Xiao Qingyu, Miao Benpeng, Bi Jie, Wang Zhen, Li Yixue
Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, P. R. China.
University of Chinese Academy of Sciences, Beijing, P. R. China.
Sci Rep. 2016 Apr 19;6:24735. doi: 10.1038/srep24735.
Protein phosphorylation is an important type of post-translational modification that is involved in a variety of biological activities. Most phosphorylation events occur on serine, threonine and tyrosine residues in eukaryotes. In recent years, many phosphorylation sites have been identified as a result of advances in mass-spectrometric techniques. However, a large percentage of phosphorylation sites may be non-functional. Systematically prioritizing functional sites from a large number of phosphorylation sites will be increasingly important for the study of their biological roles. This study focused on exploring the intrinsic features of functional phosphorylation sites to predict whether a phosphosite is likely to be functional. We found significant differences in the distribution of evolutionary conservation, kinase association, disorder score, and secondary structure between known functional and background phosphorylation datasets. We built four different types of classifiers based on the most representative features and found that their performances were similar. We also prioritized 213,837 human phosphorylation sites from a variety of phosphorylation databases, which will be helpful for subsequent functional studies. All predicted results are available for query and download on our website (Predict Functional Phosphosites, PFP, http://pfp.biosino.org/).
蛋白质磷酸化是一种重要的翻译后修饰类型，参与多种生物活动。在真核生物中，大多数磷酸化事件发生在丝氨酸、苏氨酸和酪氨酸残基上。近年来，由于质谱技术的进步，许多磷酸化位点已被鉴定出来。然而，很大一部分磷酸化位点可能是无功能的。从大量磷酸化位点中系统地筛选出功能位点对于研究它们的生物学作用将变得越来越重要。本研究着重探索功能性磷酸化位点的内在特征，以预测一个磷酸化位点是否可能具有功能。我们发现已知功能的磷酸化数据集与背景磷酸化数据集在进化保守性、激酶关联性、无序度得分和二级结构的分布上存在显著差异。我们基于最具代表性的特征构建了四种不同类型的分类器，发现它们的性能相似。我们还从各种磷酸化数据库中筛选出了213,837个人类磷酸化位点，这将有助于后续的功能研究。所有预测结果均可在我们的网站（预测功能性磷酸化位点，PFP，http://pfp.biosino.org/）上进行查询和下载。
