Takahashi Ohgi, Manabe Noriyoshi, Kirikoshi Ryota
Faculty of Pharmaceutical Sciences, Tohoku Pharmaceutical University, 4-4-1 Komatsushima, Aoba-ku, Sendai 981-8558, Japan.
Molecules. 2016 Mar 9;21(3):327. doi: 10.3390/molecules21030327.
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.
天冬酰胺（Asn）残基在肽和蛋白质中通过琥珀酰亚胺中间体自发且非酶促发生的脱酰胺反应速率，已知强烈依赖于羧基侧（Xxx）的后续残基的性质。当Xxx为甘氨酸（Gly），即最小的氨基酸残基时，琥珀酰亚胺中间体的形成是迄今为止最快的，而当Xxx为诸如异亮氨酸（Ile）和缬氨酸（Val）等体积较大的残基时则极其缓慢。在这方面，非常有趣的是，尽管组氨酸（His）体积较大，但当Xxx为His时，琥珀酰亚胺的形成肯定会加速。在本文中，我们通过计算表明，在Asn-His序列中，His侧链咪唑基团（处于中性Nε-质子化形式）可通过介导质子转移，特异性催化琥珀酰亚胺形成过程中四面体中间体的形成。以Ace-Asn-His-Nme（Ace = 乙酰基，Nme = 甲氨基）作为模型化合物，采用密度泛函理论，使用B3LYP泛函和6-31+G(d,p)基组进行了计算。我们还表明，四面体中间体一旦在NH₂基团处质子化，就很容易释放出一个氨分子，生成琥珀酰亚胺物种。
