SH2 Domains

1. Front Matter

   Pages i-xiii

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2. Overview

   1. Front Matter

      Pages 1-1

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   2. Introduction: History of SH2 Domains and Their Applications

      • Bernard A. Liu, Kazuya Machida

      Pages 3-35

   3. What Have We Learned from SH2 Domains?

      • Bruce J. Mayer

      Pages 37-43

3. Computational Approaches

   1. Front Matter

      Pages 45-45

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   2. Hidden Markov Models for Protein Domain Homology Identification and Analysis

      • Karl Jablonowski

      Pages 47-58

   3. Classification and Lineage Tracing of SH2 Domains Throughout Eukaryotes

      • Bernard A. Liu

      Pages 59-75

   4. SH2 Ligand Prediction–Guidance for In-Silico Screening

      • Shawn S. C. Li, Lei Li

      Pages 77-81

   5. An Efficient Semi-supervised Learning Approach to Predict SH2 Domain Mediated Interactions

      • Kousik Kundu, Rolf Backofen

      Pages 83-97

   6. Proteomic Clustering Analysis of SH2 Domain Datasets

      • Karl Jablonowski

      Pages 99-113

4. Experimental Tools

   1. Front Matter

      Pages 115-115

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   2. Expression and Production of SH2 Domain Proteins

      • Bernard A. Liu, Mari Ogiue-Ikeda, Kazuya Machida

      Pages 117-162

   3. Expression and Purification of Soluble STAT5b/STAT3 Proteins for SH2 Domain Binding Assay

      • Akira Asai, Kazuyuki Takakuma

      Pages 163-172

   4. Purification of SOCS (Suppressor of Cytokine Signaling) SH2 Domains for Structural and Functional Studies

      • Nicholas P. D. Liau, Artem Laktyushin, Jeffrey J. Babon

      Pages 173-182

   5. Expression and Purification of SH2 Domains Using Baculovirus Expression System

      • Mari Ogiue-Ikeda, Kazuya Machida

      Pages 183-198

   6. Functionally Altered SH2 Domains for Biochemical Studies: Loss-of-Function Mutant and Domain Concatenation

      • Mari Ogiue-Ikeda, Kazuya Machida

      Pages 199-223

   7. Creation of Phosphotyrosine Superbinders by Directed Evolution of an SH2 Domain

      • Haiming Huang, Tomonori Kaneko, Sachdev S. Sidhu, Shawn S. C. Li

      Pages 225-254

5. Structural Analysis and Binding Assays

   1. Front Matter

      Pages 255-255

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   2. Structural Characterization of Monomeric/Dimeric State of p59fyn SH2 Domain

      • Radu Huculeci, Fabien Kieken, Abel Garcia-Pino, Lieven Buts, Nico van Nuland, Tom Lenaerts

      Pages 257-267

   3. NMR Chemical Shift Mapping of SH2 Peptide Interactions

      • Marissa A. McKercher, Deborah S. Wuttke

      Pages 269-290

This volume covers an array of techniques available for studying SH2 domains and phosphotyrosine signaling. The book is divided into six parts: Part I outlines the history of SH2, technology development, and cell signaling; Part II focuses on computational approaches and tools used for identification, classification, and predictions of SH2 domain binding partners; Part III details various ways to prepare the SH2 domains as experimental reagents; Part IV presents methods for structural analysis and conventional binding assays using SH2 domains; Part V describes high-throughput and proteomics approaches to aid in analyzing SH2-mediated interactions; and Part VI covers applications for SH2 domain to functional and imaging analyzes. 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, SH2 Domains: Methods and Protocols is a valuable resource for computational biologists, biochemists, structural biologists, cell biologists, pathologists, and people interested in SH2 domains and phosphotyrosine signaling. Researchers who are investigating how protein interaction domain mediate specificity in signaling systems may also find this book informative.

• receptor tyrosine kinases (RTKs)
• phosphotyrosine signaling
• cell signaling
• structural analysis
• conventional binding assays
• high-throughput and proteomics approaches
• SH2-mediated interactions

• Department of Genetics and Genome Sciences, University of Connecticut School of Medicine, Farmington, USA

  Kazuya Machida

• Broad Institute of MIT and Harvard, Cambridge, USA

  Bernard A. Liu

Kazuya Machida, MD, PhD Dept of Genetics and Developmental Biology Univ of Connecticut Health Center Cell and Genome Sciences, Farmington, CT, USA
Tel: 860-679-1830; Email: machida@neuron.uchc.edu