※ CSS-Palm INTRODUCTION:
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.
Recently, we updated our previous CSS-Palm 2.0 (Ren, et al., 2008) into version 3.0. We manually collected the experimentally verified palmitoylation sites from scientific literature. The non-redundant training data contained 439 palmitoylation sites from 194 distinct proteins. Then the latest GPS algorithm of version 3.0 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 3.0. By comparison with our previous CSS-Palm2.0, CSS-Palm1.0 and NBA-Palm 1.0 (Ren, et al., 2008; Xue, et al., 2006; Zhou, et al., 2006), the performance of CSS-Palm 3.0 was greatly improved. Finally, the CSS-Palm 3.0 was implemented in JAVA 1.4.2 with high speed. The CSS-Palm 3.0 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 3.0 will be a great help for experimentalists. The CSS-Palm 3.0 is freely available at: http://csspalm.biocuckoo.org while the 2.0 version is also provided.
This website is linked in ExPASy Proteomics Tools page.
CSS-PALM 3.0 User Interface
For publication of results please cite the following article:
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
Computational prediction of post-translational modification sites in proteins
Yu Xue, Zexian Liu, Jun Cao, Jian Ren.
Systems and Computational Biology -
Molecular and Cellular Experimental Systems
Ning-Sun Yang (Ed.), ISBN: 978-953-307-280-7, InTech