Table of Contents
Preface vii
Chapter 1 The Basics of Translation 1
Chapter 2 Historical Milestones 5
Chapter 3 Methods of Studying Structure 15
3.1 Low-Resolution Methods 16
3.2 High-Resolution Methods 23
3.3 Computational Methods 29
Chapter 4 The Message - mRNA 33
4.1 The Genetic Code 33
4.2 Transcription 35
4.3 Processing of the Transcribed RNA 36
4.4 Translational Regulation, Reading Frame and Usage of the Genetic Code 37
Chapter 5 The Adaptor-tRNA 41
5.1 ThetRNAs 42
5.2 tRNA Structures 42
5.3 Charging - the tRNA Synthetases 46
5.4 Recognition of Amino Acids and tRNAs by Anrinoacyl-tRNA Synthetases 50
5.5 Deviations 58
Chapter 6 The Workbench - Ribosomes 61
6.1 The Composition of Ribosomes 61
6.2 rRNA 62
6.3 Ribosomal Proteins 66
6.4 The Assembly of Ribosomes 69
Chapter 7 The Structure of the Ribosome 71
7.1 Early Studies of the Structure of Ribosomal Subunits and Ribosomes 71
7.2 Crystal Structures of Ribosomes 74
7.3 The Inter-Subunit Bridges 81
7.4 The Structures of the Ribosomal RNA Molecules 86
7.5 The Structures of Ribosomal Proteins 87
7.6 The Structures of Eukaryotic and Mitochondrial Ribosomes 112
Chapter 8 Ribosomal Sites and Ribosomal States 115
8.1 The Binding of mRNA 116
8.2 The tRNA Binding Sites 120
8.3 The Peptidyl Transfer Center 131
8.4 The Polypeptide Exit Tunnel 134
8.5 The GTPase Binding Site 136
8.6 The Ribosomal States 138
Color Plates P1
Chapter 9 The Catalysts - Translation Factors 149
9.1 The trGTPases 151
9.2 Initiation Factors 168
9.3 Elongation Factors 178
9.4 Release Factors 207
9.5 Ribosome-Recycling Factor 211
9.6 tRNA Mimicry 212
9.7 Ribosome Rescue Factors/Ribosomal Protection Proteins 214
Chapter 10 Inhibitors of Protein Synthesis - Antibiotics, Resistance 229
10.1 Inhibitors of Initiation 230
10.2 Inhibitors of Ammoacyl-tRNA Binding 237
10.3 Interference with Decoding; Distortion of Fidelity 238
10.4 Inhibitors of Peptidyl Transfer 242
10.5 Inhibitors of the Exit Tunnel 247
10.6 Inhibitors of Translocation 252
10.7 Inhibitors of Translation Factors 255
Chapter 11 The Process -Translation 261
11.1 The Dynamics of Translation and the Ribosome 261
11.2 Central Assays 262
11.3 Initiation 263
11.4 Elongation 267
11.5 Termination 292
11.6 Ribosome Recycling 299
Chapter 12 Protein Processing, Folding and Targeting 303
12.1 Processing of the Nascent Peptide 303
12.2 Folding of the Nascent Chain 304
12.3 Transport of the Nascent Polypeptide 310
Chapter 13 Evolution of the Translation Apparatus 319
13.1 Evolution of the Genetic Code, tRNAs and tRNA Synthetases 321
13.2 The Evolution of Ribosomal RNAs 324
13.3 Evolution of Proteins in Translation 328
13.4 The RNA World or RNA-Dominated World 331
Appendix I 333
Appendix II 339
References 347
Index 431
