DrLLPS (相分离数据库): 第一个注释全面的液液相分离相关蛋白质数据库 (liquid-liquid phase separation database)

最新推荐文章于 2024-10-11 17:04:33 发布

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最新推荐文章于 2024-10-11 17:04:33 发布

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分类专栏：数据库工具文章标签：数据库液液相分离无膜细胞器应激颗粒 liquid-liquid phase separation

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DrLLPS (相分离数据库): a data resource of liquid-liquid phase separation in eukaryotes——第一个注释全面的液液相分离相关蛋白质数据库 (liquid-liquid phase separation database)

Abstract

Here, we presented an integrative database named DrLLPS (http://llps.biocuckoo.cn/) for proteins involved in liquid-liquid phase separation (LLPS), which is a ubiquitous and crucial mechanism for spatiotemporal organization of various biochemical reactions, by creating membraneless organelles (MLOs) in eukaryotic cells. From the literature, we manually collected 150 scaffold proteins that are drivers of LLPS, 987 regulators that contribute in modulating LLPS, and 8148 potential client proteins that might be dispensable for the formation of MLOs, which were then categorized into 40 biomolecular condensates. We searched potential orthologs of these known proteins, and in total DrLLPS contained 437 887 known and potential LLPS-associated proteins in 164 eukaryotes. Furthermore, we carefully annotated LLPS-associated proteins in eight model organisms, by using the knowledge integrated from 110 widely used resources that covered 16 aspects, including protein disordered regions, domain annotations, post-translational modifications (PTMs), genetic variations, cancer mutations, molecular interactions, disease-associated information, drug-target relations, physicochemical property, protein functional annotations, protein expressions/proteomics, protein 3D structures, subcellular localizations, mRNA expressions, DNA & RNA elements, and DNA methylations. We anticipate DrLLPS can serve as a helpful resource for further analysis of LLPS.
从文献中，我们手动收集了150种驱动LLPS的支架蛋白，987种调节LLPS的调控子，以及8148种可能对形成无膜细胞器不可或缺的潜在客户蛋白，然后将这些蛋白质分类到40种生物分子缩合物。我们搜索了这些已知蛋白的潜在直系同源物，并且总共DrLLPS在164个真核生物中包含437887个已知和潜在的LLPS相关蛋白。此外，我们使用110种广泛使用的资源（包括16个方面的蛋白质）整合的知识，仔细地注释了8种模式生物中与LLPS相关的蛋白质，包括蛋白质无序区，结构域注释，翻译后修饰（PTM），遗传变异，癌症突变，分子相互作用，疾病相关信息，药物-靶标关系，理化性质，蛋白质功能注释，蛋白质表达/蛋白质组学，蛋白质3D结构，亚细胞定位，mRNA表达，DNA和RNA元素以及DNA甲基化。我们希望DrLLPS可以作为进一步分析LLPS的有用资源。