Abstract
Protein S-palmitoylation is increasingly recognized as an important posttranslational modification, present in all eukaryotic organisms, involved in the regulation of many biological processes. The SwissPalm database centralizes the large and increasing number of published palmitoyl-proteome datasets, provides tools to compare them, and includes curated data from the literature on the identification and analysis of palmitoylated proteins. SwissPalm 2 provides an updated version, with 38 palmitoyl-proteomes at the time of release, from 17 different species, and new features such as the inclusion of orthologs.
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References
Blaskovic S, Blanc M, van der Goot FG (2013) What does S-palmitoylation do to membrane proteins? FEBS J 280:2766–2774
Schmidt MF, Schlesinger MJ (1979) Fatty acid binding to vesicular stomatitis virus glycoprotein: a new type of post-translational modification of the viral glycoprotein. Cell 17:813–819
Chamberlain LH, Shipston MJ (2015) The physiology of protein S-acylation. Physiol Rev 95:341–376
Ohno Y, Kihara A, Sano T et al (2006) Intracellular localization and tissue-specific distribution of human and yeast DHHC cysteine-rich domain-containing proteins. Biochim Biophys Acta 1761:474–483
Gottlieb CD, Linder ME (2017) Structure and function of DHHC protein S-acyltransferases. Biochem Soc Trans 45:923–928
Tabaczar S, Czogalla A, Podkalicka J et al (2017) Protein palmitoylation: palmitoyltransferases and their specificity. Exp Biol Med 242:1150–1157
Yokoi N, Fukata Y, Sekiya A et al (2016) Identification of PSD-95 depalmitoylating enzymes. J Neurosci 36:6431–6444
Davda D, Martin BR (2014) Acyl protein thioesterase inhibitors as probes of dynamic S-palmitoylation. Medchemcomm 5:268–276
Lemonidis K, Salaun C, Kouskou M et al (2017) Substrate selectivity in the zDHHC family of S-acyltransferases. Biochem Soc Trans 45:751–758
Ren J, Wen L, Gao X et al (2008) CSS-Palm 2.0: an updated software for palmitoylation sites prediction. Protein Eng Des Sel 21:639–644
Salaun C, Greaves J, Chamberlain LH (2010) The intracellular dynamic of protein palmitoylation. J Cell Biol 191:1229–1238
Levental I, Lingwood D, Grzybek M et al (2010) Palmitoylation regulates raft affinity for the majority of integral raft proteins. Proc Natl Acad Sci U S A 107:22050–22054
Gauthier-Kemper A, Igaev M, Sündermann F et al (2014) Interplay between phosphorylation and palmitoylation mediates plasma membrane targeting and sorting of GAP43. Mol Biol Cell 25(21):3284–3299
Perrody E, Abrami L, Feldman M et al (2016) Ubiquitin-dependent folding of the Wnt signaling coreceptor LRP6. elife 5
Yount JS, Zhang MM, Hang HC (2013) Emerging roles for protein S-palmitoylation in immunity from chemical proteomics. Curr Opin Chem Biol 17:27–33
Blanc M, Blaskovic S, van der Goot FG (2013) Palmitoylation, pathogens and their host. Biochem Soc Trans 41:84–88
Hornemann T (2015) Palmitoylation and depalmitoylation defects. J Inherit Metab Dis 38:179–186
Resh MD (2017) Palmitoylation of proteins in cancer. Biochem Soc Trans 45:409–416
Napoli E, Song G, Liu S et al (2017) Zdhhc13-dependent Drp1 S-palmitoylation impacts brain bioenergetics, anxiety, coordination and motor skills. Sci Rep 7:12796
Du K, Murakami S, Sun Y et al (2017) DHHC7 palmitoylates glucose transporter 4 (Glut4) and regulates Glut4 membrane translocation. J Biol Chem 292:2979–2991
Martin BR (2013) Chemical approaches for profiling dynamic palmitoylation. Biochem Soc Trans 41:43–49
Forrester MT, Hess DT, Thompson JW et al (2011) Site-specific analysis of protein S-acylation by resin-assisted capture. J Lipid Res 52:393–398
Drisdel RC, Green WN (2004) Labeling and quantifying sites of protein palmitoylation. BioTechniques 36:276–285
Roth AF, Wan J, Bailey AO et al (2006) Global analysis of protein palmitoylation in yeast. Cell 125:1003–1013
Blanc M, David F, Abrami L et al (2015) SwissPalm: protein palmitoylation database. F1000Res 4:261
Acknowledgments
This work benefited from funding from the European Research Council under the European Union’s Seventh Framework Programme (FP/2007-2013)/ERC Grant Agreement no. 340260—PalmERa. This work was also supported by grants from the Swiss National Science Foundation (to G.v.d.G), the Swiss National Centre of Competence in Research (NCCR) Chemical Biology, and the Swiss SystemsX.ch initiative evaluated by the Swiss National Science Foundation (LipidX) (to G.v.d.G). M.B. was a recipient from an EMBO Long Term Fellowship.
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Blanc, M., David, F.P.A., van der Goot, F.G. (2019). SwissPalm 2: Protein S-Palmitoylation Database. In: Linder, M. (eds) Protein Lipidation. Methods in Molecular Biology, vol 2009. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-9532-5_16
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DOI: https://doi.org/10.1007/978-1-4939-9532-5_16
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