Sh2 Domains: Methods and Protocols

Preface...
Table of Contents...
Contributing Authors...

Part I Overview

1. Introduction: History of SH2 Domains and Their Applications
Bernard A. Liu and Kazuya Machida

2. What Have We Learned from SH2 Domains?
Bruce J. Mayer

Part II Computational Approaches

3. Hidden Markov Models for Protein Domain Homology Identification and Analysis
Karl Jablonowski

4. Classification and Lineage Tracing of SH2 Domains Throughout Eukaryotes
Bernard A. Liu

5. SH2 Ligand Prediction-Guidance for In-Silico Screening
Shawn S.C. Li and Lei Li

6. An Efficient Semi-Supervised Learning Approach to Predict SH2 Domain Mediated Interactions
Kousik Kundu and Rolf Backofen

7. Proteomic Clustering Analysis of SH2 Domain DatasetsKarl Jablonowski

Part III Experimental Tools

8. Expression and Production of SH2 Domain Proteins
Bernard A. Liu, Mari Ogiue-Ikeda, and Kazuya Machida

9. Expression and Purification of Soluble STAT5b/STAT3 Proteins for SH2 Domain Binding Assay
Akira Asai and Kazuyuki Takakuma

10. Purification of SOCS (Suppressors of Cytokine Signalling) SH2 Domains for Structural and Functional Studies
Nicholas P.D. Liau, Artem Laktyushin, and Jeffrey J. Babon

11. Expression and Purification of SH2 Domains Using Baculovirus Expression System
Mari Ogiue-Ikeda and Kazuya Machida

12. Functionally Altered SH2 Domains for Biochemical Studies: Loss of Function Mutant and Domain Concatenation
Mari Ogiue-Ikeda and Kazuya Machida

13. Creation of Phosphotyrosine Superbinders by Directed Evolution of an SH2 Domain
Haiming Huang, Tomonori Kaneko, Sachdev S. Sidhu, and Shawn S.C. Li

Part IV Structural Analysis and Binding Assays

14. Structural Characterization of Monomeric/Dimeric State of p59fyn SH2 Domain
Radu Huculeci, Fabien Kieken, Abel Garcia-Pino, Lieven Buts, Nico van Nuland, and Tom Lenaerts

15. NMR Chemical Shift Mapping of SH2 Peptide Interactions
Marissa A. McKercher and Deborah S. Wuttke

16. Calorimetric Measurement of SH2 Domain Ligand Affinities
Marissa A. McKercher and Deborah S. Wuttke

17. Binding Assays Using Recombinant SH2 Domains: Far-Western, Pull Down, and Fluorescence Polarization
Kazuya Machida and Bernard A. Liu

18. In-Solution SH2 Domain Binding Assay Based on Proximity Ligation
Kazuya Machida

Part V High-Throughput Screening and Proteomics

19. Alpha-Based Multiplexed Assay for Identifying SH2 Domain Antagonists
Akira Asai and Kazuyuki Takakuma

20. Characterizing SH2 Domain Specificity and Network Interactions Using SPOT Peptide Arrays
Bernard A. Liu

21. High Throughput Quantification of SH2 Domain-Phosphopeptide Interactions with Cellulose Peptide Conjugate Microarrays
Brett W. Engelmann

22. SH2 Domains as Affinity Reagents for Phosphotyrosine Protein Enrichment and Proteomic Analysis
Mi Ke, Bizhu Chu, Lin Lin, and Ruijun Tian

23. Identification of Tyrosine Phosphorylated Proteins by SH2 Domain Affinity Purification and Mass Spectrometry
Sophia Buhs, Helwe Gerull, and Peter Nollau

24. Analysis of the Global Changes in SH2 Binding Properties Using Mass Spectrometry Supported by Quantitative Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC) Technique
Radoslaw M. Sobota

25. Using Reciprocal Protein-Peptide Array Screening to Unravel Protein Interaction Networks
Huadong Liu, Courtney Voss, and Shawn Shun-Ch