Clarke S
Department of Chemistry and Biochemistry, University of California, Los Angeles.
Int J Pept Protein Res. 1987 Dec;30(6):808-21. doi: 10.1111/j.1399-3011.1987.tb03390.x.
One mechanism for the spontaneous degradation of polypeptides is the intramolecular attack of the peptide bond nitrogen on the side chain carbonyl carbon atom of aspartic acid and asparagine residues. This reaction results in the formation of succinimide derivatives and has been shown to be largely responsible for the racemization, isomerization, and deamidation of these residues in several peptides under physiological conditions (Geiger, T. & Clarke, S. J. Biol. Chem. 262, 785-794 (1987]. To determine if similar reactions might occur in proteins, I examined the sequence and conformation about aspartic acid and asparagine residues in a sample of stable, well-characterized proteins. There did not appear to be any large bias against dipeptide sequences that readily form succinimides in small peptides. However, it was found that aspartyl and asparaginyl residues generally exist in native proteins in conformations where the peptide bond nitrogen atom cannot approach the side chain carbonyl carbon to form a succinimide ring. These orientations also represent energy minimum states, and it appears that this factor may account for a low rate of spontaneous damage to proteins by succinimide-linked reactions. The presence of aspartic acid and asparagine residues in other conformations, such as those in partially denatured, conformationally flexible regions, may lead to more rapid succinimide formation and contribute to the degradation of the molecule. The possible role of isoimide intermediates, formed by the attack of the peptide oxygen atom on the side chain carboxyl group, in protein racemization, isomerization, and deamidation is also considered.
多肽自发降解的一种机制是肽键氮对天冬氨酸和天冬酰胺残基侧链羰基碳原子的分子内攻击。该反应导致琥珀酰亚胺衍生物的形成，并且已表明在生理条件下，该反应在很大程度上导致了几种肽中这些残基的消旋、异构化和脱酰胺（盖格，T.和克拉克，S.《生物化学杂志》262，785 - 794 [1987]）。为了确定蛋白质中是否可能发生类似反应，我研究了一组稳定的、特征明确的蛋白质样品中天冬氨酸和天冬酰胺残基周围的序列和构象。对于在小肽中容易形成琥珀酰亚胺的二肽序列，似乎没有任何明显的偏向。然而，发现天冬氨酰和天冬酰胺酰残基在天然蛋白质中通常处于肽键氮原子无法接近侧链羰基碳以形成琥珀酰亚胺环的构象中。这些取向也代表能量最低状态，并且似乎这个因素可能解释了通过琥珀酰亚胺连接反应对蛋白质的自发损伤速率较低的原因。处于其他构象的天冬氨酸和天冬酰胺残基的存在，例如在部分变性的、构象灵活区域中的那些残基，可能导致更快的琥珀酰亚胺形成并促进分子的降解。还考虑了由肽氧原子攻击侧链羧基形成的异琥珀酰亚胺中间体在蛋白质消旋、异构化和脱酰胺中的可能作用。
