ab initio theoretical exploration of mechanism. Journal of the American Chemical Society, 118, 9148-9155.
[7] Takahashi, O., Kobayashi, K. and Oda, A. (2010) Modeling the enolization of succinimide derivatives, a key step of racemization of aspartic acid residues: Importance of a two-H2O mechanism. Chemistry & Biodiversity, 7, 1349-1356.
[8] Takahashi, O., Kobayashi, K. and Oda, A. (2010) Computational insight into the mechanism of serine residue racemization. Chemistry & Biodiversity, 7, 1625-1629.
[9] Takahashi, O., Kobayashi, K. and Oda, A. (2010) Computational modeling of the enolization in a direct mechanism of racemization of the aspartic acid residue. Chemistry & Biodiversity, 7, 1630-1633.
[10] Takahashi, O. and Oda, A. (2012) Amide-iminol tautomerization of the C-terminal peptide groups of aspartic acid residues. Two-water-assisted mechanism, cyclization from the iminol tautomer leading to the tetrahedral intermediate of succinimide formation, and implication to peptide group hydrogen exchange. In: Jones, J.E. and Morano, D.M., Eds., Tyrosine and Aspartic Acid: Properties, Sources and Health Benefits, Nova Science Publishers, New York, 131-147.
[11] Fujii, N., Momose, Y. and Harada, K. (1996) Kinetic study of racemization of aspartyl residues in model peptides of αA-crystallin. International Journal of Protein Research, 48, 118-122.
[12] Kuge, K., Fujii, N., Miura, Y., Tajima, S. and Saito, T. (2004) Kinetic study of racemization of aspartyl residues in synthetic elastin peptides. Amino Acids, 27, 193-197.

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