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系统水平蛋白质相互作用网络分析和分子动力学研究揭示阿魏酸与相互作用作为一种天然辐射防护剂。

System-level protein interaction network analysis and molecular dynamics study reveal interaction of ferulic acid with as a natural radioprotector.

机构信息

Center for Bioinformatics and Biostatistics, Nitte (Deemed to be University), Mangalore, Karnataka, India.

Department of Biotechnology, Siddaganga Institute of Technology, Tumakuru, Karnataka, India.

出版信息

J Biomol Struct Dyn. 2024 Apr;42(6):2765-2781. doi: 10.1080/07391102.2023.2208224. Epub 2023 May 5.

Abstract

Ferulic acid is a crucial bioactive component of broccoli, wheat, and rice bran and is also an essential natural product that has undergone significant research. Ferulic acid's precise mode of action and effect on system-level protein networks have not been thoroughly investigated. An interactome was built using the STRING database and Cytoscape tools, utilizing 788 key proteins collected from PubMed literature to identify the ferulic acid-governed regulatory action on protein interaction network (PIN). The scale-free biological network of ferulic acid-rewired PIN is highly interconnected. We discovered 15 sub-modules using the MCODE tool for sub-modulization analysis and 153 enriched signaling pathways. Further, functional enrichment of top bottleneck proteins revealed the FoxO signaling pathway involved in enhancing cellular defense against oxidative stress. The selection of the critical regulatory proteins of the ferulic acid-rewired PIN was completed by performing analyses of topological characteristics such as GO term/pathways analysis, degree, bottleneck, molecular docking, and dynamics investigations. The current research derives a precise molecular mechanism for ferulic acid's action on the body. This in-depth model would aid in understanding how ferulic acid origins its antioxidant and scavenging properties in the human body.Communicated by Ramaswamy H. Sarma.

摘要

阿魏酸是西兰花、小麦和米糠中的一种重要生物活性成分,也是一种重要的天然产物,已经进行了大量的研究。阿魏酸对系统水平蛋白质网络的精确作用方式和影响尚未得到彻底研究。使用 STRING 数据库和 Cytoscape 工具构建了相互作用组,利用从 PubMed 文献中收集的 788 个关键蛋白来识别阿魏酸对蛋白质相互作用网络(PIN)的调控作用。阿魏酸重新布线的 PIN 的无标度生物网络高度相互关联。我们使用 MCODE 工具进行子模块分析,发现了 15 个子模块和 153 个富集的信号通路。此外,对顶级瓶颈蛋白的功能富集揭示了 FoxO 信号通路参与增强细胞对氧化应激的防御。通过对关键调控蛋白进行拓扑特征分析,如 GO 术语/通路分析、度、瓶颈、分子对接和动力学研究,完成了对阿魏酸重新布线的 PIN 的关键调控蛋白的选择。本研究得出了阿魏酸在体内作用的精确分子机制。该深入模型将有助于理解阿魏酸在人体内如何产生抗氧化和清除自由基的特性。由 Ramaswamy H. Sarma 传达。

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