A readily reproducible collection of established and emerging techniques for studying the interaction between proteins and ligands, including biochemical/bulk techniques, structure analysis, spectroscopy, single-molecule studies, and theoretical/computational tools. Among the highlights are surface plasmon resonance (SPR) and reflectometric biosensor approaches, high-throughput screening with confocal optics microscopy, single molecule fluorescence and fluorescence correlation spectroscopy (FCS), atomic force microscopy (AFM), crystallography of reaction intermediates, and time-resolved x-ray crystallography. The protocols follow the successful Methods in Molecular BiologyT series format, each offering step-by-step laboratory instructions, an introduction outlining the principle behind the technique, lists of the necessary equipment and reagents, and tips on troubleshooting and avoiding known pitfalls.
1 Isothermal Titration Calorimetry Edwin A. Lewis and Kenneth P. Murphy 2 Direct Optical Detection of Protein Ligand Interactions Frank Gesellchen, Bastian Zimmermann, and Friedrich W. Herberg 3 Label-Free Detection of Protein Ligand Interactions by the Quartz Crystal Microbalance Andreas Janshoff and Claudia Steinem 4 Measurement of Solvent Accessibility at Protein Potein Interfaces Jeffrey G. Mandell, Abel Baerga-Ortiz, Arnold M. Falick, and Elizabeth A. Komives 5 Hydrophobic Interaction Chromatography: Harnessing Multivalent Protein Surface Interactions for Purification Procedures Herbert P. Jennissen 6 A Sedimentation Velocity Method in the Analytical Ultracentrifuge for the Study of Protein Protein Interactions Claus Urbanke, Gregor Witte, and Ute Curth 7 Protein Ligand Interaction Probed by Time-Resolved Crystallography Marius Schmidt, Hyotcherl Ihee, Reinhard Pahl, and Vukica Srajer 8 X-Ray Crystallography of Protein Ligand Interactions Ilme Schlichting 9 Combined Use of XAFS and Crystallography for Studying Protein Ligand Interactions in Metalloproteins Richard W. Strange and Samar S. Hasnain 10 NMR Studies of Protein Ligand Interactions Till Maurer 11 Probing Heme Protein Ligand Interactions by UV/Visible Absorption Spectroscopy Karin Nienhaus and G. Ulrich Nienhaus 12 Ultrafast Time-Resolved IR Studies of Protein Ligand Interactions Manho Lim and Philip A. Anfinrud 13 Monitoring Protein Ligand Interactions by Time-Resolved FTIR Difference Spectroscopy Carsten Kotting and Klaus Gerwert 14 Proteins In Motion: Resonance Raman Spectroscopy as a Probe of Functional Intermediates Uri Samuni and Joel M. Friedman 15 Fluorescence Polarization/Anisotropy Approaches to Study Protein Ligand Interactions: Effects of Errors and Uncertainties David M. Jameson and Gabor Mocz 16 Ligand Binding with Stopped Flow Rapid Mixing Mark S. Hargrove 17 Circular Dichroism Spectroscopy for the Study of Protein Ligand Interactions Alison Rodger, Rachel Marrington, David Roper, and Stuart Windsor 18 High-Throughput Screening of Interactions between G Protein-Coupled Receptors and Ligands Using Confocal Optics Microscopy Lenka Zemanova, Andreas Schenk, Martin J. Valler, G. Ulrich Nienhaus, and Ralf Heilker 19 Single-Molecule Study of Protein Protein and Protein DNA Interaction Dynamics H. Peter Lu 20 Application of Fluorescence Correlation Spectroscopy to Hapten Antibody Binding Theodore L. Hazlett, Qiaoqiao Ruan, and Sergey Y. Tetin 21 Atomic Force Microscopy Measurements of Protein Ligand Interactions on Living Cells Robert H. Eibl and Vincent T. Moy 22 Computer Simulation of Protein Ligand Interactions: Challenges and Applications Sergio A. Hassan, Luis Gracia, Geetha Vasudevan, and Peter J. Steinbach 23 Force Probe Molecular Dynamics Simulations Helmut Grubmuller 24 The Study of Ligand Protein Interactions by Means of Density Functional Theory and First-Principles Molecular Dynamics Carme Rovira
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