Lee Hang-mao, Dietz Karl J, Hofestädt Ralf
Bioinformatics/Medical Informatics Department, Bielefeld University, Postfach 10 01 31, Bielefeld 33615, Germany.
J Integr Bioinform. 2010 Mar 25;7(3):483. doi: 10.2390/biecoll-jib-2010-130.
A significant part of cellular proteins undergo reversible thiol-dependent redox transitions which often control or switch protein functions. Thioredoxins and glutaredoxins constitute two key players in this redox regulatory protein network. Both interact with various categories of proteins containing reversibly oxidized cysteinyl residues. The identification of thioredoxin/glutaredoxin target proteins is a critical step in constructing the redox regulatory network of cells or subcellular compartments. Due to the scarcity of thioredoxin/glutaredoxin target protein records in the public database, a tool called Reversibly Oxidized Cysteine Detector (ROCD) is implemented here to identify potential thioredoxin/glutaredoxin target proteins computationally, so that the in silico construction of redox regulatory network may become feasible. ROCD was tested on 46 thioredoxin target proteins in plant mitochondrion, and the recall rate was 66.7% when 50% sequence identity was chosen for structural model selection. ROCD will be used to predict the thioredoxin/glutaredoxin target proteins in human liver mitochondrion for our redox regulatory network construction project. The ROCD will be developed further to provide prediction with more reliability and incorporated into biological network visualization tools as a node prediction component. This work will advance the capability of traditional database- or text mining-based method in the network construction.
细胞内相当一部分蛋白质会经历可逆的硫醇依赖性氧化还原转变，这种转变常常控制或切换蛋白质的功能。硫氧还蛋白和谷氧还蛋白是这个氧化还原调节蛋白网络中的两个关键参与者。它们都与各类含有可逆氧化半胱氨酰残基的蛋白质相互作用。鉴定硫氧还蛋白/谷氧还蛋白的靶蛋白是构建细胞或亚细胞区室氧化还原调节网络的关键一步。由于公共数据库中硫氧还蛋白/谷氧还蛋白靶蛋白记录稀缺，在此实施了一种名为可逆氧化半胱氨酸检测器（ROCD）的工具，用于通过计算鉴定潜在的硫氧还蛋白/谷氧还蛋白靶蛋白，从而使氧化还原调节网络的计算机模拟构建成为可能。ROCD在植物线粒体中的46种硫氧还蛋白靶蛋白上进行了测试，当选择50%的序列同一性进行结构模型选择时，召回率为66.7%。ROCD将用于预测人类肝脏线粒体中的硫氧还蛋白/谷氧还蛋白靶蛋白，以用于我们的氧化还原调节网络构建项目。ROCD将进一步开发，以提供更可靠的预测，并作为节点预测组件纳入生物网络可视化工具。这项工作将提升传统基于数据库或文本挖掘的方法在网络构建方面的能力。
