Analytical Chemistry and Biomedicine Group, Medicine Faculty, University of Cartagena, Cartagena, Colombia.
Analytical Chemistry and Biomedicine Group, Pharmaceutical Sciences Faculty, University of Cartagena, Cartagena, Colombia.
J Mol Graph Model. 2023 Nov;124:108533. doi: 10.1016/j.jmgm.2023.108533. Epub 2023 Jun 5.
Protein oxidative modifications with reactive carbonyl species (RCS) is directly linked to metabolic processes in premature aging, cancer, neurodegenerative and infectious diseases. RCS as 4-Hydroxy-2-nonal (HNE), 4-Hydroxy-2-hexenal (HHE), 4-Oxo-2-nonenal (ONE) and Malondialdehyde (MDA) attack nucleophilic amino acids residues forming irreversible adducts with proteins as Thioredoxins (Trx). This is a class of small thiol oxide-reductases playing a key role in redox signaling and oxidative stress responses in mammals. Although proteomic studies have identified to Cys-32 residue as a target of HNE attack that inhibit its enzymatic activity, how this carbonylation affects its structure and dynamic behavior at the atomic level is unknown. Even more, the molecular bases for the atomistic behavior of these modified proteins have not been completely understood. We present molecular dynamics simulations of Trx-modified with four different RCS to analyze its global and local structural effects. For this, parameters supported in the AMBER force fields were built and validated for three non-natural cysteine residues modified with HHE, ONE and MDA. Results obtained showed a slight change in the global conformational stability of Trx modified with HNE and MDA, establishing that all modified proteins presented local regions of high mobility in the modified catalytic site and some regions far from the modification area. In addition, essential domain movement modes evidences that proteins modified with the RCS assayed induce changes in conformational flexibility. Finally, these data showed that the given conformational changes did not caused global changes in proteins but rather localized changes in particular regions.
蛋白质的氧化修饰与活性羰基化合物（RCS）直接相关，涉及代谢过程、早衰、癌症、神经退行性疾病和传染病。RCS 如 4-羟基-2-壬烯（HNE）、4-羟基-2-己烯醛（HHE）、4-氧代-2-壬烯醛（ONE）和丙二醛（MDA）攻击亲核氨基酸残基，与蛋白质形成不可逆的加合物，如硫氧还蛋白（Trx）。这是一类小的硫醇氧化物还原酶，在哺乳动物的氧化还原信号和氧化应激反应中发挥关键作用。尽管蛋白质组学研究已经确定 Cys-32 残基是 HNE 攻击的靶点，抑制其酶活性，但这种羰基化如何影响其结构和原子水平的动态行为尚不清楚。更重要的是，这些修饰蛋白的原子行为的分子基础尚未完全理解。我们对 Trx 进行了四种不同 RCS 的分子动力学模拟，以分析其全局和局部结构效应。为此，我们构建并验证了 AMBER 力场中支持的参数，用于修饰三个非天然半胱氨酸残基的 HHE、ONE 和 MDA。结果表明，HNE 和 MDA 修饰的 Trx 的全局构象稳定性略有变化，证明所有修饰的蛋白质在修饰的催化位点和远离修饰区域的一些区域都具有高迁移率的局部区域。此外，必需结构域运动模式表明，所测试的 RCS 修饰的蛋白质会引起构象灵活性的变化。最后，这些数据表明，给定的构象变化不会导致蛋白质的全局变化，而是导致特定区域的局部变化。
