蛋白质翻译后修饰棕榈酰化位点预测工具 —— CSS-Palm 2.0

 

CSS-Palm 2.0: an updated software for palmitoylation sites prediction 　 Jian Ren , Longping Wen, Xinjiao Gao, Changjiang Jin, Yu Xue and Xuebiao Yao. 　Protein Engineering, Design and Selection.2008 21(11):639-644 　 [Abstract] [Full Text] [PDF]

  As a special class of post-translational modifications (PTMs), numerous proteins could be covalently modified by a variety of lipids, including myristate (C14), palmitate (C16), farnesyl (C15), geranylgeranyl (C20) and glycosylphosphatidylinositol (GPI), etc (Casey, 1995 ; Nadolski and Linder, 2007 ; Resh, 2006 ). Although most of lipid modifications are irreversible, protein S-palmitoylation , also called as thioacylation or S-acylation, could reversibly attach 16-carbon saturated fatty acids to specific cysteine residues in protein substrates through thioester linkages (Bijlmakers and Marsh, 2003 ; Dietrich and Ungermann, 2004 ; el-Husseini Ael and Bredt, 2002 ; Greaves and Chamberlain, 2007 ; Linder and Deschenes, 2007 ; Nadolski and Linder, 2007 ; Resh, 2006 ; Resh, 2006 ; Roth, et al., 2006 ; Smotrys and Linder, 2004 ; Wan, et al., 2007 ). Palmitoylation will enhance the surface hydrophobicity and membrane affinity of protein substrates, and play important roles in modulating proteins' trafficking (Draper, et al., 2007 ; Linder and Deschenes, 2007 ), stability (Linder and Deschenes, 2007 ), and sorting (Greaves and Chamberlain, 2007 ), etc. Also, protein palmitoylation has been involved in numerous cellular processes, including signaling (Casey, 1995 ; Kurayoshi, et al., 2007 ; Resh, 2006 ), apoptosis (Chakrabandhu, et al., 2007 ; Feig, et al., 2007 ), and neuronal transmission (Roth, et al., 2006 ; Stowers and Isacoff, 2007 ), etc. Although many efforts have been made in this field, the molecular mechanism underlying protein palmitoylation still remain to be inexplicit.

     In this work, we updated our previous CSS-Palm 1.0 (Zhou, et al., 2006 ) into version 2.0 . We manually collected the experimentally verified palmitoylation sites from scientific literature. The non-redundant training data contained 263 palmitoylation sites from 109 distinct proteins. Then an improved version of CSS algorithm was deployed. The leave-one-out validation and 4-, 6-, 8-, 10-fold cross-validations were calculated to evaluate the prediction performance and system robustness of CSS-Palm 2.0 . Again, the prediction performance was also tested on an additional data set not included in the training data set, with 53 palmitoylation sites in 26 proteins. By comparison with our previous CSS-Palm1.0 and NBA-Palm 1.0 (Xue, et al., 2006 ; Zhou, et al., 2006 ), the performance of CSS-Palm 2.0 was greatly improved. Finally, the CSS-Palm 2.0 was implemented in JAVA 1.4.2 with high speed . The CSS-Palm 2.0 could predict out potential palmitoylation sites for ~1,000 proteins (with an average length of ~1000aa) within five minutes. Taken together, we proposed that the CSS-Palm 2.0 will be a great help for experimentalists. The CSS-Palm 2.0 is freely available at: http://csspalm.biocuckoo.org .

 

CSS-Palm 2.0 User Interface