Abstract
It is well established that palmitoylation plays a key role in the regulation of immune checkpoints, but the technical challenges in detecting protein palmitoylation have significantly prohibited further researches in this field. Till now, different approaches have been proposed, such as mutagenesis, antibody-based methods, bioinformatic prediction, “palmitate-centric” approaches, and “cysteine-centric” approaches. Of specific importance, high-throughput methods that allow the unbiased discovery of palmitoylation in the whole proteome should be further improved and employed. This chapter will summarize the methodological progresses for detecting protein palmitoylation, aiming to facilitate future researches in the lipid modification of immune checkpoint proteins.
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References
Blanc M, David F, Abrami L, Migliozzi D, Armand F, Bürgi J, van der Goot FG (2015) SwissPalm: protein palmitoylation database. F1000Research 4:261. https://doi.org/10.12688/f1000research.6464.1
Blanc M, David FPA, van der Goot FG (2019) SwissPalm 2: protein S-Palmitoylation database. Methods Mol Biol 2009:203–214. https://doi.org/10.1007/978-1-4939-9532-5_16
Charron G, Zhang MM, Yount JS, Wilson J, Raghavan AS, Shamir E, Hang HC (2009) Robust fluorescent detection of protein fatty-acylation with chemical reporters. J Am Chem Soc 131:4967–4975. https://doi.org/10.1021/ja810122f
Drisdel RC, Green WN (2004) Labeling and quantifying sites of protein palmitoylation. Biotechniques 36:276–285. https://doi.org/10.2144/04362RR02
Drisdel RC, Alexander JK, Sayeed A, Green WN (2006) Assays of protein palmitoylation. Methods 40:127–134. https://doi.org/10.1016/j.ymeth.2006.04.015
Fang CY, Zhang XQ, Zhang L, Gao X, Yang PY, Lu HJ (2016) Identification of palmitoylated transitional endoplasmic reticulum ATPase by proteomic technique and pan antipalmitoylation antibody. J Proteome Res 15(3):956–962. https://doi.org/10.1021/acs.jproteome.5b00979
Forrester MT, Hess DT, Thompson JW, Hultman R, Moseley MA, Stamler JS, Casey PJ (2011) Site-specific analysis of protein S-acylation by resin-assisted capture. J Lipid Res 52:393–398. https://doi.org/10.1194/jlr.d011106
Fukata Y, Dimitrov A, Boncompain G, Vielemeyer O, Perez F, Fukata M (2013) Local palmitoylation cycles define activity-regulated postsynaptic subdo-mains. J Cell Biol 202:145–161. https://doi.org/10.1083/jcb.201302071
Gao X, Hannoush RN (2014a) Single-cell in situ imaging of palmitoylation in fatty-acylated proteins. Nat Protoc 9:2607–2623. https://doi.org/10.1038/nprot.2014.179
Gao X, Hannoush RN (2014b) Method for cellular imaging of palmitoylated proteins with clickable probes and proximity ligation applied to Hedgehog, tubulin, and Ras. J Am Chem Soc 136:4544–4550. https://doi.org/10.1021/ja410068g
Hemsley PA, Weimar T, Lilley KS, Dupree P, Grierson CS (2013) A proteomic approach identifies many novel palmitoylated proteins in Arabidopsis. New Phytol 197:805–814. https://doi.org/10.1111/nph.12077
Howie J, Reilly L, Fraser NJ, Vlachaki Walker JM, Wypijewski KJ, Ashford MLJ, Calaghan SC, McClafferty H, Tian L, Shipston MJ et al (2014) Substrate recognition by the cell surface palmitoyl transferase DHHC5. Proc Natl Acad Sci U S A 111:17534–17539. https://doi.org/10.1073/pnas.1413627111
Hu LL, Wan SB, Niu S, Shi XH, Li HP, Cai YD et al (2011) Prediction and analysis of protein palmitoylation sites. Biochimie 93:489–496. https://doi.org/10.1016/j.biochi.2010.10.022
Jones ML, Collins MO, Goulding D, Choudhary JS, Rayner JC (2012) Analysis of protein palmitoylation reveals a pervasive role in Plasmodium development and pathogenesis. Cell Host Microbe 12:246–258. https://doi.org/10.1016/j.chom.2012.06.005
Kumar M, Wightman R, Atanassov I, Gupta A, Hurst CH, Hemsley PA, Turner S (2016) S-Acylation of the cellulose synthase complex is essential for its plasma membrane localization. Science 353:166–169. https://doi.org/10.1126/science.aaf4009
Kumari B, Kumar R, Kumar M (2014) PalmPred: an SVM based palmitoylation prediction method using sequence profile information. PLoS ONE 9:e89246. https://doi.org/10.1371/journal.pone.0089246
Martin BR, Cravatt BF (2009) Large-scale profiling of protein palmitoylation in mammalian cells. Nat Methods 6:135–138. https://doi.org/10.1038/nmeth.1293
Martin BR, Wang C, Adibekian A, Tully SE, Cravatt BF (2011) Global profiling of dynamic protein palmitoylation. Nat Methods 9:84–89. https://doi.org/10.1038/nmeth.1769
Morrison E, Kuropka B, Kliche S, Brügger B, Krause E, Freund C (2015) Quantitative analysis of the human T cell palmitome. Sci Rep 5:11598. https://doi.org/10.1038/srep11598
Nagano N, Ota M, Nishikawa K (1999) Strong hydrophobic nature of cysteine residues in proteins. FEBS Lett 458:69–71. https://doi.org/10.1016/s0014-5793(99)01122-9
Percher A, Ramakrishnan S, Thinon E, Yuan X, Yount JS, Hang HC (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. https://doi.org/10.1073/pnas.1602244113
Qi B, Doughty J, Hooley R (2013) A Golgi and tonoplast localized S-acyl transferase is involved in cell expansion, cell division, vascular patterning and fertility in Arabidopsis. New Phytol 200(2):444–456. https://doi.org/10.1111/nph.12385
Roth AF, Wan J, Green WN, Yates JR, Davis NG (2006a) Proteomic identification of palmitoylated proteins. Methods 40:135–142. https://doi.org/10.1016/j.ymeth.2006.05.026
Roth AF, Wan J, Bailey AO, Sun B, Kuchar JA, Green WN et al (2006b) Global analysis of protein palmitoylation in yeast. Cell 125:1003–1013. https://doi.org/10.1016/j.cell.2006.03.042
Serwa RA, Abaitua F, Krause E, Tate EW, O’Hare P (2015) Systems analysis of protein fatty acylation in herpes simplex virus-infected cells using chemical proteomics. Chem Biol 22:1008–1017. https://doi.org/10.1016/j.chembiol.2015.06.024
Shi SP, Sun XY, Qiu JD, Suo SB, Chen X, Huang SY et al (2013) The prediction of palmitoylation site locations using a multiple feature extraction method. J Mol Graph Model 40:125–130. https://doi.org/10.1016/j.jmgm.2012.12.006
Swarthout JT, Lobo S, Farh L, Croke MR, Greentree WK, Deschenes RJ, Linder ME (2005) DHHC9 and GCP16 constitute a human protein fatty acyltransferase with specificity for H- and N-Ras. J Biol Chem 280:31141–31148. https://doi.org/10.1074/jbc.M504113200
Veit M, Ponimaskin E, Schmidt MF (2008) Analysis of S-acylation of proteins. Methods Mol Biol 446:163–182. https://doi.org/10.1007/978-1-60327-084-7_12
Wan J, Roth AF, Bailey AO, Davis NG (2007) Palmitoylated proteins: purification and identification. Nat Protoc 2:1573–1584. https://doi.org/10.1038/nprot.2007.225
Wan J, Savas JN, Roth AF, Sanders SS, Singaraja RR, Hayden MR et al (2013) Tracking brain palmitoylation change: predominance of glial change in a mouse model of Huntington’s Disease. Chem Biol 20:1421–1434. https://doi.org/10.1016/j.chembiol.2013.09.018
Wright MH, Clough B, Rackham MD, Rangachari K, Brannigan JA, Grainger M et al (2014) Validation of N-myristoyltransferase as an antimalarial drug target using an integrated chemical biology approach. Nat Chem 6:112–121. https://doi.org/10.1038/nchem.1830
Yount JS, Moltedo B, Yang YY, Charron G, Moran TM, López CB et al (2010) Palmitoylome profiling reveals S-palmitoylation-dependent antiviral activity of IFITM3. Nat Chem Biol 6:610–614. https://doi.org/10.1038/nchembio.405
Zhang J, Planey SL, Ceballos C, Stevens SM Jr, Keay SK, Zacharias DA (2008) Identification of CKAP4/p63 as a major substrate of the palmitoyl acyltransferase DHHC2, a putative tumor suppressor, using a novel proteomics method. Mol Cell Proteomics 7:1378–1388. https://doi.org/10.1074/mcp.M800069-MCP200
Zhang MM, Tsou LK, Charron G, Raghavan AS, Hang HC (2010) Tandem fluores-cence imaging of dynamic S-acylation and protein turnover. Proc Natl Acad Sci U S A 107:8627–8632. https://doi.org/10.1073/pnas.0912306107
Zhang XQ, Zhang YT, Fang CY, Zhang L, Yang PY, Wang CC, Lu HJ (2018a) Ultradeep palmitoylomics enabled by Dithiodipyridine-Functionalized magnetic nanoparticles. Anal Chem 90:6161–6168. https://doi.org/10.1021/acs.analchem.8b0053429
Zhang XQ, Zhang L, Ji GH, Lei QY, Fang CY, Lu HJ (2018b) Site-specific quantification of protein palmitoylation by cysteine-stable isotope metabolic labeling. Anal Chem 90:10543–10550. https://doi.org/10.1021/acs.analchem.8b02635
Zhou F, Xue Y, Yao X, Xu Y (2006) CSS-Palm: palmitoylation site prediction with a clustering and scoring strategy (CSS). Bioinformatics 22:894–896. https://doi.org/10.1093/bioinformatics/btl013
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Lu, H., Fang, C. (2020). Methodology for Detecting Protein Palmitoylation. In: Xu, J. (eds) Regulation of Cancer Immune Checkpoints. Advances in Experimental Medicine and Biology, vol 1248. Springer, Singapore. https://doi.org/10.1007/978-981-15-3266-5_17
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