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相邻侧链对天冬酰胺基和天冬氨酸基降解的影响:肽构象与主链NH酸度之间关系的从头算研究。

Neighboring side chain effects on asparaginyl and aspartyl degradation: an ab initio study of the relationship between peptide conformation and backbone NH acidity.

作者信息

Radkiewicz J L, Zipse H, Clarke S, Houk K N

机构信息

Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, CA 90095, USA.

出版信息

J Am Chem Soc. 2001 Apr 18;123(15):3499-506. doi: 10.1021/ja0026814.

Abstract

The rate of spontaneous degradations of asparagine and aspartyl residues occurring through succinimide intermediates is dependent upon the nature of the residue on the carboxyl side in peptides. For nonglycine residues, we show here that this effect can largely be attributed to the electrostatic/inductive effect of the side chain group on the equilibrium concentration of the anionic form of the peptide bond nitrogen atom that initiates the succinimide forming reaction. However, the rate of degradation of Asn-Gly and Asp-Gly containing peptides is about an order of magnitude greater than predicted solely using this explanation. To understand the nature of the glycine effect, ab initio calculations were performed on model compounds. These calculations indicate that there is little to no change in the stability of the transition state or the tetrahedral intermediate of succinimide formation with Asn-/Asp-Gly and Asn-/Asp-Ala derivatives. However, we have found that the acidity of the backbone peptide nitrogen NH is highly dependent upon the conformation of the molecule. Since glycine residues lack the beta-carbon common to all other protein amino acids, these residues can sample additional regions of conformational space where it is possible to further stabilize the backbone amide anion and thus increase the rate of degradation. These results provide the first rationale for the particular rate enhancement of degradation in peptidyl Asn-/Asp-Gly sequences. The results also can be applied to asparagine and aspartyl residues in proteins where the 3-dimensional structure provides additional constraints on conformation that can either increase or decrease the equilibrium concentration of the backbone amide anion and thus their rate of degradation via succinimide intermediates. Understanding this chemistry will assist attempts to minimize the deleterious effect of aging at the molecular level. The relationship between these results and proton exchange experiments is discussed in the Appendix.

摘要

通过琥珀酰亚胺中间体发生的天冬酰胺和天冬氨酰残基的自发降解速率取决于肽中羧基侧残基的性质。对于非甘氨酸残基,我们在此表明,这种效应在很大程度上可归因于侧链基团对引发琥珀酰亚胺形成反应的肽键氮原子阴离子形式平衡浓度的静电/诱导效应。然而,含天冬酰胺-甘氨酸和天冬氨酸-甘氨酸的肽的降解速率比仅用这种解释预测的要大一个数量级左右。为了理解甘氨酸效应的本质,对模型化合物进行了从头算。这些计算表明,天冬酰胺/天冬氨酸-甘氨酸和天冬酰胺/天冬氨酸-丙氨酸衍生物形成琥珀酰亚胺的过渡态或四面体中间体的稳定性几乎没有变化。然而,我们发现主链肽氮NH的酸度高度依赖于分子的构象。由于甘氨酸残基缺乏所有其他蛋白质氨基酸共有的β-碳,这些残基可以占据构象空间的其他区域,在这些区域有可能进一步稳定主链酰胺阴离子,从而提高降解速率。这些结果为肽中天冬酰胺/天冬氨酸-甘氨酸序列降解速率的特别提高提供了首个理论依据。这些结果也可应用于蛋白质中的天冬酰胺和天冬氨酰残基,其中三维结构对构象提供了额外的限制,这可以增加或降低主链酰胺阴离子的平衡浓度,从而影响它们通过琥珀酰亚胺中间体的降解速率。理解这种化学性质将有助于在分子水平上尽量减少衰老的有害影响。这些结果与质子交换实验之间的关系在附录中进行了讨论。

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