Accelerated Racemization of Aspartic Acid and Asparagine Residues via Succinimide Intermediates:  An ab Initio Theoretical Exploration of Mechanism

Abstract

Aspartic acid and asparagine residues racemize rapidly relative to other amino acid residues in proteins and peptides. This has been attributed to the increased acidity of the α-carbons of succinimide residues derived from the spontaneous cyclizations of these residues. To understand the basis of this effect, the acidities of model compounds were calculated using ab initio quantum mechanics (RHF/6-31+G*). The results were also checked with DFT (Becke3LYP/6-31+G*) and solvent cavity models (IPCM and SCIPCM). The geometries of succinimide, 2-pyrrolidinone, and the derived enolate anions were optimized, and the gas phase deprotonation energies were calculated. The imide is more acidic than the amide by 18 kcal/mol in the gas phase. Since there is a qualitative correlation between gas phase and aqueous acidities, this result provides an explanation for the experimental observations that the rate of peptidyl succinimide racemization can be ∼10 5 times greater than that of unmodified aspartic acid residues. To quantitate the source of the succinimide acidity, the geometries and CH acidities of various conformations of N -formylacetamide and acetamide, acyclic models of succinimide and 2-pyrrolidinone, and 3-oxobutanal and acetone, acyclic models lacking the nitrogen atom, were studied. The importance of resonance effects for increasing the acidity of the α-carbon of succinimide was established, but electrostatic and inductive effects also have an important influence on acidities. The acidity of succinimide is compared to the acidities of several peptide models. Isosuccinimide, an alternative degradation product of aspartic acid and asparagine residues, is also be expected to be racemization prone by similar mechanisms.