Computational studies on nonenzymatic succinimide-formation mechanisms of the aspartic acid residues catalyzed by two water molecules

Biochim Biophys Acta Proteins Proteom. 2020 Sep;1868(9):140459. doi: 10.1016/j.bbapap.2020.140459. Epub 2020 May 29.


In the biological proteins, aspartic acid (Asp) residues are prone to nonenzymatic isomerization via a succinimide (Suc) intermediate. Asp-residue isomerization causes the aggregation and the insolubilization of proteins, and is considered to be involved in various age-related diseases. Although Suc intermediate was considered to be formed by nucleophilic attack of the main-chain amide nitrogen of N-terminal side adjacent residue to the side-chain carboxyl carbon of Asp residue, previous studies have shown that the nucleophilic attack is more likely to proceed via iminol tautomer when the water molecules act as catalysts. However, the full pathway to Suc-intermediate formation has not been investigated, and the experimental analyses for the Asp-residue isomerization mechanism at atomic and molecular levels, such as the analysis of the transition state geometry, are difficult. In the present study, we computationally explored the full pathways for Suc-intermediate formation from Asp residues. The calculations were performed two types of reactant complexes, and all energy minima and TS geometries were optimized using B3LYP density functional methods. As a result, the SI-intermediate formation was divided into three processes, i.e., iminolization, cyclization, and dehydration processes, and the activation energies were calculated to be 26.1 or 28.4 kcal mol-1. These values reproduce the experimental data. The computational results show that abundant water molecules in living organisms are effective catalysts for the Asp-residue isomerization.

Keywords: Density functional theory; Isomerization; Nonenzymatic reaction; Reaction mechanism; Tautomerization; d-aspartic acid.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amides
  • Aspartic Acid / chemistry*
  • Catalysis
  • Cyclization
  • Isomerism
  • Models, Chemical*
  • Models, Molecular
  • Nitrogen
  • Proteins / chemistry
  • Succinimides / chemical synthesis*
  • Water / chemistry*


  • Amides
  • Proteins
  • Succinimides
  • Water
  • succinimide
  • Aspartic Acid
  • Nitrogen