About Book

Any interaction between two protein molecules enabled by electrostatic forces like hydrophobic effect is known as protein-protein interaction. The examples of these interactions are cell metabolism, single transduction, muscle contraction, transport across membranes, etc. The process is used in many subjects namely quantum chemistry, molecular dynamics, biochemistry, etc. Protein–protein interactions (PPIs) play crucial roles in fundamental processes in living cells. PPIs perform multi-functions, such as modifying the kinetic properties of enzymes, catalysing metabolic reactions, activating or suppressing a protein, changing the specificity of a protein, regulating upstream and downstream levels and transporting molecules. Computational analysis of PPI networks is increasingly becoming a mandatory tool to understand the functions of unexplored proteins. At present, protein-protein interaction (PPI) is one of the key topics for the development and progress of modern system’s biology. This book is a compilation of chapters that discuss the most vital concepts in the field of protein-protein interactions. It discusses in detail the various applications and techniques of the subject. It deals with bioluminescent proteins, peptidomimetics, ubiquitin pathways, membrane proteins, dynamic light scattering, electron paramagnetic resonance, computational methods, transient protein-protein interactions, salt solutions and assays. Different approaches, evaluations and methodologies and advanced studies on the subject have been included in it. Coherent flow of topics, student-friendly language and extensive use of examples make this book an invaluable source of knowledge. For someone with an interest and eye for detail, this book covers the most significant topics in this field. It will serve as a reference to a broad spectrum of readers.

Preface............................................................................................................v

Chapter 1 Introductory Chapter: Protein-Protein Interactions and Assays......1

1. Introduction............................................................................................1

2. Protein-protein interaction assays......................................................2

Acknowledgements...............................................................................5

Authors’ contributions..........................................................................5

Chapter 2 Coordination of DNA Base Excision Repair by Protein-Protein Interactions...................................................................................................8

Abstract...................................................................................................8

1. Introduction............................................................................................9

2. Main steps of BER and proteins iNvol-ved..................................10

3. Proteins involved in BER interact directly with each other......12

4. Interactions of BER proteins with noncanonical factors contribute

to the regulation of DNA repair......................................................19

5. Intersection of posttranslational modifications and protein-

protein interactions in BER coordination.......................................21

6. Conclusions..........................................................................................23

Acknowledgements.............................................................................24

Conflict of interest..............................................................................24

Chapter 3 Protein-Protein Interactions in Salt Solutions .................................37

1. Introduction..........................................................................................37

2. Historical background........................................................................39

3. Some theoretical explanations for protein-protein interactions in

salt solutions........................................................................................43

4. Molecular mechanism for protein-ion interactions......................45

5. From protein-ion interactions to protein-protein interactions ..47

6. Conclusions..........................................................................................52

7. Acknowledgements.............................................................................54

Chapter 4 In Vivo Imaging of Protein-Protein Interactions .............................59

1. Introduction..........................................................................................59

2. Fluorescence imaging of PPI ...........................................................60

3. Bioluminescence imaging (BLI) of PPI...........................................67

4. PET imaging of PPI ...........................................................................73

5. Conclusion ...........................................................................................75

Chapter 5 Computational Approaches to Elucidating Transient Protein-

Protein Interactions, Predicting Receptor-Ligand Pairings.............81

1. Introduction..........................................................................................81

2. Current computational approaches for predicting protein-protein

interaction ............................................................................................82

3. Phylogenetics and beyond, how multiple kernel learning can

improve predictions of receptor-ligand pairings ........................89

4. Conclusion ...........................................................................................93

5. Acknowledgments ............................................................................95

Chapter 6 Inferring Protein-Protein Interactions (PPIs) Based on

Computational Methods ......................................................................100

1. Introduction........................................................................................100

2. Computational methods to infer PPIs .........................................101

3. Computational methods to infer protein flexibility...................111

4. PPI prediction from protein flexibility ........................................113

5. Conclusion..........................................................................................121

Chapter 7 Site-Directed Spin Labeling and Electron Paramagnetic Resonance

(EPR) Spectroscopy: A Versatile Tool to Study Protein-Protein

Interactions...............................................................................................127

1. Introduction........................................................................................127

2. Site-Directed Spin Labeling (SDSL)...............................................128

3. EPR analysis of spin labeled proteins..........................................132

4. SDSL EPR in protein interaction studies.....................................141

5. Acknowledgement.............................................................................144

Chapter 8 Characterization of Protein-Protein Interactions via Static and

Dynamic Light Scattering.....................................................................154

1. Introduction........................................................................................154

2. Theory of light scattering from biomacromolecules in

solution................................................................................................155

3. Composition-gradient light scattering instrumentation............164

4. Practical challenges of composition-gradient light scattering..167

5. CG-MALS examples.........................................................................174

6. Conclusion..........................................................................................183

7. Acknowledgement.............................................................................183

Chapter 9 Approaches to Analyze Protein-Protein Interactions of Membrane

Proteins ....................................................................................................187

1. Introduction ......................................................................................187

2. Determination of membrane protein-protein interactions ......188

3. Characterization of membrane protein-protein interactions ...194

4. Conclusions and outlook ...............................................................203

5. Acknowledgment .............................................................................204

Chapter 10 Bioluminescent Proteins: High Sensitive Optical Reporters for

Imaging Protein-Protein Interactions and Protein Foldings in

Living Animals .......................................................................................215

1. Introduction ......................................................................................215

2. Molecular imaging .........................................................................225

3. Bioluminescent assays to study protein-protein interactions .233

4. Bioluminescence resonance energy transfer ...............................246

5. Future directions in bioluminescence imaging ..........................248

Citation......................................................................................................259

Index...........................................................................................................261

About Author

Herbert Minh pursued his M.Sc. in Systems Biology and Bioinformatics from Science Research University, Krasnoyarsk. He conducted researches on proteomics and bioinformatics. He is a Visiting Professor at Community College, Dnipro. Minh was awarded the “Dean’s Award for Distinguished Teaching” for his outstanding contribution to the student community in the field of proteomics. He has produced numerous articles, research papers and books in the field of proteomics. He has also been an invited speaker at various international conferences.