Proteome-wide prediction of novel DNA/RNA-binding proteins using amino acid composition and periodicity in the hyperthermophilic archaeon Pyrococcus furiosus.
Proteome-wide prediction of novel DNA/RNA-binding proteins using amino acid composition and periodicity in the hyperthermophilic archaeon Pyrococcus furiosus.
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DOI：
10.1093/dnares/dsm011
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发表时间：
2007-06-30
期刊：
影响因子：
--
通讯作者：
Kanai A
中科院分区：
文献类型：
--
作者：
Fujishima K;Komasa M;Kitamura S;Suzuki H;Tomita M;Kanai A
蛋白质在复杂的生物系统中起着关键作用，但在公开的数据库中，约有一半的蛋白质被注释为功能未知。因此，利用生物信息学方法进行蛋白质组功能分类正成为揭示未知蛋白质功能的重要方法。以极端嗜热古菌Pyrococcusfuriosus为模型物种，以氨基酸组成和周期性为特征向量，采用支持向量机（SVM）方法对DNA/RNA结合蛋白和其他功能蛋白进行了识别。我们将该值定义为组成评分（CO）和周期性评分（PD）。根据CO评分和PD评分的二维相关性分析，将P. furiosus蛋白分为3类（I-III）。结果，发现分类为I类蛋白质（CO评分+ PD评分> 0.6）的功能已知蛋白质中约87%是DNA/RNA结合蛋白质。通过对994个蛋白质的二维相关性分析，预测了151个蛋白质可能是新的DNA/RNA结合蛋白。随机选择的假设蛋白质的DNA/RNA结合活性进行了实验验证。在I类中的七个候选蛋白中有六个具有DNA/RNA结合活性，支持我们的方法的有效性。
Proteins play a critical role in complex biological systems, yet about half of the proteins in publicly available databases are annotated as functionally unknown. Proteome-wide functional classification using bioinformatics approaches thus is becoming an important method for revealing unknown protein functions. Using the hyperthermophilic archaeon Pyrococcus furiosus as a model species, we used the support vector machine (SVM) method to discriminate DNA/RNA-binding proteins from proteins with other functions, using amino acid composition and periodicities as feature vectors. We defined this value as the composition score (CO) and periodicity score (PD). The P. furiosus proteins were classified into three classes (I–III) on the basis of the two-dimensional correlation analysis of CO score and PD score. As a result, approximately 87% of the functionally known proteins categorized as class I proteins (CO score + PD score > 0.6) were found to be DNA/RNA-binding proteins. Applying the two-dimensional correlation analysis to the 994 hypothetical proteins in P. furiosus, a total of 151 proteins were predicted to be novel DNA/RNA-binding protein candidates. DNA/RNA-binding activities of randomly chosen hypothetical proteins were experimentally verified. Six out of seven candidate proteins in class I possessed DNA/RNA-binding activities, supporting the efficacy of our method.
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