Adp-Ribosylation and Nad+ Utilizing Enzymes: Methods and Protocols

ISBN-13: 9781493985876 / Angielski / Twarda / 2018 / 417 str.

Paul Chang

Spis treści

Preface…

Table of Contents…

Contributing Authors…

Part I Introduction

1. Vitamin B3 in Health and Disease: Toward the Second Century of Discovery

Myron K. Jacobson and Elaine L. Jacobson

Part II ADPribose Binding Domains as Tools

2. Monitoring Poly(ADP-Ribosyl)ation in Response to DNA Damage in Live Cells Using Fluorescently-Tagged Macrodomains

Rebecca Smith and Gyula Timinszky

3. In Vitro Techniques for ADP-Ribosylated Substrate Identification

Giovanna Grimaldi, Giulianan Catara, Carmen Valente, and Daniela Corda

4. Assessment of Intracellular Auto-Modification Levels of ARTD10 using Mono-ADP-Ribose-Specific Macrodomains 2 and 3 of Murine Artd8

Mareike Bütepage, Sarah Krieg, laura Eckei, Jinyu Li, Giulia Rossetti, Patricia Verheugd, and Bernhard Lüscher

5. Biochemical and Biophysical Assays of PAR-WWE Domain Interactions and Production of iso-ADPr for PAR Binding Analysis

Zhizhi Wang and Wenqing Xu

Part III Enzymatic Assays of NAD+ Utilizing Enzymes

6. Assays for NAD-Dependent Reactions and NAD Metabolites

Michael B. Schultz, Yuancheng Lu, Nady Braidy, and David A Sinclair

7. Generating Protein-Linked and Protein-Free Mono-, Oligo-, and Poly(ADP-Ribose) In Vitro

Ken Y. Lin, Dan Huang, and W. Lee Kraus

8. Methods to Study TCDD-Inducible Poly-ADP-Ribose Polymerase (TIPARP) Mono-ADP-Ribosyltransferase Activity

David Hutin, Giulia Grimaldi, and Jason Matthews

9. Dictyostelium as a Model to Assess Site-Specific ADP-Ribosylation Events

Anna-Lena Kolb, Duen-Wei Hsu, Ana B.A. Wallis, Seiji Ura, Alina Rakhimova, Catherine J. Pears, and Nicholas D. Lakin

10. Mono-ADP-Ribosylation Catalyzed by Arginine-Specific ADP-Ribosyltransferases

Linda A. Stevens and Joel Moss

11. Monitoring Expression and Enzyme Activity of Ecto-ARTCs

Stephan Menzel, Sahil Abriouch, Peter Bannas, Friedrich Haag, and Friedrich Koch-Nolte

12. ADP-Ribosyl-Acceptor Hydrolase Activities Catalyzed by the ARH Family of Proteins

Masato Mashimo and Joel Moss

13. Mono-ADP-Ribosylhydrolase Assays

Jeannette Abplanalp, Ann-Katrin Hopp, and Michael O. Hottiger

14. Hydrolysis of ADP-Ribosylation by Macrodomains

Melanija Posavec Marjanović, Gytis Jankevicius, and Ivan Ahel

15. HPLC-Based Enzyme Assays for Sirtuins

Jun Young Hong, Xiaoyu Zhang, and Hening Lin

Part IV Small Molecule Screening Assays of NAD+ Utilizing Enzymes

16. Small Molecule Screening Assay for Mono-ADP-Ribosyltransferases

Haikarainen Teemu, Murphy Sudarshan, Maksimainen Mirko, and Lari Lehtiö

17. ¬A Simple, Sensitive, and Generalizable Plate Assay for Screening PARP Inhibitors

Ilsa T. Kirby, Rory K. Morgan, and Michael S. Cohen

Part V Mass Spectrometry Techniques for Detection of Mono-ADP-Ribosylation

18. Non-Localized Searching of HCD Data for Fast and Sensitive Identification of ADP-Ribosylated Peptides

Thomas Colby, Juan José Bonfiglio, and Ivan Matic

19. Quantitative Determination of MAR Hydrolase Residue Specificity In Vitro by Tandem Mass Spectrometry

Robert Lyle Mcpherson, Shao-En Ong, and Anthony K.L. Leung

Part VI Mono-ADP-Ribose and Disease

20. Detection of ADP-Ribosylating Bacterial Toxins

Chen Chen and Joseph T. Barbieri

21. Preparation of Recombinant Alphaviruses for Functional Studies of ADP-Ribosylation

Rachy Abraham, Robert L. McPherson, Easwaran Sreekumar, Anthony K.L. Leung, and Diane E. Griffin

22. Monitoring the Sensitivity of T Cell Populations towards NAD+ Released during Cell Preparation

Björn Rissiek, Marco Lukowiak, Friedrich Haag, Tim Magnus, and Friedrich Koch-Nolte

23. Identifying Target RNAs of PARPs

Florian J. Bock and Paul Chang

Part VII NAD+ Analogue Approaches and Chemical Synthesis

24. ADPr-Peptide Synthesis

Hans A.V. Kistemaker, Jim Voorneveld, and Dmitri V. Filippov

25. Identifying Genomic Sites of ADP-Ribosylation Mediated by Specific Nuclear PARP Enzymes Using Click-ChIP

Ryan A. Rogge, Bryan A. Gibson, and W. Lee Kraus

Part VIII NAD+ Sensors

26. Methods for Using a Genetically-Encoded Fluorescent Biosensor to Monitor Nuclear NAD+

Michael S. Cohen, Melissa L. Stewart, Richard H. Goodman, and Xiaolu A. Cambronne

Blurb

This volume focuses on mono-ADP-ribosylation and enzymes that use NAD+ including Sirtuins, PARPs, and bacterial and eukaryotic ADP-ribosyltransferases. The chapters in this book are organized into eight parts, and offer detailed descriptions of key protocols used to study topics such as in vitro techniques for ADP-ribosylation substrate identification; biochemical and biophysical assays of PAR-WWE domain interactions; monitoring expression and enzyme activity of ecto-ARTCs; HPLC-based enzymes assays for Sirtuins; and identifying target RNAs of PARPs. 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 thorough, ADP-ribosylation and NAD+ Utilizing Enzymes: Methods and Protocols is a valuable resource for anyone interested in this developing and expanding field.