Thermodynamics and Mechanisms of Protonated Asparaginyl-Glycine Decomposition
Thermodynamics and Mechanisms of Protonated Asparaginyl-Glycine Decomposition
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DOI：
10.1021/acs.jpcb.6b03253
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发表时间：
2016-07-14
影响因子：
3.3
通讯作者：
Armentrout, P. B.
中科院分区：
文献类型：
--
作者：
Boles, Georgia C.;Wu, R. R.;Armentrout, P. B.
天冬酰胺残基的脱酰胺化是蛋白质自发的翻译后修饰，在各种生物过程和退行性疾病中发挥着重要作用。在目前的工作中，我们提出了一个完整的描述脱酰胺过程，以及其他关键的碎片（脱水，肽键裂解，和损失2 NH3）从质子化天冬酰胺酰甘氨酸，H+（AsnGly），通过研究其动能依赖的碰撞诱导解离（CID）与质子化天冬酰胺使用引导离子束串联质谱仪。这些结果进行了比较与那些持续的非共振辐照（SORI）-CID的H+（AsnGly）与Ar在傅里叶变换离子回旋共振质谱仪。在B3 LYP/6- 31 G（d）水平上，采用模拟退火方法和一系列弛豫势能扫描，确定了每个关键反应的中间态和过渡态结构.在B3 LYP和B3 LYP-GD 3BJ/6-311+G（d，p）水平上对所有物种进行了优化。在B3 LYP、B3 P86、MP2（full）和B3 LYP-GD 3BJ理论水平上计算了所有主要反应物种的单点能量，并使用M06-2X作为限速物种。中间体，TS，和产品的相对能量允许H+（AsnGly）分解的基本和限速步骤的表征。通过结合实验和计算结果，H+（AsnGly）脱酰胺和其他碎片的完整的机械性质进行了探索，并与以前研究的H+（Asn）复杂。水溶剂化对关键TS的影响也进行了探讨。在一个基本的水平上，这种分析将有助于了解脱酰胺，脱水和其他重要的肽片段化中涉及的关键分子内相互作用的热力学和动力学特征。
Deamidation at asparagine residues, a spontaneous post-translational modification in proteins, plays a significant role in various biological processes and degenerative diseases. In the current work, we present a full description of the deamidation process as well as other key fragmentations (dehydration, peptide bond cleavage, and loss of 2 NH3) from protonated asparaginyl-glycine, H+(AsnGly), by studying its kinetic energy dependent collision-induced dissociation (CID) with Xe using a guided ion beam tandem mass spectrometer. These results are compared with those for sustained off-resonance irradiation (SORI)-CID of H+(AsnGly) with Ar in a Fourier transform ion cyclotron resonance mass spectrometer. Computationally, simulating annealing methodology and a series of relaxed potential energy scans at the B3LYP/6-31G(d) level were performed to identify all intermediate and transition state (TS) structures for each key reaction. All species were further optimized at the B3LYP and B3LYP-GD3BJ/6-311+G(d,p) levels of theory. Single point energies of all major reaction species were calculated at the B3LYP, B3P86, MP2(full), and B3LYP-GD3BJ levels of theory and using M06-2X for rate-limiting species. Relative energies of intermediates, TSs, and products allow characterization of the elementary and rate limiting steps in H+(AsnGly) decomposition. By combining experimental and computational results, the complete mechanistic nature of H+(AsnGly) deamidation and other fragmentations is explored and compared to the previously studied H+(Asn) complex. The influence of water solvation on key TSs is also explored. On a fundamental level, this analysis will aid in understanding the thermodynamic and kinetic characteristics of the key intramolecular interactions involved in deamidation, dehydration, and other important fragmentations of peptides.