Proteins are the cell’s workers, their messengers and overseers. In these roles, proteins specifically bind small molecules, nucleic acid and other protein partners. Cellular systems are closely regulated and biologically significant changes in populations of particular protein complexes correspond to very small variations of their thermodynamics or kinetics of reaction. Interfering with the interactions of proteins is the dominant strategy in the development of new pharmaceuticals. Protein Ligand Interactions: Methods and Applications, Second Edition provides a complete introduction to common and emerging procedures for characterizing the interactions of individual proteins. From the initial discovery of natural substrates or potential drug leads, to the detailed quantitative understanding of the mechanism of interaction, all stages of the research process are covered with a focus on those techniques that are, or are anticipated to become, widely accessible and performable with mainstream commercial instrumentation. Written in the highly successful Methods in Molecular Biology series format, chapters contain introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and notes on troubleshooting and avoiding known pitfalls.
Authoritative and accessible, Protein Ligand Interactions: Methods and Applications, Second Edition serves as an ideal guide for researchers new to the field of biophysical characterization of protein interactions – whether they are beginning graduate students or experts in allied areas of molecular cell biology, microbiology, pharmacology, medicinal chemistry or structural biology.
Part I. Introduction and Overview
1. Protein-Ligand Interactions: Fundamentals
Mark A. Williams
2. Protein Sample Characterization
Tina Daviter and Rémi Fronzes
3. Measurement of Protein-Ligand Complex Formation
Peter N. Lowe, Cara Vaughan, and Tina Daviter
Part II. Quantitation of Thermodynamics and Kinetics
4. Isothermal Titration Calorimetry for Studying Protein-Ligand Interactions
Luminita Damian
5. Rapid Mixing Kinetic Techniques
Stephen R. Martin and Maria J. Schilstra
6. Protein-Ligand Interactions Using SPR Systems
Åsa Frostell, Lena Vinterbäck and Hans Sjöbom
Part III. Spectroscopic Methods
7. Fluorescence Techniques in Analysis of Protein-Ligand Interactions
Gabor Mocz and Justin A. Ross
8. Circular and Linear Dichroism Spectroscopy for the Study of Protein-Ligand Interactions
Tina Daviter, Nikola Chmel, and Alison Rodger
9. Analyzing Protein-Ligand Interactions by Dynamic NMR Spectroscopy
Anthony Mittermaier and Erick Meneses
10. Studying Metal Ion - Protein Interactions: Electronic Absorption, Circular Dichroism and Electron Paramagnetic Resonance
Lilliana Quintanar and Lina Rivillas-Acevedo
11. Monitoring Protein-Ligand Interactions by Time-resolved FTIR Difference Spectroscopy
Carsten Kötting and Klaus Gerwert
Part IV. Ligand Discovery
12. Biophysical Methods in Drug Discovery from Small Molecule to Pharmaceutical
Geoffrey Holdgate, Stefan Geschwindner, Alex Breeze, Gareth Davies, Nicola Colclough, David Temesi, and Lara Ward
13. Biophysical Screening for the Discovery of Small-Molecule Ligands
Alessio Ciulli
14. Screening Protein-Small Molecule Interactions by NMR
Ben Davis
Part V. Molecules in Cellular Environments
15. Model Membrane Systems
Heiko Keller, Remigiusz Worch, and Petra Schwille
16. Quantitative Fluorescence Co-localization to Study Protein-Receptor Complexes
Shanica N. Pompey, Peter Michaely, and Katherine Luby-Phelps
Part VI. Structural & Computational Methods
17. Studying Protein-Ligand Interactions Using X-Ray Crystallography
Andrew P. Turnbull and Paul Emsley
18. Molecular Fields in Ligand Discovery
Paul J. Gane and A. W. Edith Chan
19. Structure-Based Virtual Screening for Novel Ligands
William R. Pitt, Mark D. Calmiano, Boris Kroeplien, Richard D. Taylor, James P. Turner, and Michael A. King
