ADP-ribosylation and NAD+ utilizing enzymes : methods and protocols
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Bibliographic Information
ADP-ribosylation and NAD+ utilizing enzymes : methods and protocols
（Methods in molecular biology / John M. Walker, series editor, 1813）（Springer protocols）
Humana Press, c2018
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Includes bibliographical references and index
Description and Table of Contents
Description
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.
Table of Contents
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 Butepage, Sarah Krieg, laura Eckei, Jinyu Li, Giulia Rossetti, Patricia Verheugd, and Bernhard Luscher
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 Marjanovic, 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 Lehtioe
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 Jose 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
Bjoern 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
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