Table Of ContentPROTEIN INTERACTIONS
Edited by
Jianfeng Cai and
Rongsheng E. Wang
PROTEIN INTERACTIONS
Edited by Jianfeng Cai
and Rongsheng E. Wang
Protein Interactions
Edited by Jianfeng Cai and Rongsheng E. Wang
Published by InTech
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Copyright © 2012 InTech
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Publishing Process Manager Marina Jozipovic
Technical Editor Teodora Smiljanic
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First published March, 2012
Printed in Croatia
A free online edition of this book is available at www.intechopen.com
Additional hard copies can be obtained from [email protected]
Protein Interactions, Edited by Jianfeng Cai and Rongsheng E. Wang
p. cm.
ISBN 978-953-51-0244-1
Contents
Preface IX
Part 1 Examples of Protein Interactions 1
Chapter 1 MOZ-TIF2 Fusion Protein Binds to
Histone Chaperon Proteins CAF-1A
and ASF1B Through Its MOZ Portion 3
Hong Yin, Jonathan Glass and Kerry L. Blanchard
Chapter 2 Autophagy-Mediated Defense Response
of Mouse Mesenchymal Stromal Cells (MSCs)
to Challenge with Escherichia coli 23
N.V. Gorbunov, B.R. Garrison, M. Zhai, D.P. McDaniel,
G.D. Ledney, T.B. Elliott and J.G. Kiang
Chapter 3 The Use of Reductive Methylation of
Lysine Residues to Study Protein-Protein Interactions
in High Molecular Weight Complexes by Solution NMR 45
Youngshim Lee, Sherwin J. Abraham and Vadim Gaponenko
Chapter 4 Regulation of Protein-Protein Interactions
by the SUMO and Ubiquitin Pathways 53
Yifat Yanku and Amir Orian
Chapter 5 Functional Protein Interactions
in Steroid Receptor-Chaperone Complexes 71
Thomas Ratajczak, Rudi K. Allan,
Carmel Cluning and Bryan K. Ward
Chapter 6 The TPR Motif as a Protein Interaction
Module – A Discussion of Structure and Function 103
Natalie Zeytuni and Raz Zarivach
Chapter 7 The Two DUF642 At5g11420 and
At4g32460-Encoded Proteins Interact In Vitro
with the AtPME3 Catalytic Domain 119
Esther Zúñiga-Sánchez and Alicia Gamboa-de Buen
VI Contents
Chapter 8 Protein-Protein Interactions and Disease 143
Aditya Rao, Gopalakrishnan Bulusu,
Rajgopal Srinivasan and Thomas Joseph
Chapter 9 AApeptides as a New Class of Peptidomimetics
to Regulate Protein-Protein Interactions 155
Youhong Niu, Yaogang Hu, Rongsheng E. Wang,
Xiaolong Li, Haifan Wu, Jiandong Chen and Jianfeng Cai
Chapter 10 Protein Interactions in S-RNase-Based
Gametophytic Self-Incompatibility 171
Thomas L. Sims
Chapter 11 Direct Visualization of Single-Molecule
DNA-Binding Proteins Along DNA to
Understand DNA–Protein Interactions 195
Hiroaki Yokota
Chapter 12 Defining the Cellular Interactome of
Disease-Linked Proteins in Neurodegeneration 215
Verena Arndt and Ina Vorberg
Chapter 13 Biochemical, Structural
and Pathophysiological Aspects
of Prorenin and (Pro)renin Receptor 243
A.H.M. Nurun Nabi and Fumiaki Suzuki
Chapter 14 Cholesterol-Binding
Peptides and Phagocytosis 275
Antonina Dunina-Barkovskaya
Part 2 Studying Protein Interactions 291
Chapter 15 One-by-One Sample Preparation
Method for Protein Network Analysis 293
Shun-Ichiro Iemura and Tohru Natsume
Chapter 16 Live In-Cell Visualization of Proteins
Using Super Resolution Imaging 311
Catherine H. Kaschula, Dirk Lang and M. Iqbal Parker
Chapter 17 Approaches to Analyze Protein-Protein
Interactions of Membrane Proteins 327
Sabine Hunke and Volker S. Müller
Chapter 18 Relating Protein Structure and Function
Through a Bijection and Its Implications
on Protein Structure Prediction 349
Marco Ambriz-Rivas, Nina Pastor and Gabriel del Rio
Contents VII
Chapter 19 Protein-DNA Interactions Studies
with Single Tethered Molecule Techniques 369
Guy Nir, Moshe Lindner and Yuval Garini
Chapter 20 Characterization of Protein-Protein Interactions
via Static and Dynamic Light Scattering 401
Daniel Some and Sophia Kenrick
Chapter 21 Site-Directed Spin Labeling and Electron
Paramagnetic Resonance (EPR) Spectroscopy:
A Versatile Tool to Study Protein-Protein Interactions 427
Johann P. Klare
Chapter 22 Modification, Development,
Application and Prospects of
Tandem Affinity Purification Method 447
Xiaoli Xu, Xueyong Li, Hua Zhang and Lizhe An
Preface
Protein interactions, including interactions between proteins and proteins, nucleic acids,
lipids, carbohydrates, are essential to all aspects of biological processes, such as cell
growth, differentiation, and apoptosis. Therefore, investigation and modulation of protein
interactions are of significance as it not only reveals the mechanism governing cellular
activity, but also leads to potential agents for the treatment of various diseases. In recent
years, the development of biochemistry knowledge and instrumentation techniques has
greatly facilitated the research in protein interactions. To provide some background
information on the protein interactions, and also highlight the examples in the study of
protein interactions, this book reviews some latest development in protein interactions,
including modulation of protein interactions, applications of analytical techniques, and
computer-assisted simulations. It aims to inspire the further development of technologies
and methodologies in the understanding and regulation of protein interactions.
Although the chapters included in this book are all addressing protein interactions, we
try to separate them into two parts according to their objectives. Chapters in part 1
mainly focus on the investigation of some specific protein-protein or protein-nucleic
acid interactions, and try to elucidate the mechanism of specific cellular processes. Part
1 provides some insight of why and how to study protein interactions, and illustrates
some approaches to modulate protein interactions. The second part is devoted to the
development of various methods for the investigation of protein interactions,
including computational modeling. Methods used to study protein interactions often
evolve rapidly and many innovative methods or approaches are emerging in this field.
The chapters shown in this part would shed light on the further development and
application of analytical techniques and computer simulations.
I would like to thank every author because they have devoted their effort and expertise
to prepare the outstanding chapters included in this book. I also thank Dr. Rongsheng E.
Wang, the co-Editor of this volume, for his tremendous help on the review and editing of
the book. Meanwhile, I want to express my deep appreciation to Ms. Marina Jozipovic
for her tireless efforts in distributing, organizing, and processing all of the chapters.
Jianfeng Cai
Assistant Professor, Department of Chemistry,
University of South Florida, Tampa, FL
USA
