Abstract

The rates of deamidation reactions of asparagine (Asn) residues which occur spontaneously and nonenzymatically in peptides and proteins via the succinimide intermediate are known to be strongly dependent on the nature of the following residue on the carboxyl side (Xxx). The formation of the succinimide intermediate is by far the fastest when Xxx is glycine (Gly), the smallest amino acid residue, while extremely slow when Xxx is bulky such as isoleucine (Ile) and valine (Val). In this respect, it is very interesting to note that the succinimide formation is definitely accelerated when Xxx is histidine (His) despite its large size. In this paper, we computationally show that, in an Asn–His sequence, the His side-chain imidazole group (in the neutral Nε-protonated form) can specifically catalyze the formation of the tetrahedral intermediate in the succinimide formation by mediating a proton transfer. The calculations were performed for Ace−Asn−His−Nme (Ace = acetyl, Nme = methylamino) as a model compound by the density functional theory with the B3LYP functional and the 6-31+G(d,p) basis set. We also show that the tetrahedral intermediate, once protonated at the NH2 group, easily releases an ammonia molecule to give the succinimide species.

Highlights

  • IntroductionSuccinimide (SI)-mediated reactions of asparagine (Asn) and aspartic acid (Asp) residues in peptides and proteins (Scheme 1) have been extensively studied in many fields of chemical, biological, and pharmaceutical sciences [1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38]

  • Geometry optimizations were performed by using the B3LYP functional and the 6-31+G(d,p) basis set, and relative energies were corrected for the zero-point energy (ZPE) and the hydration free energy calculated by the SM8 continuum model [47,48]

  • The reactant, transition state, intermediate, and product are abbreviated as R, TS, INT, and P, respectively, and PC stands for the product complex formed between P, an NH3 molecule, and a proton

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Summary

Introduction

Succinimide (SI)-mediated reactions of asparagine (Asn) and aspartic acid (Asp) residues in peptides and proteins (Scheme 1) have been extensively studied in many fields of chemical, biological, and pharmaceutical sciences [1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38] These reactions occur spontaneously and nonenzymatically both in vivo and in vitro, and produce biologically uncommon L-β-Asp, D-Asp, and D-β-Asp residues. Since the rate of Asn deamidation varies widely depending on the peptide and protein structures, it has been proposed that this reaction functions as a molecular clock by regulating the timing of biological events such as protein turnover [18,25]

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