Table of Contents
Foreword xi
Preface xiii
About the Author xix
Chapter 1 Historical Perspectives 1
1.1 Introduction to Proteomics 3
1.2 Proteome and Proteomics 7
1.3 Genetics of Proteins 9
1.4 Molecular Biology of Genes and Proteins 20
1.5 Protein Chemistry Before Proteomics 24
References 34
Further Reading 37
Chapter 2 Proteomics - Relation to Genomics, Bioinformatics 39
2.1 Genomics 40
2.2 Bioinformatics and Computational Biology 57
References 58
Further Reading 59
Chapter 3 Methodology for Separation and Identification of Proteins and their Interactions 61
3.1 Separation of Proteins Via a Multidimensional Approach 61
3.2 Determination of the Primary Structure of Proteins 70
3.3 Determination of the 3D Structure of a Protein 83
3.4 Determination of the Amount of Proteins 86
3.5 Structural and Functional Proteomics 89
References 99
Further Reading 101
Chapter 4 Proteomics of Protein Modifications 103
4.1 Phosphorylation and Phosphoproteomics 104
4.2 Glycosylation and Glycoproteomics 107
4.3 Ubiquitination and Ubiquitinomics 110
4.4 Miscellaneous Modifications of Proteins 112
References 113
Further Reading 113
Chapter 5 Proteomics of Protein-Protein Interactions/Interactomes 115
5.1 Protein-Protein Interactions (PPI) in Vivo 116
5.2 Analysis of Protein Interactions in Vitro 118
5.3 Analysis of Protein Interactions in Silico 124
5.4 Synthetic Genetic Methods to Determine Protein Interactions 125
5.5 Interactomes 125
5.6 Evolution and Conservation of Interactomes 132
5.7 Interactomes and the Complexity of Organisms: It is the Number of Interactomes that Matters in Understanding the Complexity of an Organism and not the Number of Genes 133
5.8 Interaction of Proteins with Small Molecules 133
References 134
Further Reading 134
Chapter 6 Applications of Proteomics I: Proteomics, Human Disease, and Medicine 137
6.1 Diseasome 139
6.2 Medical Proteomics 139
6.3 Clinical Proteomics 148
6.4 Metaproteomics and Human Health 153
6.5 Proteomics in Biotechnology and Industry of Drug Production 154
6.6 Metaproteomics of Microbial Fermentation 155
6.7 Beef Industry 158
6.8 Bioterrorism and Biodefense 158
References 159
Further Reading 160
Chapter 7 Proteomics - Future Developments 163
7.1 Technical Scope of Proteomics-Beyond Protein Identification 163
7.2 Scientific Scope of Proteomics-Control of Epigenesis 165
7.3 Medical Scope of Proteomics 166
7.4 Proteomics, Energy Production, and Bioremediation 169
7.5 Proteomics and Biodefense 170
References 170
Further Reading 170
Index 171
