Protein Lipidation: Methods and Protocols

ISBN-13: 9781493995318 / Angielski / Twarda / 2019 / 327 str.

Maurine Linder

Spis treści

Preface…

Table of Contents…

Contributing Authors…

PART I DETECTION OF LIPID MODIFICATIONS

1. Determination of Protein S-Acylation State by Enhanced Acyl-Switch Methods

Charlotte H. Hurst, Dionne Trumbull, and Piers A. Hemsley

2. Detection of Heterogeneous Protein S-Acylation in Cells

Jennifer Greaves and Nicholas C. O. Tomkinson

3. Optimization of Metabolic Labeling with Alkyne-Containing Isoprenoid Probes

Mina Ahmadi, Kiall Francis Suazo, and Mark D. Distefano

4. Chemical Proteomic Analysis of S-Fatty Acylated Proteins and their Modification Sites

Emmanuelle Thinon and Howard C. Hang

  

5. Direct Analysis of Protein S-Acylation by Mass Spectrometry

Yuhaun Ji and Cheng Lin

6. Enrichment of S-Palmitoylated Proteins for Mass Spectrometry Analysis

Melanie 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) Assay

Takashi Kanadome, Norihiko Yokoi, Yuko Fukata, and Masaki Fukata

8. Measuring S-Depalmitoylation Activity In Vitro and In Live Cells with Fluorescent Probes

Rahul S. Kathayat and Bryan C. Dickinson

9. Dynamic Radiolabeling of S-Palmitoylated Proteins

Laurence Abrami, Robin A. Denhardt-Eriksson, Vassily Hatzimanikatis, and F. Gisou van der Goot

10. Fluorogenic Assays for the Defatty-Acylase Activity of Sirtuins

Jun Young Hong, Ji Cao, and Hening Lin

 

11. Global Profiling of Sirtuin Deacylase Substrates Using Chemical Proteomic Strategy and Validation by Fluorescent Labeling

Shuai 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- qPCR

Heather McClafferty and Michael J. Shipston

13. In Vitro Assays to Monitor the Enzymatic Activities of zDHHC Protein Acyltransferases

David A. Mitchell, Laura C. Pendleton, and Robert J. Deschenes

14. Purification of Recombinant zDHHC Proteins Using an Insect Cell Expression System

Martin Ian P. Malgapo and Maurine E. Linder

15. Bioinformatic Identification of Functionally and Structurally Relevant Residues and Motifs in Protein S-Acyltransferases

Rodrigo Quiroga and Javier Valdez Taubas

PART IV ONLINE RESOURCE

16. SwissPalm 2: Protein S-Palmitoylation Database

Mathieu 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 ELISA

Aaron H. Nile and Rami N. Hannoush

18. Biochemical Assays for Ghrelin Acylation and Inhibition of Ghrelin O-Acyltransferase

Michelle 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 System

William 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 Ste24

Erh-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 Chemistry

Akiyuki Nishimura and Maurine E. Linder

23. Purification of the Rhodopsin-Transducin Complex for Structural Studies

Yang Gao, Jon W. Erickson, Richard A. Cerione, and Sekar Ramanchandran

24. Reconstitution of the Rhodopsin-Transducin Complex into Lipid Nanodiscs

Yang Gao, Jon W. Erickson, Richard A. Cerione, and Sekar Ramanchandran

Blurb

This volume explores techniques used to detect lipids attached to proteins, to analyze the function of lipid modifications, and to characterize the enzymes that add and remove lipids from proteins. The book is organized into seven parts: Part One describes chemically-based strategies to identify substrates for protein lipidation that can be applied to individual proteins or globally using proteomics. Part Two focuses on the enzymes that remove fatty acids from proteins and provides methods to monitor protein biogenesis and palmitate turnover. Part Three addresses biochemical and cellular characterization of DHHC S-acyltransferases, a family of enzymes with 23 members encoded by the human genome. Part Four presents the SwissPalm 2 database and tips on how to use it effectively. Part Five focuses on fatty acylation that occurs in the lumen of the secretory pathway. Parts Six and Seven conclude the book with methods to produce and assay lipid-modified and integral membrane proteins. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.

Cutting-edge and authoritative, Protein Lipidation: Methods and Protocols is a valuable resource for experts in the field and for investigators who encounter protein lipidation through their research on a particular cellular process or favorite protein.