Protein-Protein Interactions: A Molecular Cloning Manual

by Golemis, Erica A; Adams, Peter D

• ISBN13: 9780879697235
• ISBN10: 0879697237
• Edition: 2nd
• Format: Paperback
• Copyright: 2005-10-26
• Publisher: Cold Spring Harbor Laboratory Press

Summary

This is an updated edition of a manual that provides a thorough collection of the technical and theoretical issues involved in the study of protein associations, including standard methods, biophysical approaches, and, in a final section, a collection of computational methods for integrating and analyzing interactions.

Table of Contents

Preface	ix
Section 1 Protein--Protein Interactions in Biological Context
Protein--Protein Interactions: A Common Theme in Cell Biology	1	(12)
Tony Pawson
Gerald D. Gish
Building a Better Web: Progress in the Concept and Methodology of Protein Interaction Studies	13	(24)
Elena N. Pugacheva
Erica A. Golemis
Section 2 Standard Technologies to Probe Protein Interactions
Identification of Protein--Protein Interactions by Conventional Column Chromatography	37	(18)
Valery Sudakin
Identification of Associated Proteins by Coimmunoprecipitation	55	(12)
Peter D. Adams
Rugang Zhang
Maxim V. Poustovoitov
Steven H. Seeholzer
Michael Ohh
Chromatin Immunoprecipitation of Protein Complexes	67	(14)
Achim Breiling
Valerio Orlando
Identification of Protein--Protein Interactions with Glutathione-S-Transferase Fusion Proteins	81	(24)
Margret B. Einarson
Elena N. Pugacheva
Jason R. Orlinick
Protein Interactions Captured by Chemical Cross-linking	105	(24)
Owen W. Nadeau
Gerald M. Carlson
Identification of Protein--Protein Interactions by Overlay Screening of λ Phage cDNA Expression Libraries	129	(12)
Jiyong Zhao
Phage-display Methodology for the Study of Protein-Protein Interactions	141	(26)
Carl S. Goodyear
Gregg J. Silverman
Yeast Two-Hybrid System for Studying Protein--Protein Interactions	167	(28)
Ilya Serebriiskii
Bacterial Two-Hybrid System for Studying and Modifying Protein--Protein Interactions	195	(22)
Astrid V. Giesecke
J. Keith Joung
Genetic Approaches to Identify Protein--Protein Interactions in Budding Yeast	217	(12)
Randy Strich
Section 3 Biophysical Approaches to Probe Protein Interactions
Calorimetry-based Approaches in Analysis of Protein--Protein Interactions	229	(24)
Jens Holger Trankle
Christian Herrmann
Analytical Ultracentrifugation in the Study of Protein Self-association and Heterogeneous Protein--Protein Interactions	253	(26)
Andrea Balbo
Peter Schuck
Monitoring Protein--Protein Interactions by Time-resolved FTIR Difference Spectroscopy	279	(22)
Carsten Kotting
Klaus Gerwert
Protein Co-crystallization for X-ray Structure Determination	301	(16)
Kehao Zhao
Ronen Marmorstein
Characterization of Multiprotein Complexes by Mass Spectrometry	317	(12)
Carol V. Robinson
Identification of Novel Protein Complexes and Protein--Protein Interactions by Mass Spectrometry	329	(26)
Sherry Niessen
Ian Mcleod
John R. Yates III
Measurement of Protein--Protein Interactions Using Surface Plasmon Resonance Spectroscopy	355	(22)
John T. Simpson
Robert J. Fisher
Advancement and Utilization of Biosensors for Protein Interaction Analysis and Proteomics	377	(22)
Simon Cocklin
Tetsuya Ishino
Mauro Sergi
Dobrin Nedelkov
Randall W. Nelson
Irwin Chaiken
Probing Ligand--Receptor Interactions with Atomic Force Microscopy	399	(16)
Xiaohui Zhang
Aileen Chen
Ewa Wojcikiewicz
Midhat H. Abdulreda
Sirshendu Banerjee
Vincent T. Moy
Analysis of Protein--DNA Interactions by Optical Tweezers: Application to Chromatin Fibers	415	(14)
Martin L. Bennink
Sanford H. Leuba
Jordanka Zlatanova
Evanescent Field Fluorescence Microscopy for Analysis of Protein--DNA Interactions at the Single-Molecule Level	429	(16)
Haocheng Zheng
Miroslav Tomschik
Jordanka Zlatanova
Sanford H. Leuba
Section 4 Novel High-Throughput Approaches to Probe Protein Interactions
Using Genetically Engineered Kinases to Screen for Novel Protein Kinase Substrates	445	(24)
Scott T. Eblen
N. Vinay Kumar
Michael J. Weber
The Split-Ubiquitin Membrane-based Yeast Two-Hybrid System	469	(30)
Lukas Burkle
John P. Miller
Daniel Auerbach
Igor Stagljar
A Bacterial Two-Hybrid System Based on a cAMP Signaling Cascade	499	(18)
Gouzel Karimova
Daniel Ladant
In Vitro Selection and Evolution of Protein--Ligand Interactions by Ribosome Display	517	(32)
Christiane Schaffitzel
Christian Zahnd
Patrick Amstutz
Beatrice Luginbuhl
Andreas Pluckthun
Protein-dependent Ribozymes as Reporters of Protein--Protein Interactions	549	(12)
Jorg S. Hartig
Section 5 Interactions of Proteins and Peptides
Screening Kinase Phosphorylation Motifs Using Peptide Libraries	561	(14)
Isaac A. Manke
Michael B. Yaffe
Using Peptide Aptamers to Study Proteins and Protein Networks	575	(16)
Aleric H. Soans
Clement A. Stanyon
Huamei Zhang
Russell L. Finley, Jr.
Analysis of Protein Interactions with Immobilized Peptide Arrays Synthesized on Membrane Supports	591	(18)
Ronald Frank
Stefan Dubel
Section 6 In Vivo Imaging of Protein Interactions
Imaging Protein Interactions by FRET Microscopy	609	(28)
Peter J. Verveer
Oliver Rocks
Ailsa G. Harpur
Philippe I.H. Bastiaens
Detection of Protein Interactions and Library Screening with Protein-fragment Complementation Assays	637	(36)
Ingrid Remy
F.X. Campbell-Valois
Galia Ghaddar
Stephanie Aquin
Stephen W. Michnick
Direct Visualization of Protein Interactions in Living Cells Using Bimolecular Fluorescence Complementation Analysis	673	(22)
Chang-Deng Hu
Tom K. Kerppola
Imaging Protein--Protein Interactions in Living Animals	695	(20)
Ramasam Paulmurugan
Pritha Ray
Abhijit De
Carmel T. Chan
Sanjir Sam Gambhir
Electron Microscopy Tomography and Localization of Proteins and Macromolecular Complexes in Cells	715	(26)
Willie J.C. Geerts
Abraham J. Koster
Arie J. Verkleij
Bruno M. Humbel
Section 7 Genome-wide and Computer-based Analysis of Protein Interactions
Genome-wide Analysis of Protein-Protein Interactions Using a Two-Hybrid Array	741	(20)
Tony R. Hazbun
John P. Miller
Tandem Affinity Purification Strategy for Protein Complex Characterization	761	(14)
Bertrand Seraphin
Mercedes Pamblanco
Celine Faux
Andrzej Dziembowski
Combining Phage Display and Unrelated Orthogonal Approaches to Determine Interaction Networks Mediated by Protein Recognition Modules	775	(22)
Simona Panni
Serena Paoluzi
Luisa Castagnoli
Gianni Cesareni
Exploiting Synthetic Genetic Interactions to Predict Pathways and Complexes	797	(16)
Gary D. Bader
Amy Tong
Lan V. Zhang
Frederick P. Roth
Brenda Andrews
Charles Boone
Analysis of Genome-wide Protein Interactions Using Computational Approaches	813	(26)
Anton J. Enright
Christos A. Ouzounis
Visualization and Integration of Protein Interaction Networks	839	(18)
Trey Ideker
Kai Tan
Peter Uetz
Section 8 Design of Novel Interactions and Inhibitors in Drug Discovery
Engineering Antibodies with Preferred Antigen Specificity	857	(16)
Stefan Knackmuss
Fabrice Le Gall
Sergey M. Kipriyanov
Discovery of a Growth Hormone Antagonist Using a Structure--Function Approach	873	(12)
Darlene E. Berryman
John J. Kopchick
Computational Docking of Biomolecular Complexes with AutoDock	885	(8)
David S. Goodsell
Exploiting Protein--Protein Interactions to Design an Activator of p53	893	(14)
David C. Fry
Bradford J. Graves
Lyubomir T. Vassilev
Appendix: Cautions	907	(12)
Index	919