Kinase Signaling Networks

ISBN-13: 9781493971527 / Angielski / Twarda / 2017 / 537 str.

Aik-Choon Tan; Paul H. Huang

Opis

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.

Spis treści

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 Jørgensen

 

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 Renvoisé, Ludovic Bonhomme, Marlène 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 Noël, Matheus H. Dias, Layra L. Albuquerque, Amanda S. Guimarães, 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