GPS-YNO2: computational prediction of tyrosine nitration sites in proteins
GPS-YNO2: computational prediction of tyrosine nitration sites in proteins
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GPS-YNO2：蛋白质中酪氨酸硝化位点的计算预测
DOI：
10.1039/c0mb00279h
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发表时间：
2011-01-01
影响因子：
--
通讯作者：
Xue, Yu
中科院分区：
文献类型：
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作者：
Liu, Zexian;Cao, Jun;Xue, Yu
蛋白质酪氨酸硝化（PTN）是一种重要的、普遍存在的翻译后修饰（PTM），在免疫应答、细胞死亡、衰老和神经退行性变等生理和病理过程中发挥着重要作用。鉴定位点特异性硝化底物是理解PTN分子机制和生物学功能的基础。与劳动密集型和耗时的实验方法相比，在这里，我们报告了新的软件包GPS-YNO 2预测PTN网站的发展。该软件的准确性为76.51%，敏感性为50.09%，特异性为80.18%。作为一个应用实例，我们预测了数百个硝化底物的潜在PTN位点，这些底物已在小规模或大规模研究中通过实验检测到，尽管实际硝化位点尚未确定。通过与一氧化氮（NO）依赖的S-亚硝基化可逆修饰的统计功能比较，我们观察到PTN更喜欢攻击某些基本的生物过程和功能。这些预测和分析结果可能有助于进一步的实验研究。最后，GPS-YNO 2 1.0的在线服务和本地软件包是用JAVA实现的，可在http://yno2.biocuckoo.org/上免费获得。
The last decade has witnessed rapid progress in the identification of protein tyrosine nitration (PTN), which is an essential and ubiquitous post-translational modification (PTM) that plays a variety of important roles in both physiological and pathological processes, such as the immune response, cell death, aging and neurodegeneration. Identification of site-specific nitrated substrates is fundamental for understanding the molecular mechanisms and biological functions of PTN. In contrast with labor-intensive and time-consuming experimental approaches, here we report the development of the novel software package GPS-YNO2 to predict PTN sites. The software demonstrated a promising accuracy of 76.51%, a sensitivity of 50.09% and a specificity of 80.18% from the leave-one-out validation. As an example application, we predicted potential PTN sites for hundreds of nitrated substrates which had been experimentally detected in small-scale or large-scale studies, even though the actual nitration sites had still not been determined. Through a statistical functional comparison with the nitric oxide (NO) dependent reversible modification of S-nitrosylation, we observed that PTN prefers to attack certain fundamental biological processes and functions. These prediction and analysis results might be helpful for further experimental investigation. Finally, the online service and local packages of GPS-YNO2 1.0 were implemented in JAVA and freely available at: http://yno2.biocuckoo.org/.