Recently, elucidation of protein palmitoylation-dependent functional roles has been emerging as an intriguing puzzle. Protein palmitoylation, also known as S-acylation, is one of the most ubiquitous post-translational modifications (PTM), reversibly attaching a 16-carbon saturated fatty acid as lipid palmitate (C16:0) to cysteine residues in protein substrates through thioester linkage (Bijlmakers and Marsh, 2003; Dietrich and Ungermann, 2004; el-Husseini Ael and Bredt, 2002; Linder and Deschenes, 2003; Smotrys and Linder, 2004). Biochemically, palmitoylation enhances the surface hydrophobicity of protein substrates and promotes their interaction with membranes (Kleuss and Krause, 2003). It can also regulate proteins’ intracellular trafficking (Kang, et al., 2004), sorting (Schneider, et al., 2005), subcellular localizations (Van Itallie, et al., 2005) and functional activities (Sudo, et al., 1992). Moreover, palmitoylation has been implicated in a variety of biological and physiological processes, including signal transduction (Vazquez, et al., 2005), mitosis (Caron, et al., 2001), neuronal development (el-Husseini Ael and Bredt, 2002), endocytosis (Yik, et al., 2002), and apoptosis (Wang and Sebti, 2005), etc.

    Identification of palmitoylation sites provides a solid foundation of understanding the molecular regulatory functions of palmitoylation process. To date, very few palmitoylation sites have been verified experimentally. Although several efficient techniques, such as mass spectrometry (MS), have been employed recently, most of the known palmitoylation sites are mapped by mutagenesis of candidate cysteine residues with conventional biochemical methods. And the features for palmitoylation are quite elusive and almost all of previous studies proposed that there is no common and canonical consensus sequence/motif for palmitoylation (Bijlmakers and Marsh, 2003; el-Husseini Ael and Bredt, 2002; Linder and Deschenes, 2003; Smotrys and Linder, 2004; ten Brinke, et al., 2002). Moreover, the molecular machinery for palmitoylation is still inexplicit. Palmitoylation of proteins might be carried out in both enzyme- and nonenzyme-dependent manners (Bijlmakers and Marsh, 2003; el-Husseini Ael and Bredt, 2002; Linder and Deschenes, 2003; Smotrys and Linder, 2004). Without the protein palmitoyltransferases identified in budding yeast (Dietrich and Ungermann, 2004), fruit fly (Linder and Deschenes, 2003), and mammalians (Fukata, et al., 2004; Huang, et al., 2004), palmitoylation of proteins could still take place in vivo & in vitro spontaneously (el-Husseini Ael and Bredt, 2002; Smotrys and Linder, 2004). These intrinsic and disordered characteristics of palmitoylation introduce great difficulties into choosing appropriate candidate cysteine residues in the substrates for further experimental manipulation. Thus, in silico prediction of palmitoylation sites implemented in an apt algorithm/approach is in urgent need and insightful for the further experimental design.

    In this work, we present a novel and comprehensive system CSS-Palm - Palmitoylation Sites Prediction with Clustering and Scoring Strategy. The detailed description of the algorithm could be found in the supplementary materials. Its prediction performance on the curated date set of 210 experiment-verified palmitoylation sites from 83 distinct proteins is quite satisfying with Jack Knife sensitivity 82.16% and specificity 83.17% respectively. For experimentalists' convenience, we have developed this easy-to-use web server, CSS-Palm.