Comparison of the activation energy barrier for succinimide formation from α- and β-aspartic acid residues obtained from density functional theory calculations

Biochimica Et Biophysica Acta. Proteins and Proteomics
Tomoki NakayoshiAkifumi Oda

Abstract

The l-α-Asp residues in peptides or proteins are prone to undergo nonenzymatic reactions to form l-β-Asp, d-α-Asp, and d-β-Asp residues via a succinimide five-membered ring intermediate. From these three types of isomerized aspartic acid residues, particularly d-β-Asp has been widely detected in aging tissue. In this study, we computationally investigated the cyclization of α- and β-Asp residues to form succinimide with dihydrogen phosphate ion as a catalyst (H2PO4-). We performed the study using B3LYP/6-31+G(d,p) density functional theory calculations. The comparison of the activation barriers of both residues is discussed. All the calculations were performed using model compounds in which an α/β-Asp-Gly sequence is capped with acetyl and methylamino groups on the N- and C-termini, respectively. Moreover, H2PO4- catalyzes all the steps of the succinimide formation (cyclization-dehydration) acting as a proton-relay mediator. The calculated activation energy barriers for succinimide formation of α- and β-Asp residues are 26.9 and 26.0kcalmol-1, respectively. Although it was experimentally confirmed that β-Asp has higher stability than α-Asp, there was no clear difference between the activation barriers. Therefore, the higher sta...Continue Reading

Citations

Mar 3, 2018·International Journal of Molecular Sciences·Ryota KirikoshiOhgi Takahashi
Jan 10, 2021·International Journal of Molecular Sciences·Tomoki NakayoshiAkifumi Oda
Jun 1, 2020·Biochimica Et Biophysica Acta. Proteins and Proteomics·Tomoki NakayoshiAkifumi Oda
Jul 1, 2020·Biochimica Et Biophysica Acta. Proteins and Proteomics·Tomoki NakayoshiAkifumi Oda
Sep 30, 2020·International Journal of Molecular Sciences·Koichi KatoAkifumi Oda
May 22, 2021·Molecular Informatics·Pablo Andrei NogaraJoão Batista Teixeira Rocha
Mar 28, 2019·The Journal of Physical Chemistry. B·Tomoki NakayoshiAkifumi Oda

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