Institute of Systems Biology, Shanghai University, Shanghai, China.
Biochimie. 2011 Mar;93(3):489-96. doi: 10.1016/j.biochi.2010.10.022. Epub 2010 Nov 12.
Palmitoylation is a universal and important lipid modification, involving a series of basic cellular processes, such as membrane trafficking, protein stability and protein aggregation. With the avalanche of new protein sequences generated in the post genomic era, it is highly desirable to develop computational methods for rapidly and effectively identifying the potential palmitoylation sites of uncharacterized proteins so as to timely provide useful information for revealing the mechanism of protein palmitoylation. By using the Incremental Feature Selection approach based on amino acid factors, conservation, disorder feature, and specific features of palmitoylation site, a new predictor named IFS-Palm was developed in this regard. The overall success rate thus achieved by jackknife test on a newly constructed benchmark dataset was 90.65%. It was shown via an in-depth analysis that palmitoylation was intimately correlated with the feature of the upstream residue directly adjacent to cysteine site as well as the conservation of amino acid cysteine. Meanwhile, the protein disorder region might also play an import role in the post-translational modification. These findings may provide useful insights for revealing the mechanisms of palmitoylation.
棕榈酰化是一种普遍而重要的脂质修饰，涉及一系列基本的细胞过程，如膜运输、蛋白质稳定性和蛋白质聚集。在后基因组时代，新的蛋白质序列呈雪崩式增长，因此非常需要开发计算方法来快速有效地识别未表征蛋白质的潜在棕榈酰化位点，以便及时提供揭示蛋白质棕榈酰化机制的有用信息。本文基于氨基酸因素、保守性、无序特征和棕榈酰化位点的特定特征，采用基于氨基酸因素的递增特征选择方法，开发了一种新的预测器 IFS-Palm。在新构建的基准数据集上通过交叉验证测试，总体成功率达到 90.65%。通过深入分析表明，棕榈酰化与半胱氨酸位点直接相邻的上游残基的特征以及氨基酸半胱氨酸的保守性密切相关。同时，蛋白质无序区域在后翻译修饰中也可能发挥重要作用。这些发现可能为揭示棕榈酰化机制提供有用的见解。
