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Preface

Section 1: Protein–Protein Interactions in Biological Context

Chapter 1: Protein–Protein Interactions: A Common Theme in Cell Biology

Chapter 2: Building a Better Web: Progress in the Concept and Methodology of Protein Interaction Studies

Section 2: Standard Technologies to Probe Protein Interactions

Chapter 3: Identification of Protein–Protein Interactions by Conventional Column Chromatography

Chapter 4: Identification of Associated Proteins by Coimmunoprecipitation

Chapter 5: Chromatin Immunoprecipitation of Protein Complexes

Chapter 6: Identification of Protein–Protein Interactions with Glutathione-S-Transferase Fusion Proteins

Chapter 7: Protein Interactions Captured by Chemical Cross-linking

Chapter 8: Identification of Protein–Protein Interactions by Overlay Screening of λ Phage cDNA Expression Libraries

Chapter 9: Phage-display Methodology for the Study of Protein–Protein Interactions

Chapter 10: Yeast Two-Hybrid System for Studying Protein–Protein Interactions

Chapter 11: Bacterial Two-Hybrid System for Studying and Modifying Protein–Protein Interactions

Chapter 12: Genetic Approaches to Identify Protein–Protein Interactions in Budding Yeast

Section 3: Biophysical Approaches to Probe Protein Interactions

Chapter 13: Calorimetry-based Approaches in Analysis of Protein–Protein Interactions

Chapter 14: Analytical Ultracentrifugation in the Study of Protein Self-association and Heterogeneous Protein–Protein Interactions

Chapter 15: Monitoring Protein–Protein Interactions by Time-resolved FTIR Difference Spectroscopy

Chapter 16: Protein Co-crystallization for X-ray Structure Determination

Chapter 17: Characterization of Multiprotein Complexes by Mass Spectrometry

Chapter 18: Identification of Novel Protein Complexes and Protein–Protein Interactions by Mass Spectrometry

Chapter 19: Measurement of Protein–Protein Interactions Using Surface Plasmon Resonance Spectroscopy

Chapter 20: Advancement and Utilization of Biosensors for Protein Interaction Analysis and Proteomics

Chapter 21: Probing Ligand–Receptor Interactions with Atomic Force Microscopy

Chapter 22: Analysis of Protein–DNA Interactions by Optical Tweezers: Application to Chromatin Fibers

Chapter 23: Evanescent Field Fluorescence Microscopy for Analysis of Protein–DNA Interactions at the Single-Molecule Level

Section 4: Novel High-Throughput Approaches to Probe Protein Interactions

Chapter 24: Using Genetically Engineered Kinases to Screen for Novel Protein Kinase Substrates

Chapter 25: The Split-Ubiquitin Membrane-based Yeast Two-Hybrid System

Chapter 26: A Bacterial Two-Hybrid System Based on a cAMP Signaling Cascade

Chapter 27: In Vitro Selection and Evolution of Protein–Ligand Interactions by Ribosome Display

Chapter 28: Protein-dependent Ribozymes as Reporters of Protein–Protein Interactions

Section 5: Interactions of Proteins and Peptides

Chapter 29: Screening Kinase Phosphorylation Motifs Using Peptide Libraries

Chapter 30: Using Peptide Aptamers to Study Proteins and Protein Networks

Chapter 31: Analysis of Protein Interactions with Immobilized Peptide Arrays Synthesized on Membrane Supports

Section 6: In Vivo Imaging of Protein Interactions

Chapter 32: Imaging Protein Interactions by FRET Microscopy

Chapter 33: Detection of Protein Interactions and Library Screening with Protein-fragment Complementation Assays

Chapter 34: Direct Visualization of Protein Interactions in Living Cells Using Bimolecular Fluorescence Complementation Analysis

Chapter 35: Imaging Protein–Protein Interactions in Living Animals

Chapter 36: Electron Microscopy Tomography and Localization of Proteins and Macromolecular Complexes in Cells

Section 7: Genome-wide and Computer-based Analysis of Protein Interactions

Chapter 37: Genome-wide Analysis of Protein–Protein Interactions Using a Two-Hybrid Array

Chapter 38: Tandem Affinity Purification Strategy for Protein Complex Characterization

Chapter 39: Combining Phage Display and Unrelated Orthogonal Approaches to Determine Interaction Networks Mediated by Protein Recognition Modules

Chapter 40: Exploiting Synthetic Genetic Interactions to Predict Pathways and Complexes

Chapter 41: Analysis of Genome-wide Protein Interactions Using Computational Approaches

Chapter 42: Visualization and Integration of Protein Interaction Networks

Section 8: Design of Novel Interactions and Inhibitors in Drug Discovery

Chapter 43: Engineering Antibodies with Preferred Antigen Specificity

Chapter 44: Discovery of a Growth Hormone Antagonist Using a Structure–Function Approach

Chapter 45: Computational Docking of Biomolecular Complexes with AutoDock

Chapter 46: Exploiting Protein–Protein Interactions to Design an Activator of p53

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