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

Abstract

Racemization of aspartic acid (Asp) residues in proteins plays an important role in the molecular biology of aging. In the widely accepted mecha- nism of the Asp racemization, a succinimide (SI) intermediate is the species which actually un- dergo the direct racemization. In the present stu- dy, a two-water-assisted mechanism of the SI racemization was computationally investigated using a model compound in which an amino- succinyl (Asu) residue is capped with acetyl and NMe groups on the N- and C-termini, respective- ly. The two water molecules catalyze the enoliza- tion of the Hα−Cα−C=O portion in the Asu resi- due by mediating proton relay from the α-carbon atom to the carboxyl oxygen atom. After the eno- lization, 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 fol- lowing ketonization. The overall activation bar- rier (28.2 kcal·mol−1) corresponds to the enoliza- tion and ketonization steps, and falls within the available experimental activation energies (21.4 - 29.0 kcal·mol−1). Therefore, the two-water-assis- ted mechanism investigated here is plausible for the in vivo and in vitro racemization reactions of the SI intermediates formed in peptides and pro- teins.