Abstract
S-palmitoylation is a reversible lipid posttranslational modification (PTM) that can mediate protein localization, trafficking, interaction with membranes, and a host of other biophysical characteristics. Over the past decade, a suite of chemoproteomic strategies have uncovered the breadth of S-palmitoylation, revealing widespread susceptibility to modification by this PTM throughout the human proteome. A focal point of research toward understanding the role of S-palmitoylation in varied cellular processes has focused on understanding how “writer” and “eraser” proteins function together to control the levels of S-palmitoylation of target proteins. The spatial and temporal regulation of S-palmitoylation by its “erasers”—acyl protein thioesterases (APTs)—is not fully understood. Tools which enable monitoring of the activity levels of the APTs in real-time in live cells illuminate how spatial control of these enzymes redecorate the lipidation state of the local proteome. To this end, we have developed fluorescence-based depalmitoylation probes (DPPs), which report S-depalmitoylase activity in live cells. Using DPPs, we have demonstrated that S-depalmitoylase activity changes in response to growth factor stimulation, unveiling potential regulation of cell growth and metabolism by APTs. Additionally, we recently discovered APTs in mitochondria using targeted DPPs, indicating new roles for S-depalmitoylation in this critical cellular compartment. Here, we present detailed protocols on how to carry out in vitro S-depalmitoylase activity assays and live cell fluorescence imaging employing the growing DPP toolbox.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
Blanc M, David F, Abrami L et al (2015) SwissPalm: protein palmitoylation database. F1000Res 4:261
Linder ME, Deschenes RJ (2007) Palmitoylation: policing protein stability and traffic. Nat Rev Mol Cell Biol 8:74–84
Lanyon-Hogg T, Faronato M, Serwa RA, Tate EW (2017) Dynamic protein acylation: new substrates, mechanisms, and drug targets. Trends Biochem Sci 42:566–581
Sanders SS, Martin DD, Butland SL et al (2015) Curation of the mammalian palmitoylome indicates a pivotal role for palmitoylation in diseases and disorders of the nervous system and cancers. PLoS Comput Biol 11(8):e1004405. https://doi.org/10.1371/journal.pcbi.1004405
Hernandez JL, Majmudar JD, Martin BR (2013) Profiling and inhibiting reversible palmitoylation. Curr Opin Chem Biol 17:20–26
Peng T, Thinon E, Hang HC (2016) Proteomic analysis of fatty-acylated proteins. Curr Opin Chem Biol 30:77–86
Gottlieb CD, Linder ME (2017) Structure and function of DHHC protein S-acyltransferases. Biochem Soc Trans 45:923–928
Rana MS, Kumar P, Lee CJ et al (2018) Fatty acyl recognition and transfer by an integral membrane S-acyltransferase. Science 359(6372):eaao6326
Zheng B, DeRan M, Li X et al (2013) 2-Bromopalmitate analogues as activity-based probes to explore palmitoyl acyltransferases. J Am Chem Soc 135:7082–7085
Duncan JA, Gilman AG (2002) Characterization of Saccharomyces cerevisiae acyl-protein thioesterase 1, the enzyme responsible for G protein alpha subunit deacylation in vivo. J Biol Chem 277:31740–31752
Lin DT, Conibear E (2015) ABHD17 proteins are novel protein depalmitoylases that regulate N-Ras palmitate turnover and subcellular localization. elife 4:e11306
Toyoda T, Sugimoto H, Yamashita S (1999) Sequence, expression in Escherichia coli, and characterization of lysophospholipase II. Biochim Biophys Acta 1437:182–193
Verkruyse LA, Hofmann SL (1996) Lysosomal targeting of palmitoyl-protein thioesterase. J Biol Chem 271:15831–15836
PMID 27307232, https://www.ncbi.nlm.nih.gov/pubmed/?term=27307232
Kathayat RS Cao Y, Elvira PD et al (2018) Active and dynamic mitochondrial S-depalmitoylation revealed by targeted fluorescent probes. Nat Commun 9:334
El-Husseini Ael D, Schnell E, Dakoji S et al (2002) Synaptic strength regulated by palmitate cycling on PSD-95. Cell 108:849–863
Ponimaskin E, Dityateva G, Ruonala MO et al (2008) Fibroblast growth factor-regulated palmitoylation of the neural cell adhesion molecule determines neuronal morphogenesis. J Neurosci 28:8897–8907
Drisdel RC, Green WN (2004) Labeling and quantifying sites of protein palmitoylation. BioTechniques 36:276–285
Wan J, Roth AF, Bailey AO, Davis NG (2007) Palmitoylated proteins: purification and identification. Nat Protoc 2:1573–1584
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
Percher A, Ramakrishnan S, Thinon E et al (2016) Mass-tag labeling reveals site-specific and endogenous levels of protein S-fatty acylation. Proc Natl Acad Sci U S A 113:4302–4307
Charron G, Wilson J, Hang HC (2009) Chemical tools for understanding protein lipidation in eukaryotes. Curr Opin Chem Biol 13:382–391
Martin BR, Wang C, Adibekian A, Tully SE, Cravatt BF (2011) Global profiling of dynamic protein palmitoylation. Nat Methods 9:84–89
Yap MC, Kostiuk MA, Martin DD et al (2010) Rapid and selective detection of fatty acylated proteins using omega-alkynyl-fatty acids and click chemistry. J Lipid Res 51:1566–1580
Kathayat RS, Elvira PD, Dickinson BC (2017) A fluorescent probe for cysteine depalmitoylation reveals dynamic APT signaling. Nat Chem Biol 13:150–152
Qiu T, Kathayat RS, Cao Y, Beck MW, Dickinson BC (2018) A fluorescent probe with improved water solubility permits the analysis of protein S-depalmitoylation activity in live cells. Biochemistry 57:221–225
Adibekian A, Martin BR, Chang JW et al (2012) Confirming target engagement for reversible inhibitors in vivo by kinetically tuned activity-based probes. J Am Chem Soc 134:10345–10348
Garland M, Schulze CJ, Foe IT et al (2018) Development of an activity-based probe for acyl-protein thioesterases. PLoS One 13:e0190255
Creaser SP, Peterson BR (2002) Sensitive and rapid analysis of protein palmitoylation with a synthetic cell-permeable mimic of SRC oncoproteins. J Am Chem Soc 124:2444–2445
Dekker FJ, Rocks O, Vartak N (2010) Small-molecule inhibition of APT1 affects Ras localization and signaling. Nat Chem Biol 6:449
Görmer K, Bürger M, Kruijtzer JA et al (2012) Chemical-biological exploration of the limits of the Ras de- and repalmitoylating machinery. Chembiochem 13:1017–1023
Beck M, Kathayat RS, Cham CM, Chang EB, Dickinson BC (2017) Michael addition-based probes for ratiometric fluorescence imaging of protein S-depalmitoylases in live cells and tissues. Chem Sci 8:7588–7592
Acknowledgments
This work was supported by the University of Chicago, the National Institute of General Medical Sciences (R35 GM119840) of the National Institutes of Health, and a Research Fellowship from the Alfred P. Sloan Foundation.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2019 Springer Science+Business Media, LLC, part of Springer Nature
About this protocol
Cite this protocol
Kathayat, R.S., Dickinson, B.C. (2019). Measuring S-Depalmitoylation Activity In Vitro and In Live Cells with Fluorescent Probes. 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_8
Download citation
DOI: https://doi.org/10.1007/978-1-4939-9532-5_8
Published:
Publisher Name: Humana, New York, NY
Print ISBN: 978-1-4939-9531-8
Online ISBN: 978-1-4939-9532-5
eBook Packages: Springer Protocols