Computational studies on cyclic imide formation mechanism of glutamic acid residues catalyzed by two water molecules

Abstract

Aspartic acid (Asp) residues in peptides and proteins are prone to nonenzymatic stereoinversion and/or isomerization to form three types of isomerized Asp residues (L-β-Asp, D-α-Asp, and D-β-Asp) via a five-membered ring succinimide intermediate. These isomerized Asp residues are detected more frequently in aged tissues. However, stereoinversion and/or isomerization of glutamic acid (Glu) residues having a chemical structure similar to Asp residues are hardly detected in proteins. In this study, we investigate computationally the formation mechanism of the cyclic imide, i.e., amino-glutarimidyl (Agl) from Glu residues, with water molecules as catalyst. We study the reaction mechanism by using quantum chemical B3LYP/6-31+G(d,p) density functional theory calculations. All calculations are performed by using model compounds in which a Glu residue is capped with acetyl and methylamino groups on the N- and C-termini, respectively. Agl formation consists of the three steps of iminolization, cyclization, and dehydration, and two water molecules acting as proton-relay mediators catalyze all three steps. The calculated activation energy for Agl formation from Glu residues is 30.3 kcal mol−1, which is somewhat greater than found experimentally for Asp-residue stereoinversion. This calculation suggests that in vivo Glu-residue stereoinversion is unlikely to occur because of the high activation barrier.