The past 25 years has seen the emergence of a wealth of data suggesting that novel biological functions of known proteins play important roles in biology and medicine. This ability of proteins to exhibit more than one unique biological activity is known as protein moonlighting. Moonlighting proteins can exhibit novel biological functions, thus extending the function of the proteome, and are also implicated in the pathology of a growing number of idiopathic and infectious diseases. This book, written by a cell biologist, protein evolutionary biologist and protein bioinformatician, brings together the latest information on the structure, evolution and biological function of the growing numbers of moonlighting proteins that have been identified, and their roles in human health and disease. This information is revealing the enormous importance protein moonlighting plays in the maintenance of human health and in the induction of disease pathology. Protein Moonlighting in Biology and Medicine will be of interest to a general readership in the biological and biomedical research community.

Brian Henderson is Professor of Biochemistry at University College London. He started his research career as a cell biologist, migrating to become an immunologist then pharmacologist with six years experience in the pharmaceutical industry. In the early 1990s studies of bacteria-host interactions identified a bacterial molecular chaperone, chaperonin 60, as a potent signalling molecule able to induce osteoclast formation and bone remodelling. This was Henderson's introduction to protein moonlighting and he has spent the past twenty years exploring the roles of bacterial and human moonlighting proteins in human health and disease.

Mario Fares is a Principal Investogator in the Evolutionary Genetics and Bioinformatics Laboratory at Trinity College. His research is focused on the understanding of the selective forces shaping the evolution of proteins, proteomes and genomes. Most of the concepts dealt with in his laboratory are related to the field of molecular evolution and the complexity of mutations relationships. Taking these interests and concepts to the level of comparative genomics and proteomics adds the dimension of systems biology to his research.

Andrew Martin is a researcher in the Bloomsbury Center for Bioinformatics at University College, London. His research focuses on structural bioinformatics: developing tools to investigate and understand the relationship between protein sequence, structure and function. Within this general area, his main interests are protein modelling, structural analysis, structural immunology, effects of mutation on protein structure and disease, application of relational databases, automation and software development.

Preface xi

1 An Introduction to the Protein Molecule 1

1.1 Why Study Protein Moonlighting? 1

1.2 A Brief History of Proteins 2

1.3 Protein Biology 4

1.4 Protein Structure and Function 6

1.5 Protein Sequence Determination, Structures, and Bioinformatics 9

1.6 Regulation of Protein Synthesis 11

1.7 Conclusions 12

References 12

2 How Proteins Evolve? 15

2.1 Introduction 15

2.2 A Darwinian View of Molecular Evolution 16

2.3 The Neutral and Nearly Neutral Theories of Molecular Evolution 18

2.4 Mutation, Fitness, and Evolution 20

2.5 Proteins Evolve at Different Rates 24

2.6 Protein Evolution by Gene Duplication 25

2.7 Conclusions 26

References 26

3 A Brief History of Protein Moonlighting 31

3.1 Introduction 31

3.2 Protein Moonlighting: The Early Beginnings 31

3.3 Eye Lens Proteins and Gene Sharing 33

3.4 Multifunctional Metabolic Proteins and Molecular Chaperones 35

3.5 The Return of Moonlighting 37

3.6 A Current View of Protein Moonlighting 39

3.7 The Current Population of Moonlighting Proteins 40

3.8 Conclusions 40

References 40

4 The Structural Basis of Protein Moonlighting 45

4.1 Introduction 45

4.2 The Structural Biology of Protein Moonlighting 48

4.2.1 Exploiting Protein Bulk 49

4.2.2 Catalytic Promiscuity 49

4.2.3 Exploiting Separate Functional Sites 50

4.2.4 Exploiting Alternatively Folded Forms 55

4.2.5 Alternative Oligomerization 56

4.2.6 Posttranslational Modifications 57

4.3 Predicting and Engineering Moonlighting 57

4.4 Conclusions 58

References 60

5 Protein Moonlighting and New Thoughts about Protein Evolution 63

5.1 Introduction 63

5.2 A Darwinian Perspective of Protein Moonlighting 65

5.3 Origin and Evolutionary Stability of Protein Moonlighting 67

5.4 Mutational Robustness and the Persistence of Moonlighting Proteins 68

5.5 Proteins Robust to Mutations Are Highly Evolvable 70

5.6 Moonlighting Proteins and the Rate of Protein Evolution 72

5.7 Molecular Chaperones Buffer the Effects of Mutations on Proteins, Expediting Their Rate of Evolution and Enabling Moonlighting 74

5.8 Protein Moonlighting Can Lead to Functional Specialization 76

5.9 Conclusions 76

References 77

6 Biological Consequences of Protein Moonlighting 81

6.1 Introduction 81

6.2 The Human Genome, Protein?]Coding Genes, and Cellular Complexity 81

6.3 How Many Moonlighting Proteins Exist/What Proportion of the Proteome Moonlights? 83

6.4 Secretion of Moonlighting Proteins: A Major Problem Seeking Solution 86

6.5 How Does Protein Moonlighting Influence Systems Biology? 90

6.5.1 Systems Biology and Protein Moonlighting 91

6.5.2 Analysis of the Systems Biology of the Moonlighting Protein Glycerol Kinase 95

6.6 Role of Moonlighting Proteins in the Control of the Biology of the Healthy Cell 97

6.6.1 Do Moonlighting Protein Exhibit Novel Biological Functions? 97

6.6.2 Moonlighting Proteins and Normal Cellular Functions 104

6.6.2.1 Secreted Moonlighting Proteins 105

6.6.2.2 Moonlighting Proteins on the Plasma Membrane 106

6.6.2.3 Moonlighting Proteins in the Nucleus or Interacting with Nucleic Acids 110

6.6.2.4 Moonlighting Proteins in Cellular Vesicular Trafficking 113

6.6.2.5 Moonlighting in the Cell Cytoplasm 113

6.6.2.6 Ribosomal Moonlighting Proteins 115

6.6.2.7 Moonlighting in Cell Division 118

6.6.2.8 Moonlighting Proteins Existing in Multiple Cellular Compartments 118

6.7 Moonlighting Proteins in the Biology of Single?]Celled Eukaryotes 119

6.8 Moonlighting Proteins Interacting with Moonlighting Proteins 119

6.9 Moonlighting Proteins and Vision: Are ...