This comprehensive and highly illustrated book provides a basic and up-to-date summary of translation on bacterial ribosomes, with emphasis on the structural insights. It is an attempt to present the ribosome and its functional activities in a coherent manner. Two types of illustrations are used to describe the translation field: simplified black-and-white illustrations to depict aspects of translation and color plates to give correct structural representations.
The book presents essentially all aspects of the translation system, focusing on the relation between structure and function. Upper level undergraduates and graduate students with an interest in protein synthesis will find this lecture notes volume invaluable. The book is also an essential source of information for researchers who want to get an overview of translation.
Author(s): Anders Liljas
Edition: 1
Publisher: World Scientific
Year: 2004
Language: English
Commentary: 1
Pages: 339
City: Singapore; Hackensack, NJ
Preface......Page 8
Contents......Page 10
List of Abbreviations......Page 16
1 The Basics of Translation......Page 18
2 Historical Milestones......Page 22
3 Methods to Study Structure......Page 29
Surface accessibility to enzymes and chemical modifications......Page 30
Proximity information by chemical and spectroscopic methods......Page 31
Electron microscopy......Page 32
Neutron scattering......Page 33
Nuclear magnetic resonance......Page 34
X-ray diffraction......Page 35
4.1 The genetic code......Page 38
4.3 Processing of the transcribed RNA......Page 40
4.4 Reading frame and usage of the genetic code......Page 41
5.1 Structure......Page 44
5.2 tRNA conformations when bound to the ribosome......Page 47
5.3 Synthesis......Page 48
5.5 Charging — the tRNA synthetases......Page 49
Classes and subclasses......Page 50
Amino acid recognition: not a simple matter......Page 52
Deviations......Page 53
Editing......Page 54
6.1 The composition of ribosomes......Page 55
6.2 rRNA......Page 56
The identification and number of ribosomal proteins......Page 59
6.4 The assembly of ribosomes......Page 63
7.1 Early studies of the structure of ribosomal subunits and ribosomes......Page 64
Some steps in the history of ribosome crystallography......Page 66
The small subunit......Page 68
The large subunit......Page 69
The inter-subunit bridges......Page 71
7.3 The structures of the ribosomal RNA molecules......Page 73
7.4 The structures of ribosomal proteins......Page 75
Relationships between ribosomal proteins......Page 76
Protein-RNA interactions......Page 78
S1......Page 80
S12......Page 81
L10......Page 82
L12......Page 83
The P proteins......Page 87
L25–CTC......Page 89
8 Ribosomal Sites and Ribosomal States......Page 92
The binding site for mRNA — the decoding site......Page 93
8.2 The tRNA binding sites......Page 95
The T-site......Page 97
The A-site......Page 99
The P-site......Page 100
The E-site......Page 101
Hybrid tRNA sites......Page 102
8.3 The peptidyl transfer center (PTC)......Page 103
8.4 The polypeptide exit tunnel......Page 105
8.5 The GTPase binding site......Page 108
Free subunits and translating ribosomes, initiation......Page 110
The pre- and post-translocation states......Page 111
The locked and unlocked states......Page 112
The restrictive and ram states......Page 113
Color Plates......Page 116
9 The Catalysts — Translation Factors......Page 148
9.1 The GTPases......Page 149
The consensus elements. Nucleotide and Mg2+ binding......Page 154
Which tGTPase should bind?......Page 156
The induction of GTP hydrolysis — the ribosomal GAP......Page 157
GTP hydrolysis by tGTPases......Page 159
Nucleotide exchange......Page 161
9.2 Initiation factors......Page 162
IF2......Page 163
IF3......Page 166
EF-Tu......Page 168
Structure......Page 170
Ternary complexes......Page 171
Antibiotics targetting EF-Tu......Page 172
Binding of EF-Tu to the ribosome......Page 173
GTP hydrolysis by EF-Tu......Page 175
EF-Ts......Page 177
SelB......Page 179
EF-G......Page 182
Antibiotics targetting EF-G and EF2......Page 183
Structure......Page 184
EF-G bound to the ribosome......Page 188
GTP hydrolysis and translocation......Page 190
EF-G mutants......Page 191
9.4 Release factors......Page 192
9.5 Ribosome recycling factor (RRF)......Page 194
9.6 tRNA mimicry......Page 196
9.7 Additional ribosome-binding GTPases......Page 198
Tet(O)/Tet(M)......Page 200
Stringent response......Page 201
tmRNA......Page 204
Ribosome Modulation Factor — RMF......Page 205
RbfA......Page 206
CsdA......Page 207
10 Inhibitors of Protein Synthesis, Antibiotics, Resistance......Page 208
10.1 Inhibitors of initiation......Page 210
10.2 Interference with decoding. Distortion of fidelity......Page 211
Streptomycin (Str)......Page 212
Tetracycline......Page 213
10.4 Inhibitors of peptidyl transfer......Page 214
Anisomycin......Page 215
Virginamycin M......Page 216
10.5 Inhibitors of the exit tunnel — the macrolides......Page 217
16-membered lactone rings......Page 218
Macrolide resistance......Page 219
Pactamycin (Ptc)......Page 220
Thiostrepton......Page 221
Inhibitors binding to EF-G and EF2......Page 222
11.1 The dynamics of translation and the ribosome......Page 224
11.2 Central assays......Page 225
11.3 Initiation......Page 226
11.4 Elongation......Page 230
Fidelity related states of the small subunit......Page 231
The mechanism for decoding......Page 232
Initial recognition......Page 233
GTP hydrolysis......Page 235
Proofreading......Page 237
Peptidyl transfer......Page 238
The acceptor ends and hybrid states......Page 241
Is translocation a spontaneous process inherent in the ribosome?......Page 244
EF-G catalyzed translocation......Page 247
The relationship between EF-Tu and EF-G......Page 251
11.5 Termination......Page 253
11.6 Ribosome recycling......Page 255
12.1 Folding of the nascent chain......Page 257
Trigger factor......Page 258
DnaK......Page 259
12.2 Transport of the product......Page 260
13 Evolution of the Translation Apparatus......Page 265
13.1 Evolution of codons, tRNAs and tRNA synthetases......Page 266
13.2 Evolutionary relationship between tRNAs and ribosomal RNAs......Page 267
13.3 Evolutionary relationship of ribosomal proteins......Page 268
13.4 The RNA world......Page 270
Appendix I......Page 271
Appendix II......Page 278
References......Page 280
Index......Page 330
