Impact of Structural Flexibility on Tunneling Contribution to the Reaction Mechanism of Spontaneous Succinimide Formation in Asn-Gly-Containing Peptides

Abstract

Spontaneous deamidation and isomerization of asparagine (Asn) residues is a major pathway of nonenzymatic protein aging, where Asn-Gly-containing peptides (NG motifs) represent the most reactive sequence. In this context, the first step of isomerization is succinimide formation, which is initiated by a concerted proton-transfer and nucleophilic activation step. Although the overall mechanism is established, the detailed nature of the rate-determining succinimide formation step and the possible role of nuclear quantum effects remain unclear. Here, we combine density functional theory (DFT), intrinsic reaction coordinate (IRC) analysis, and quantitative NMR kinetics to investigate hydrogen/deuterium (H/D) substitution effects on NG isomerization in different model peptides, which represent both conformationally flexible and restricted systems. Deuteration preserves the reaction pathway and structural evolution, indicating an invariant classical reaction coordinate. However, kinetic isotope effects in the flexible peptide system reveal a mixed classical–tunneling mechanism in the rate-determining step with observable deviations from classical over-the-barrier behavior. In contrast, the conformationally restricted peptide shows suppressed tunneling contributions. These findings demonstrate that conformational accessibility modulates proton tunneling in spontaneous peptide rearrangements and extends nuclear quantum effects beyond enzymatic systems to nonenzymatic processes associated with protein aging.