Protein Lipidation: Methods and Protocols

Preface...Table of Contents...Contributing Authors...
PART I DETECTION OF LIPID MODIFICATIONS

1.Determination of Protein S-Acylation State by Enhanced Acyl-Switch MethodsCharlotte H. Hurst, Dionne Trumbull, and Piers A. Hemsley
2.Detection of Heterogeneous Protein S-Acylation in CellsJennifer Greaves and Nicholas C. O. Tomkinson
3.Optimization of Metabolic Labeling with Alkyne-Containing Isoprenoid ProbesMina Ahmadi, Kiall Francis Suazo, and Mark D. Distefano
4.Chemical Proteomic Analysis of S-Fatty Acylated Proteins and their Modification SitesEmmanuelle Thinon and Howard C. Hang  5.Direct Analysis of Protein S-Acylation by Mass SpectrometryYuhaun Ji and Cheng Lin
6.Enrichment of S-Palmitoylated Proteins for Mass Spectrometry AnalysisMelanie Cheung See Kit and Brent R. Martin
PART II REVERSIBLE FATTY ACYLATION

7.Systematic Screening of Depalmitoylating Enzymes and Evaluation of their Activities by the Acyl-PEGyl Exchange Gel-Shift (APEGS) AssayTakashi Kanadome, Norihiko Yokoi, Yuko Fukata, and Masaki Fukata
8.Measuring S-Depalmitoylation Activity In Vitro and In Live Cells with Fluorescent ProbesRahul S. Kathayat and Bryan C. Dickinson
9.Dynamic Radiolabeling of S-Palmitoylated ProteinsLaurence Abrami, Robin A. Denhardt-Eriksson, Vassily Hatzimanikatis, and F. Gisou van der Goot
10.Fluorogenic Assays for the Defatty-Acylase Activity of SirtuinsJun Young Hong, Ji Cao, and Hening Lin 11.Global Profiling of Sirtuin Deacylase Substrates Using Chemical Proteomic Strategy and Validation by Fluorescent LabelingShuai Zhang, Nicole A. Spiegelman, and Hening Lin
PART III zDHHC S-ACYLTRANSFERASES
12.siRNA Knockdown of Mammalian zDHHCs and Validation of mRNA Expression by RT-qPCRHeather McClafferty and Michael J. Shipston
13.In Vitro Assays to Monitor the Enzymatic Activities of zDHHC Protein AcyltransferasesDavid A. Mitchell, Laura C. Pendleton, and Robert J. Deschenes
14.Purification of Recombinant zDHHC Proteins Using an Insect Cell Expression SystemMartin Ian P. Malgapo and Maurine E. Linder
15.Bioinformatic Identification of Functionally and Structurally Relevant Residues and Motifs in Protein S-AcyltransferasesRodrigo Quiroga and Javier Valdez Taubas
PART IV ONLINE RESOURCE

16.SwissPalm 2: Protein S-Palmitoylation DatabaseMathieu Blanc, Fabrice P. A. David, and F. Gisou van der Goot
PART V FATTY ACYLATION IN THE LUMEN OF THE SECRETORY PATHWAY
17.Probing Interaction of Lipid-Modified Wnt Protein and Its Receptors by ELISAAaron H. Nile and Rami N. Hannoush
18.Biochemical Assays for Ghrelin Acylation and Inhibition of Ghrelin O-AcyltransferaseMichelle A. Sieburg, Elizabeth R. Cleverdon, and James L. Hougland
19.In Vitro Analysis of Hedgehog Acyltransferase and Porcupine Fatty Acyltransferase Activities James John Asciolla, Kalpana Rajanala, and Marilyn D. Resh
PART VI PRENYLATION AND POST-PRENYLATION PROCESSING 
20.Production of Farnesylated and Methylated Proteins in an Engineered Insect Cell SystemWilliam Gillette, Peter Frank, Shelley Perkins, Matthew Drew, Carissa Grose, and Dominic Esposito
21.A Quantitative FRET Assay for the Upstream Cleavage Activity of the Integral Membrane Proteases Human ZMPSTE24 and Yeast Ste24Erh-Ting Hsu, Jeffrey S. Vervacke, Mark D. Distefano, and Christine A. Hrycyna
PART VII BIOCHEMISTRY OF PROTEIN LIPIDATION

22.Monitoring RhoGDI Extraction of Lipid-Modified Rho GTPases from Membranes using Click ChemistryAkiyuki Nishimura and Maurine E. Linder
23.Purification of the Rhodopsin-Transducin Complex for Structural StudiesYang Gao, Jon W. Erickson, Richard A. Cerione, and Sekar Ramanchandran
24.Reconstitution of the Rhodopsin-Transducin Complex into Lipid NanodiscsYang Gao, Jon W. Erickson, Richard A. Cerione, and Sekar Ramanchandran