A Computational DFT Study of the Stereoinversion of Succinimide Residues Formed in Proteins and Peptides Catalyzed by a Hydrogen Phosphate Ion: An Unsymmetrical S_E1 Mechanism

Succinimide residues formed spontaneously from aspartic acid (Asp) and asparagine (Asn) residues in proteins and peptides are stereochemically unstable, undergoing partial l-to-d stereoinversion, and this is responsible for the d-Asp and d-β-Asp residues found in long-lived proteins. These stereoinverted abnormal amino acid residues are believed to be related to aging and some age-related diseases such as cataracts. Although the succinimide stereoinversion is nonenzymatic, a catalyst is required for it to occur at physiological temperature. In this study, it was found by density functional theory (DFT) calculations that a hydrogen phosphate ion (HPO₄²⁻) can effectively catalyze the stereoinversion of the succinimide intermediate. The HPO₄²⁻ ion abstracts a proton from the asymmetric carbon atom of the succinimide residue to form an enolate intermediate. Then, while the resultant dihydrogen phosphate ion (H₂PO₄⁻) remains bound to the enolate ion, a water molecule donates a proton to the enolate intermediate on the opposite side from the phosphate (which is the rate-determining step) to produce the inverted carbon atom. The calculated activation barrier (ca. 90 kJ mol⁻¹) is consistent with a slow in vivo reaction. The present found mechanism can be termed the “unsymmetrical S_E1” or “pseudo-S_E2” mechanism.