Baltoumas Fotis A, Sofras Dimitrios, Apostolakou Avgi E, Litou Zoi I, Iconomidou Vassiliki A
Section of Cell Biology & Biophysics, Department of Biology, School of Sciences, National & Kapodistrian University of Athens, Panepistimiopolis, 15701 Athens, Greece.
Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center "Alexander Fleming", 34 Fleming St., 16672 Athens, Greece.
Membranes (Basel). 2023 Jan 3;13(1):62. doi: 10.3390/membranes13010062.
The nuclear envelope (NE) is a double-membrane system surrounding the nucleus of eukaryotic cells. A large number of proteins are localized in the NE, performing a wide variety of functions, from the bidirectional exchange of molecules between the cytoplasm and the nucleus to chromatin tethering, genome organization, regulation of signaling cascades, and many others. Despite its importance, several aspects of the NE, including its protein-protein interactions, remain understudied. In this work, we present NucEnvDB, a publicly available database of NE proteins and their interactions. Each database entry contains useful annotation including a description of its position in the NE, its interactions with other proteins, and cross-references to major biological repositories. In addition, the database provides users with a number of visualization and analysis tools, including the ability to construct and visualize protein-protein interaction networks and perform functional enrichment analysis for clusters of NE proteins and their interaction partners. The capabilities of NucEnvDB and its analysis tools are showcased by two informative case studies, exploring protein-protein interactions in Hutchinson-Gilford progeria and during SARS-CoV-2 infection at the level of the nuclear envelope.
核膜（NE）是围绕真核细胞细胞核的双层膜系统。大量蛋白质定位于核膜，执行各种各样的功能，从细胞质与细胞核之间分子的双向交换到染色质拴系、基因组组织、信号级联调节等等。尽管核膜很重要，但其几个方面，包括其蛋白质-蛋白质相互作用，仍未得到充分研究。在这项工作中，我们展示了NucEnvDB，一个公开可用的核膜蛋白及其相互作用的数据库。每个数据库条目都包含有用的注释，包括其在核膜中的位置描述、与其他蛋白质的相互作用以及到主要生物数据库的交叉引用。此外，该数据库为用户提供了许多可视化和分析工具，包括构建和可视化蛋白质-蛋白质相互作用网络以及对核膜蛋白及其相互作用伙伴的簇进行功能富集分析的能力。通过两个信息丰富的案例研究展示了NucEnvDB及其分析工具的功能，这些研究在核膜水平上探索了哈钦森-吉尔福德早衰症和新冠病毒感染期间的蛋白质-蛋白质相互作用。
