Protein-Ligand Interactions: Methods and Applications

ISBN-13: 9781071611999 / Angielski / Miękka / 2021

Daviter, Tina

Opis

This third edition provides new and updated chapters detailing a complete introduction to common and emerging procedures for characterizing the interactions of individual proteins with their natural ligands, drugs or other binding partners. Chapters detail natural substrates, potential drug leads, quantitative understanding of the mechanism of interaction, and different techniques. 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. Authoritative and accessible, Protein Ligand Interactions: Methods and Applications, Third Edition serves as an ideal guide for researchers new to the field of biophysical characterization of protein interactions.

Spis treści

Part I : Overview

1. Assessing and Improving Protein Sample Quality

Bertrand Raynal, Sébastien Brûlé, Stephan Uebel, and Stefan H. Knauer

 

2. A Familiar Protein-Ligand Interaction Revisited with Multiple Methods

Xiaochun Li-Blatter, Ludovit Zweifel, and Timothy Sharpe

 

Part II: Universal Methods For Protein Interactions

3. Interactions of a Signal Transduction Protein Investigated by Fluorescence Stopped-Flow Kinetics

Stephen R. Martin and Maria J. Schilstra

 

4. Kinetic Methods of Deducing Binding Mechanisms Involving Intrinsically Disordered Proteins

Elin Karlsson and Per Jemth

 

5. Isothermal Titration Calorimetry

Christopher M. Johnson

 

6. Measuring the K_d of Protein-Ligand Interactions Using Microscale Thermophoresis

Shih-Chia Tso and Chad A. Brautigam

 

7. Quartz Crystal Microbalance with Dissipation Monitoring (QCM-D); Preparing Functionalized Lipid Layers for the Study of Complex Protein-Ligand Interactions

Holly L Birchenough and Thomas A Jowitt

 

Part III: Screening For Ligand Binding

8. Indirect Detection of Ligand Binding by Thermal Melt Analysis Joseph Shaw and Christopher Stubbs

 

9. The Use of Acoustic Mist Ionization Mass Spectrometry for High-throughput Screening

Helen Plant, David Murray, Hannah Semple, Gareth Davies, Ian Sinclair, and Geoffrey A. Holdgate

 

10. Ligand Discovery – High Through-put Binding: Fluorescence Polarization (Anisotropy)

Geoffrey A. Holdgate and Paul E. Hemsley

 

11. Fragment Screening by NMR

Ben J. Davis

 

Part IV: Nucleotide Binding and Hydrolysis

12. A Quick Primer in Fluorescence-based Equilibrium and Pre-Steady State Methods for Determining Protein-Nucleotide Affinities

Harland E. Brandon and Hans-Joachim Wieden

 

13. Measurement of Nucleotide Hydrolysis using Fluorescent Biosensors for Phosphate

Simone Kunzelmann

 

Part V: Binding Nucleic Acids

14. Gel-based Analysis of Protein-Nucleic Acid Interactions

James A.W. Stowell, Terence T.L. Tang, Maximilian Seidel, and Lori A. Passmore

 

15. Biophysical Studies of the Binding of Viral RNA with the 80S Ribosome using SwitchSENSE

Emma Schenckbecher, Guillaume Bec, Taiichi Sakamoto, Benoit Meyer, and Eric Ennifar

 

16. Biolayer Interferometry: Protein-RNA Interactions

Stephen R. Martin, Andres Ramos, and Laura Masino

 

17. Analysis of Protein-DNA Interactions Using Surface Plasmon Resonance and a ReDCaT Chip

Clare E. M. Stevenson and David M. Lawson

 

18. Characterization of Protein Nucleic Acid complexes by Size-Exclusion Chromatography Coupled with Light Scattering, Absorbance and Refractive Index Detectors 

Ewa Folta-Stogniew

 

19. Analytical Ultracentrifugation for Analysis of Protein Nucleic Acid Interactions

Andrea Bogutzki and Ute Curth

 

20. Studying RNA-Protein Complexes Using X-ray Crystallography

Andrew P. Turnbull and Xiaoqiu Wu

 

Part VI: Membrane Binding

21. Flow Linear Dichroism of Protein-membrane Systems

Matthew R.Hicks, Sarah R. Dennison, Adewale Olamoyesan, and Alison Rodger

 

22. Probing Protein-Membrane Interactions and Dynamics Using Hydrogen-Deuterium eXchange Mass Spectrometry (HDX-MS)

Jordan TB Stariha, Reece M Hoffmann, David J Hamelin, and John E Burke