PROTEIN INTERACTIONS Edited by Jianfeng Cai and Rongsheng E. Wang Protein Interactions Edited by Jianfeng Cai and Rongsheng E. Wang Published by InTech Janeza Trdine 9, 51000 Rijeka, Croatia Copyright © 2012 InTech All chapters are Open Access distributed under the Creative Commons Attribution 3.0 license, which allows users to download, copy and build upon published articles even for commercial purposes, as long as the author and publisher are properly credited, which ensures maximum dissemination and a wider impact of our publications. After this work has been published by InTech, authors have the right to republish it, in whole or part, in any publication of which they are the author, and to make other personal use of the work. Any republication, referencing or personal use of the work must explicitly identify the original source. As for readers, this license allows users to download, copy and build upon published chapters even for commercial purposes, as long as the author and publisher are properly credited, which ensures maximum dissemination and a wider impact of our publications. Notice Statements and opinions expressed in the chapters are these of the individual contributors and not necessarily those of the editors or publisher. No responsibility is accepted for the accuracy of information contained in the published chapters. The publisher assumes no responsibility for any damage or injury to persons or property arising out of the use of any materials, instructions, methods or ideas contained in the book. Publishing Process Manager Marina Jozipovic Technical Editor Teodora Smiljanic Cover Designer InTech Design Team 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 orders@intechopen.com 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 [...]... but it is not known if the interaction between the homologous proteins in 8 Protein Interactions mammalian cells, MOZ and CAF-1A, takes place in human cells and if any interaction occurs between the MOZ-TIF2 fusion protein and CAF-1A To address these areas we looked for interactions by co-immunoprecipitation using transfections with the Fig 1 Protein interaction between MOZ and CAF-1A or ASF1B in the... another protein, ASF1B, which interacted with the MOZ-1/759 fragment To verify the interaction between MOZ 12 Protein Interactions and ASF1B and to examine if the MOZ-TIF2 fusion protein also interacts with ASF1B, we conducted pull down assays and examined co-localization of proteins similar to the studies with CAF-1A A S-tag fusion cDNA with ASF1B was created in the pET-30c vector and the fusion protein. .. domains) Bone morphogenetic protein 1 Interleukin 8 receptor, beta NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 6, 17kDa calreticulin Actin binding LIM protein 1 Ribosome binding protein 1 homolog 180kDa (dog) vesicle amine transport protein 1 homolog (T californica) Calreticulin histone cluster 1, H2bi insulin-like growth factor binding protein 2, 36kDa Inversin PTK2B protein tyrosine kinase 2... phosphorimager MOZ-TIF2 Fusion Protein Binds to Histone Chaperon Proteins CAF-1A and ASF1B Through Its MOZ Portion 7 2.6 In Vitro protein binding assay with S-tagged fusion protein The S-tagged fusion of ASF1B was expressed from pET-30c-ASF1B in E coli BL21CodonPlus® (DE3)-RIL cells after induction with 0.8 mM of IPTG and purification with Stagged agarose beads The fusion protein on agarose beads was... Carnitine palmitoyltransferase 1B (muscle) PCTAIRE protein kinase 1 Neutrophil cytosolic factor 4, 40kDa neurogranin (protein kinase C substrate, RC3) Tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, epsilon polypeptide Mediator complex subunit 21 Insulin-like growth factor binding protein 2, 36kDa acylphosphatase 2, muscle type FK506 binding protein 1A, 12kDa Neurochondrin Syntaxin 5... following exposure of MSCs to E coli 2.3 Analysis of the cell proteins Proteins from MSCs were extracted in accordance with the protocol described previously (30) The aliquoted proteins (20 μg total protein per gel well) were separated on SDSpolyacrylamide slab gels (NuPAGE 4-12% Bis-Tris; Invitrogen, Carlsbad, CA) After electrophoresis, proteins were blotted onto a PDVF membrane and the blots were... translation system and interactions detected with a GST pull down assay (Figure 3C) For equivalent amounts of fusion peptides more MOZ-1/313 was bound to CAF-1A than MOZ-488/703 (Figure 3C) As a percentage of the input radioactivity, MOZ-1/313 pulled down about 30 % of the [35S]methionine labeled CAF-1A while MOZ-488/703 pulled down only 14% Further 10 Protein Interactions analysis of domain interactions showed... [35S]-methionine labeled p150 protein was produced from a T7driven pET-30 plasmid with an in vitro translation system A, binding assay was conducted with [35S]-methionine labeled p150 and the GST-tagged MOZ fragments The input lane is 10% of the [35S] methionine p150 protein added to the binding assay A, schematic structure MOZ-TIF2 Fusion Protein Binds to Histone Chaperon Proteins CAF-1A and ASF1B Through... homolog B (ASF1B) Both of these proteins were verified to interact with the MOZ partner of MOZ-TIF2 fusion in the yeast two-hybrid system The interaction has been further characterized by coimmunoprecipitation, protein pull-down assays, and co-localization by immunohistochemistry The differences in the interactions of CAF-1A and ASF1B with wild type MOZ and the MOZ-TIF2 fusion proteins may contribute to... centrifugation at 15,000 rpm for 30 minutes at 4˚C GST fusion proteins were purified with the GST Purification Module (Amersham Pharmacia Biotech, Piscataway, NJ) Purified GST fusion proteins were examined with SDS-PAGE followed by Coomassie Blue staining To perform GST pull down affinity assays [35S]Methionine-labeled proteins were first produced with Single Tube Protein System 3 or EcoProTM T7 system (EMD Biosciences, . 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. 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. 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