Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario N9B 3P4, Canada.
J Phys Chem B. 2024 Jun 13;128(23):5545-5556. doi: 10.1021/acs.jpcb.3c07628. Epub 2024 May 30.
Spontaneous deamidation of amino acids is a physiologically important process, particularly for protein aging and diseases. Despite its widespread occurrence, the mechanism of glutamine deamidation particularly within proteins remains poorly understood. We have used a multiscale computational approach to investigate glutamine deamidation in the tripeptide Glycine-Glutamine-Glycine (Gly-Gln-Gly) and γS-Crystallin protein. Specifically, both the 5- and 6-membered water-assisted deamidation pathways in the tripeptide have been elucidated and compared. Both are found to occur in three stages: iminol formation, cyclization, and deamination. The rate-limiting step in each mechanism is nucleophilic attack of the backbone iminol nitrogen, formed in the first stage, at the glutamine's side-chain carbonyl carbon. For the 6- and 5-membered mechanisms, this occurs with a free energy cost of 136.4 and 179.5 kJ mol, respectively. Thus, overall, in the Gly-Gln-Gly tripeptide, the 6-membered pathway is preferred. Furthermore, the free energies for forming cyclic intermediates and products at selected Gln residues (based on experimentally reported % deamidation) in γS-Crystallin have been obtained. It is found that the 5-membered product complex is exergonic at -25.3 kJ mol, while the 6-membered product complex is calculated to be endergonic at 90.7 kJ mol. Thus, the deamidation pathway in folded and constrained proteins may not exclusively follow the 6-membered route. Molecular dynamics (MD) simulations of γS-Crystallin indicate that deamidation is more likely to occur when two or more water molecules are in the proximity of the glutamine residue. Consequently, significant conformational changes are found to accompany Gln120 deamidation in γS-Crystallin. This in turn can influence water availability at the other Gln residues considered and hence potentially their deamidation. Collectively, these results provide comprehensive insights into spontaneous water-assisted deamidation of glutamine residues in peptides and into the role and impact of Gln deamidation in proteins.
氨基酸的自发脱酰胺作用是一种重要的生理过程，特别是对蛋白质的老化和疾病。尽管它的发生很普遍，但谷氨酰胺脱酰胺作用的机制，特别是在蛋白质中的机制，仍然知之甚少。我们使用一种多尺度计算方法来研究三肽甘氨酸-谷氨酰胺-甘氨酸（Gly-Gln-Gly）和 γS-晶体蛋白中的谷氨酰胺脱酰胺作用。具体来说，已经阐明并比较了三肽中的 5-和 6-元水分子辅助脱酰胺途径。这两种途径都被发现分三个阶段发生：亚氨基的形成、环化和脱氨。每个机制的限速步骤是在第一阶段形成的骨架亚氨基氮对谷氨酰胺侧链羰基碳的亲核攻击。对于 6-元和 5-元机制，这分别需要 136.4 和 179.5 kJ mol 的自由能成本。因此，总的来说，在 Gly-Gln-Gly 三肽中，6-元途径是首选的。此外，还获得了在 γS-晶体蛋白中选定 Gln 残基（基于实验报道的%脱酰胺）形成环状中间体和产物的自由能。结果发现，5-元产物络合物的自由能为-25.3 kJ mol，而 6-元产物络合物的自由能为 90.7 kJ mol。因此，折叠和约束蛋白质中的脱酰胺途径可能并不完全遵循 6-元途径。γS-晶体蛋白的分子动力学（MD）模拟表明，当两个或更多水分子接近谷氨酰胺残基时，脱酰胺作用更有可能发生。因此，在 γS-晶体蛋白中，发现 Gln120 脱酰胺作用伴随着显著的构象变化。这反过来又会影响其他考虑到的 Gln 残基的水分子可用性，从而可能影响它们的脱酰胺作用。总的来说，这些结果提供了对肽中谷氨酰胺残基自发水分子辅助脱酰胺作用的全面了解，并对蛋白质中 Gln 脱酰胺作用的作用和影响有了更深入的认识。
