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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
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Last update: Mar. 18th, 2011