title: A Computational Study of the Mechanism of Succinimide Formation in the Asn-His Sequence: Intramolecular Catalysis by the His Side Chain.
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.
authors.affiliation: Faculty of Pharmaceutical Sciences, Tohoku Pharmaceutical University, 4-4-1 Komatsushima, Aoba-ku, Sendai 981-8558, Japan. ohgi@tohoku-pharm.ac.jp.
authors.forename: Ohgi
authors.initials: O
authors.lastname: Takahashi
authors.affiliation: Faculty of Pharmaceutical Sciences, Tohoku Pharmaceutical University, 4-4-1 Komatsushima, Aoba-ku, Sendai 981-8558, Japan. manabe@tohoku-pharm.ac.jp.
authors.forename: Noriyoshi
authors.initials: N
authors.lastname: Manabe
authors.affiliation: Faculty of Pharmaceutical Sciences, Tohoku Pharmaceutical University, 4-4-1 Komatsushima, Aoba-ku, Sendai 981-8558, Japan. kirikoshi@tohoku-pharm.ac.jp.
authors.forename: Ryota
authors.initials: R
authors.lastname: Kirikoshi
mesh_terms: D000595:Amino Acid Sequence; D001216:Asparagine / Q000737:chemistry*; D002384:Catalysis; D006639:Histidine / Q000737:chemistry*; D008956:Models, Chemical; D010455:Peptides / Q000737:chemistry; D011506:Proteins / Q000737:chemistry; D013388:Succinimides / Q000737:chemistry*
chemical_list: D010455:Peptides; D011506:Proteins; D013388:Succinimides; C032620:succinimide; D006639:Histidine; D001216:Asparagine
keywords: Asn–His sequence; asparagine residue; computational chemistry; deamidation; density functional theory; histidine imidazole group; intramolecular catalysis; nonenzymatic reaction; proton-transfer mediator; succinimide