Protein-Ligand Interactions: Methods and Applications
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Part I Overview
1. Assessing and Improving Protein Sample Quality
Bertrand Raynal, S嶵astien Br? 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 Kd 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 JowittPart 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 InteractionsJames 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-Stogniew19. 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
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