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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
WWW Resources

Figures

Chapters 1–13
	Figure 1-3. SH2 domain-containing proteins grouped according to biochemical activity
	Figure 2-2. Novitas characterization flowchart
	Figure 6-2. GST pull-down assay
	Figure 7-2. Flowchart for cross-linking screening
	Figure 8-1. Identification of interacting proteins by screening λ phage cDNA expression libraries
	Figure 9-1. Engineering of proteins based on structural information
	Figure 10-2. Flowchart, controls, and library screen
	Figure 12-1. Suppressor strategies
	Figure 12-3. Mutant phenotypes for suppressor analysis
	Figure 13-1. Schematic of an isothermal titration calorimeter
	Figure 13-7. Energy landscape of Ras/Raf contact surface
Chapters 14–20
	Figure 14-2. Sedimentation velocity profiles
	Figure 14-3. Sedimentation coefficient distribution
	Figure 15-1. Time-resolved infrared absorbance difference spectra
	Figure 16-1. X-ray structure determination of macromolecules
	Figure 17-1. Different pressure regimes in the modified Q-TOF 2 mass spectrometer
	Figure 18-1. AP-MS procedure
	Figure 19-2. Interaction monitored as a sensorgram
	Figure 20-1. HIV-1 attachment and entry into cells
	Figure 20-2. SPR-based gp120/Env interaction assays
	Figure 20-3. Sensorgram overlays for gp120 JR-FL binding to 17b mAb surface
Chapters 21–25
	Figure 21-1. Schematic of AFM
	Figure 21-2. Functionalization of AFM tips with ConA
	Figure 21-3. Interaction between streptavidin-functionalized tip and biotinylated agarose bead
	Figure 22-1. Operation principles of optical tweezers
	Figure 22-2. Experimental setup, flow system, and flow cell
	Figure 23-2. Concept of spFRET
	Figure 24-2. Sequence alignment of ATP-binding site of protein kinases
	Figure 24-3. Analog inhibition assay
	Figure 25-1. Membrane-based yeast two-hybrid system
Chapters 26–31
	Figure 26-1. Bacterial two-hybrid system
	Figure 26-2. Cloning strategy and screening/selection procedures for bacterial two-hybrid system
	Figure 27-1. Ribosome display
	Figure 27-3. Ribosome display construct for assembly PCR
	Figure 28-1. Hammerhead ribozyme
	Figure 28-2. Ribozymes for detection of protein interactions
	Figure 29-2. Matrix and graphic representation of amino acid selectivity data
	Figure 30-1. Aptamer analysis of protein interactions
	Figure 31-2. Manual SPOT synthesis
	Figure 31-5. Classic epitope analysis experiment
	Figure 31-6. Dual-positional-scanning peptide library experiment
Chapters 32–35
	Figure 32-1. FRET efficiency
	Figure 32-2. Acceptor photobleaching experiment
	Figure 32-6. FLIM images of live cells
	Figure 33-4. GFP PCA-based library screening strategy
	Figure 33-5. In vivo β-lactamase PCA applications
	Figure 34-1. BiFC assay
	Figure 34-5. Multicolor fluorescence complementation analysis
	Figure 35-1. Imaging of protein interactions in living animals
	Figure 35-2. Imaging in living mice by two-hybrid approach
Chapters 36–40
	Figure 36-1. Specimen preparation for EM tomography
	Figure 36-9. Manual contouring of membrane structures in tomograms
	Figure 37-1. Protein–protein interactions by two-hybrid and MS techniques
	Figure 37-5. Array-based screening procedure
	Figure 38-1. Overview of TAP method
	Figure 39-1. Determining interaction networks mediated by protein recognition modules
	Figure 39-4. Comparison of networks obtained by two orthogonal approaches
	Figure 40-1. The SGA method
	Figure 40-3. SGA screen enriched for genes related to BIM1
Chapters 41–46
	Figure 41-1. Computational prediction of protein interaction
	Figure 42-1. Physical interactions involving proteins
	Figure 42-3. 2358 protein–protein interactions in yeast
	Figure 42-4. Kohn's symbols
	Figure 44-3. Human GH binding to the receptor
	Figure 44-6. Space-filling model of the third α-helix
	Figure 45-1. AutoDockTools
	Figure 45-2. AutoGrid
	Figure 46-1. Regulation of p53 by MDM2
	Figure 46-3. X-ray structure of MDM2/Nutlin-2 complex

Tables

Interaction domain recognition of posttranslational protein modifications
p53-interacting proteins
FPLC columns
Cross-linkers
Recognition specificity of domains involved in protein interaction
Computational resources
Parameters of molecules and molecular interactions
Protein interaction databases
Protein network visualization and analysis tools

Protocols

Protein–Protein Interactions: A Molecular Cloning Manual, Second Edition—Protocols [Supplementary material]
	Chapter 11: Bacterial Two-Hybrid System for Studying and Modifying Protein–Protein Interactions
	Chapter 14: Analytical Ultracentrifugation in the Study of Protein Self-Association and Heterogeneous Protein–Protein Interactions
	Chapter 20: Advancement and Utilization of Biosensors for Protein Interaction Analysis and Proteomics
	Chapter 35: Imaging Protein–Protein Interactions in Living Animals
Protein–Protein Interactions: A Molecular Cloning Manual, First Edition—Chapters
	Chapter 2: Signal Transduction and Mammalian Cell Growth: Problems and Paradigms
	Chapter 3: Impact of Protein Interaction Technologies on Cancer Biology and Pharmacogenetics
	Chapter 11: Detection of Homotypic Protein Interactions with Green Fluorescent Protein Proximity Imaging (GFP-PRIM)
	Chapter 15: Analysis of Protein Interactions Using a Quartz Crystal Microbalance Biosensor
	Chapter 16: Protease Footprinting
	Chapter 17: Tandem Affinity Purification to Enhance Interacting Protein Identification
	Chapter 18: Protein Purification by Inverse Transition Cycling
	Chapter 19: Using In Vitro Expression Cloning to Identify Interacting Proteins
	Chapter 20: Using Xenopus Egg Extracts to Modify Recombinant Proteins
	Chapter 21: Using λ Repressor Fusions to Isolate and Characterize Self-assembling Domains
	Chapter 23: Protein Interactions in Live Cells Monitored by β-Galactosidase Complementation
	Chapter 24: Identification of Protein Single-chain Antibody Interactions In Vivo Using Two-hybrid Protocols
	Chapter 28: Generation of Protein Fragment Libraries by Incremental Truncation
	Chapter 29: Catalytic Antibodies: New Characters in the Protein Repertoire
	Chapter 32: Protein Bundling to Enhance the Detection of Protein–Protein Interactions
	Chapter 35: Modulating Protein–Protein Interactions to Develop New Therapeutic Approaches

Links

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WWW Resources
	Chapter 2: Building a Better Web: Progress in the Concept and Methodology of Protein Interaction Studies
	Chapter 5: Chromatin Immunoprecipitation of Protein Complexes
	Chapter 10: Yeast Two-Hybrid System for Studying Protein–Protein Interactions
	Chapter 12: Genetic Approaches to Identify Protein–Protein Interactions in Budding Yeast
	Chapter 16: Protein Co-crystallization for X-ray Structure Determination
	Chapter 18: Identification of Novel Protein Complexes and Protein–Protein Interactions by Mass Spectrometry
	Chapter 25: The Split-Ubiquitin Membrane-based Yeast Two-Hybrid System
	Chapter 29: Screening Kinase Phosphorylation Motifs Using Peptide Libraries
	Chapter 30: Using Peptide Aptamers to Study Proteins and Protein Networks
	Chapter 35: Imaging Protein–Protein Interactions in Living Animals
	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 42: Visualization and Integration of Protein Interaction Networks
	Chapter 43: Engineering Antibodies with Preferred Antigen Specificity
	Chapter 45: Computational Docking of Biomolecular Complexes with AutoDock

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