SH2 Domains

ISBN-13: 9781071633922 / Angielski / Twarda / 2023

Opis

This volume looks at the latest methods used to study and modulate the biological function and mechanisms of SH2 domains. The chapters in this book are organized into five parts. Part One presents methodology aimed at determining the structures and dynamics of SH2 domains and their complexes with phosphopeptides. Part Two discusses techniques to understand and predict interactions of SH2 domains by measuring or calculating their affinity to phosphopeptides. Part Three focuses on inhibitors of SH2 domains that lead the way for chemical tool development and drug discovery. Part Four describes how to evolve and engineer SH2 domains with specific binding properties, and Part Five explores how to measure the regulation of protein tyrosine phosphatase activity through allosteric binding of peptides to SH2 domains and condensation. 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 comprehensive, SH2 Domains: Functional Modules and Evolving Tools in Biology is a valuable resource for researchers, working in the biophysical and biochemical field, who want to learn more about this exciting and versatile class of regulatory and signaling domains. 

Spis treści

Preface…
Table of Contents…
Contributing Authors…

Part I Structure and Dynamics of SH2 Domains

1. Methods for Structure Determination of SH2 Domain–Phosphopeptide Complexes by NMR
Vittoria Nanna, Michelangelo Marasco, John P. Kirkpatrick, and Teresa Carlomagno

2. NMR Methods to Study the Dynamics of SH2 Domain–Phosphopeptide Complexes
Michelangelo Marasco, John P. Kirkpatrick, Vittoria Nanna, and Teresa Carlomagno

3. Crystal Structure Analysis of SH2 Domains in Complex with Phosphotyrosine Peptides
Miki Senda and Toshiya Senda

4. Revealing Allostery in PTPN11 SH2 Domains from MD Simulations
Massimiliano Anselmi and Jochen S. Hub

5. Structure Determination of SH2–Phosphopeptide Complexes by X-Ray Crystallography: The Example of p120RasGAP
Amy L. Stiegler and Titus J. Boggon

Part II Biophysics and Bioinformatics of SH2 Domain–Phosphopeptide Binding

6. Fluorescence Anisotropy and Polarization in the Characterization of Biomolecular Association Processes and Their Application to Study SH2 Domain Binding Affinity
Sara Bobone, Claudia Storti, Paolo Calligari, and Lorenzo Stella

7. Computational Evaluation of Peptide-Protein Binding Affinities: Application of Potential of Mean Force Calculations to SH2 Domains
Paolo Calligari, Lorenzo Stella, and Gianfranco Bocchinfuso

8. NMR Relaxation Dispersion Experiments to Study Phosphopeptide Recognition by SH2 Domains: The Grb2-SH2–Phosphopeptide Encounter Complex
Fabio C. L. Almeida, Karoline Sanches, Icaro P. Caruso, and Fernando A. Melo

9. Using Linear Motif Database Resources to Identify SH2 Domain Binders
Hugo Sámano-Sánchez, Toby J. Gibson, and Lucía B. Chemes

10. Using Surface Plasmon Resonance to Study SH2 Domain-Peptide Interactions
Gabrielle M. Watson, Menachem J. Gunzburg, and Jacqueline A. Wilce

Part III Small-Molecule Binders and Inhibitors of SH2 Domains

11. Inhibitor Library Screening of SH2 Domains through Denaturation-Based Assays
Elvin D. de Araujo, Anna Orlova, Qirat F. Ashraf, Richard Moriggl, and Patrick T. Gunning

12. Dissecting Selectivity Determinants of Small-Molecule Inhibitors of SH2-Domains via Fluorescence Polarization Assays
Angela Berg, Julian Gräb, Barbara Klüver, and Thorsten Berg

13. Lipid Binding of SH2 Domains
Wonhwa Cho, Kyli Berkley, and Ashutosh Sharma

14. Exploring the Binding Interaction between Phosphotyrosine Peptides and SH2 Domains by Proximal Crosslinking
Rui Wang, Yishu Bao, and Jiang Xia

15. Synthesis and Biochemical Evaluation of Monocarboxylic GRB2 SH2 Domain Inhibitors
Tao Xiao, Min Zhang, and Haitao Ji

Part IV Engineering SH2 Domains

16. Engineering of SH2 Domains for the Recognition of Protein Tyrosine O-Sulfation Sites
Sean Paul Waldrop, Wei Niu, and Jiantao Guo

17. Engineering SH2 Domains with Tailored Specificities and Affinities
Gregory D. Martyn, Gianluca Veggiani, and Sachdev S. Sidhu

Part V SH2-Domain Containing Proteins and Regulation of Activity

18. Measuring Protein Tyrosine Phosphatase Activity Dependent on SH2 Domain-Mediated Regulation
Pablo Rios, Azin Kiani, and Maja Köhn

19. Peptides as Baits for the Co-Precipitation of SH2 Domain-Containing Proteins
Azin Kiani, Pablo Rios, and Maja Köhn

20. Biomolecular Condensation of SH2 Domain-Containing Proteins on Membranes
Longhui Zeng and Xiaolei Su

Subject Index List…