Main description:

This detailed volume describes cutting-edge techniques in three distinct and complementary areas of contemporary kinase biology research. Beginning with a section on synthetic biology, chemical biology, and screening approaches to kinase signaling networks, the book continues with sections on mass spectrometry and metabolic analysis of kinase signaling as well as computational analysis of kinase signaling networks. Written for the highly successful Methods in Molecular Biology series, 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.
Authoritative and practical, Kinase Signaling Networks aims to provide scientists with the tools necessary to overcome the technological bottlenecks that limit our ability to gain a deeper mechanistic understanding of kinase biology.

Contents:

Part I: Synthetic Biology, Chemical Biology, and Screening Approaches

1. Optogenetic Control of Ras/Erk Signaling Using the Phy-PIF System

Alexander G. Goglia, Maxwell Z. Wilson, Daniel B. DiGiorno, and Jared E. Toettcher

2. Dissecting Kinase Effector Signaling Using the RapRTAP Methodology

Anne-Marie Ray, Jennifer E. Brinks-Klomp, Kerrie B. Collins, and Andrei V. Karginov

3. Single-Cell Imaging of ERK Signaling Using Fluorescent Biosensors

Michael Pargett, Taryn E. Gillies, Carolyn K. Teragawa, Breanne Sparta, and John G. Albeck

4. Quantification of Cell Signaling Networks Using Kinase Activity Chemosensors

Jon R. Beck, Edward N. Harris, and Cliff I. Stains

5. Expression of Recombinant Phosphoproteins for Signal Transduction Studies

Karl W. Barber and Jesse Rinehart

6. Allosteric Modulation of Src-Family Kinases with ATP-Competitive Inhibitors

Ames C. Register, Sujata Chakraborty, and Dustin J. Maly

7. Characterization of Ligand Binding to Pseudokinases Using a Thermal Shift Assay

Isabelle S. Lucet and James M. Murphy

8. Proteomic Profiling of Protein Kinase Inhibitor Targets by Mass Spectrometry

Martin Golkowski, Dustin J. Maly, and Shao-En Ong

9. Utilizing the Luminex Magnetic Bead-Based Suspension Arrays for Rapid Multiplexed Phosphoprotein Quantification

Adam Stewart and Udai Banerji

10. High-Content Imaging and RNAi Screens for Investigating Kinase Network Plasticity

Simon R. Stockwell and Sibylle Mittnacht

11. Analysis of Drug Resistance Using Kinome-Wide Functional Screens

Katherine R. Singleton, Keith T. Earley, and Lynn E. Heasley

12. Identification and Validation of Driver Kinases from Next Generation Sequencing Data

Andri Leonidou, Barrie Peck, and Rachael Natrajan

Part II: Mass Spectrometry and Metabolic Analysis of Kinase Signaling

13. Label-Free Phosphoproteomic Approach for Kinase Signaling Analysis

Edmund Wilkes and Pedro R. Cutillas

14. Cell-Specific Labeling for Analyzing Bidirectional Signaling by Mass Spectrometry

Christopher J. Tape and Claus Jorgensen

15. Characterization of the Phospho-Adhesome by Mass Spectrometry-Based Proteomics

Joseph Robertson, Jonathan D. Humphries, Nikki R. Paul, Stacey Warwood, David Knight, Adam Byron, and Martin J. Humphries

16. Analysis of Phosphotyrosine Signaling Networks in Lung Cancer Cell Lines

Malgorzata Broncel and Paul H. Huang

17. Targeted Analysis of Phosphotyrosine Signaling by Multiple-Reaction-Monitoring Mass Spectrometry

Leo S. Payne and Paul H. Huang

18. Phosphoproteomic Analysis of Isolated Mitochondria in Yeast

Margaux Renvoise, Ludovic Bonhomme, Marlene Davanture, Michel Zivy, and Claire Lemaire

19. A Methodology for Comprehensive Analysis of Toll-Like Receptor Signaling in Macrophages

Marijke Koppenol-Raab and Aleksandra Nita-Lazar

20. Absolute Phosphorylation Stoichiometry Analysis by Motif-Targeting Quantitative Mass Spectrometry

Chia-Feng Tsai, Wei-Chi Ku, Yu-Ju Chen, and Yasushi Ishihama

21. Identification of Plant Kinase Substrates Based on Kinase Assay-Linked Phosphoproteomics

Chuan-Chih Hsu, Justine V. Arrington, Liang Xue, and W. Andy Tao

22. Mass Spectrometry Analysis of Spatial Protein Networks by Colocalization Analysis (COLA)

Faraz K. Mardakheh

23. Development of Selected Reaction Monitoring Methods to Systematically Quantify Kinase Abundance and Phosphorylation Stoichiometry in Human Samples

Kirsten Beck, Nathan Camp, Michael Bereman, James Bollinger, Jarrett Egertson, Michael MacCoss, and Alejandro Wolf-Yadlin

24. Analysis of Signaling Networks at the Single Cell Level Using Mass Cytometry

Shovik Bandyopadhyay, Daniel A.C. Fisher, Olga Malkova, and Stephen T. Oh

25. Magnetic Resonance Spectroscopy (MRS)-Based Methods for Examining Cancer Metabolism in Response to Oncogenic Kinases Drug Treatment

Yuen-Li Chung

26. Deconstructing the Metabolic Networks of Oncogenic Signaling Using Targeted Liquid-Chromatography Tandem Mass Spectrometry (LC-MS/MS)

George Poulogiannis

Part III: Computational Analysis of Kinase Signaling Networks

27. Modeling of Receptor Tyrosine Kinase Signaling: Computational and Experimental Protocols

Dirk Fey, Edita Aksamitiene, Anatoly Kiyatkin, and Boris N. Kholodenko

28. An Interdisciplinary Approach for Designing Kinetic Models of the Ras/MAPK Signaling Pathway

Marcelo S. Reis, Vincent Noel, Matheus H. Dias, Layra L. Albuquerque, Amanda S. Guimaraes, Lulu Wu, Junior Barrera, and Hugo A. Armelin

29. Databases and Computational Tools for Evolutionary Analysis of Protein Phosphorylation

Chris Tan Soon Heng

30. Informatics Approaches for Predicting, Understanding, and Testing Cancer Drug Combinations

Jing Tang

31. Target Inhibition Maps Based on Responses to Kinase Inhibitors

Noah Berlow and Ranadip Pal

32. Partial Least Squares Regression Models for the Analysis of Kinase Signaling

Danielle L. Bourgeois and Pamela K. Kreeger