Computational Study on the Function of Palmitoylation on the Envelope Protein in SARS-CoV-2,Journal of Chemical Theory and Computation

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Computational Study on the Function of Palmitoylation on the Envelope Protein in SARS-CoV-2
Journal of Chemical Theory and Computation ( IF 5.7 ) Pub Date : 2021-09-13 , DOI: 10.1021/acs.jctc.1c00359
Shengjie Sun ₁ , Chitra Karki ₁ , Javier Aguilera ₂ , Alan E Lopez Hernandez ₁ , Jianjun Sun ₂ , Lin Li _{1,

3}

Affiliation

SARS-CoV-2 that caused COVID-19 has spread since the end of 2019. Its major effects resulted in over four million deaths around the whole world by August 2021. Therefore, understanding virulence mechanisms is important to prevent future outbreaks and for COVID-19 drug development. The envelope (E) protein is an important structural protein, affecting virus assembly and budding. The E protein pentamer is a viroporin, serving as an ion transferring channel in cells. In this work, we applied molecular dynamic simulations and topological and electrostatic analyses to study the effects of palmitoylation on the E protein pentamer. The results indicate that the cation transferring direction is more from the lumen to the cytosol. The structure of the palmitoylated E protein pentamer is more stable while the loss of palmitoylation caused the pore radius to reduce and even collapse. The electrostatic forces on the two sides of the palmitoylated E protein pentamer are more beneficial to attract cations in the lumen and to release cations into the cytosol. The results indicate the importance of palmitoylation, which can help the drug design for the treatment of COVID-19.

中文翻译：

SARS-CoV-2 包膜蛋白棕榈酰化功能的计算研究

引起 COVID-19 的 SARS-CoV-2 自 2019 年底以来一直在传播。截至 2021 年 8 月，其主要影响导致全世界超过 400 万人死亡。因此，了解毒力机制对于预防未来的疫情爆发和预防新冠病毒的爆发非常重要。 19 药物开发。包膜（E）蛋白是一种重要的结构蛋白，影响病毒的组装和出芽。 E蛋白五聚体是一种病毒孔蛋白，充当细胞中的离子传输通道。在这项工作中，我们应用分子动力学模拟以及拓扑和静电分析来研究棕榈酰化对 E 蛋白五聚体的影响。结果表明，阳离子转移方向更多的是从管腔到细胞质。棕榈酰化E蛋白五聚体的结构更加稳定，而棕榈酰化的丧失导致孔隙半径减小甚至塌陷。棕榈酰化E蛋白五聚体两侧的静电力更有利于吸引管腔中的阳离子并将阳离子释放到胞质溶胶中。结果表明棕榈酰化的重要性，它可以帮助设计治疗 COVID-19 的药物。

更新日期：2021-10-12

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