CSS-Palm 2.0: an updated software for palmitoylation sites prediction

Abstract

Protein palmitoylation is an essential post-translational lipid modification of proteins, and reversibly orchestrates a variety of cellular processes. Identification of palmitoylated proteins with their sites is the foundation for understanding molecular mechanisms and regulatory roles of palmitoylation. Contrasting to the labor-intensive and time-consuming experimental approaches, in silico prediction of palmitoylation sites has attracted much attention as a popular strategy. In this work, we updated our previous CSS-Palm into version 2.0. An updated clustering and scoring strategy (CSS) algorithm was employed with great improvement. The leave-one-out validation and 4-, 6-, 8- and 10-fold cross-validations were adopted to evaluate the prediction performance of CSS-Palm 2.0. Also, an additional new data set not included in training was used to test the robustness of CSS-Palm 2.0. By comparison, the performance of CSS-Palm was much better than previous tools. As an application, we performed a small-scale annotation of palmitoylated proteins in budding yeast. The online service and local packages of CSS-Palm 2.0 were freely available at: http://bioinformatics.lcd-ustc.org/css_palm.

The IQD Family of Calmodulin-Binding Proteins Links Calcium Signaling to Microtubules, Membrane Subdomains, and the Nucleus

“…Membrane tethering of IQD proteins is possibly stabilized by S-acylation (or palmitoylation), which attaches fatty acids to internal Cys residues. In silico analyses using the GPS-Lipid and CSS-Palm tools (Ren et al, 2008;Xie et al, 2016) predicted the presence of Sacylation sites in several IQD family members (Supplemental Table S1). Experimental support for the lipidation of IQD proteins is provided by a large-scale proteomics data set, which reported S-acylation of IQD32 (Hemsley et al, 2013).…”

Annotation of microsporidian genomes using transcriptional signals

“…For post-translational modifications, we looked for GPI anchors (http://mendel.imp.ac.at/sat/gpi/gpi_server. html) 53 , myristoylation (http://web.expasy.org/myristoylator/) 54 , palmitoylation (http://csspalm.biocuckoo.org/) 55 and prenylation (http://mendel.imp.ac.at/sat/ PrePS/index.html) 56 .…”

A component of the mitochondrial outer membrane proteome of T. brucei probably contains covalent bound fatty acids

“…According to the NMT algorithm (http://mendel.imp.ac.at/myristate/), which predicts myristoylation sites, the glycine residue on the second position (G2) is subject to myristoylation with a high level of confidence (probability of false positive 0.03%). The cysteine residue on position three (C3) is a predicted palmitoylation site with ≥95% confidence level when analyzed using the CSSPalm algorithm (Ren et al, 2008). Consistent with this prediction, POMP39 was identified as one of 124 proteins enriched by streptavidin chromatography following an acyl-biotin exchange-reaction of whole cell lysates (Emmer et al, 2011).…”