Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, 13400-970 Piracicaba, SP, Brazil.
BMC Bioinformatics. 2009 Dec 31;10:454. doi: 10.1186/1471-2105-10-454.
Protein-protein interactions (PPIs) constitute one of the most crucial conditions to sustain life in living organisms. To study PPI in Arabidopsis thaliana we have developed AtPIN, a database and web interface for searching and building interaction networks based on publicly available protein-protein interaction datasets.
All interactions were divided into experimentally demonstrated or predicted. The PPIs in the AtPIN database present a cellular compartment classification (C3) which divides the PPI into 4 classes according to its interaction evidence and subcellular localization. It has been shown in the literature that a pair of genuine interacting proteins are generally expected to have a common cellular role and proteins that have common interaction partners have a high chance of sharing a common function. In AtPIN, due to its integrative profile, the reliability index for a reported PPI can be postulated in terms of the proportion of interaction partners that two proteins have in common. For this, we implement the Functional Similarity Weight (FSW) calculation for all first level interactions present in AtPIN database. In order to identify target proteins of cytosolic glutamyl-tRNA synthetase (Cyt-gluRS) (AT5G26710) we combined two approaches, AtPIN search and yeast two-hybrid screening. Interestingly, the proteins glutamine synthetase (AT5G35630), a disease resistance protein (AT3G50950) and a zinc finger protein (AT5G24930), which has been predicted as target proteins for Cyt-gluRS by AtPIN, were also detected in the experimental screening.
AtPIN is a friendly and easy-to-use tool that aggregates information on Arabidopsis thaliana PPIs, ontology, and sub-cellular localization, and might be a useful and reliable strategy to map protein-protein interactions in Arabidopsis. AtPIN can be accessed at http://bioinfo.esalq.usp.br/atpin.
蛋白质-蛋白质相互作用（PPIs）是维持生物体内生命的最重要条件之一。为了研究拟南芥中的蛋白质-蛋白质相互作用，我们开发了 AtPIN，这是一个基于公开的蛋白质-蛋白质相互作用数据集进行搜索和构建相互作用网络的数据库和网络界面。
所有的相互作用都分为实验证实或预测的。AtPIN 数据库中的蛋白质-蛋白质相互作用呈现出细胞区室分类（C3），根据其相互作用证据和亚细胞定位将蛋白质-蛋白质相互作用分为 4 类。文献表明，一对真正相互作用的蛋白质通常具有共同的细胞功能，而具有共同相互作用伙伴的蛋白质具有共享共同功能的高概率。在 AtPIN 中，由于其集成的特性，可以根据两个蛋白质共同的相互作用伙伴的比例来推测报告的蛋白质-蛋白质相互作用的可靠性指数。为此，我们对 AtPIN 数据库中所有一级相互作用实施了功能相似性权重（FSW）计算。为了鉴定细胞质谷氨酰-tRNA 合成酶（Cyt-gluRS）（AT5G26710）的靶蛋白，我们结合了两种方法，AtPIN 搜索和酵母双杂交筛选。有趣的是，蛋白质谷氨酰胺合成酶（AT5G35630）、一种抗病蛋白（AT3G50950）和一种锌指蛋白（AT5G24930）被 AtPIN 预测为 Cyt-gluRS 的靶蛋白，也在实验筛选中被检测到。
AtPIN 是一个友好易用的工具，它聚合了拟南芥蛋白质-蛋白质相互作用、本体论和亚细胞定位的信息，可能是映射拟南芥蛋白质-蛋白质相互作用的有用和可靠策略。AtPIN 可在 http://bioinfo.esalq.usp.br/atpin 访问。
