Structural Aspects of Protein Synthesis

by Liljas, Anders

• ISBN13: 9789812388636
• ISBN10: 981238863X
• Edition: 1st
• Format: Hardcover
• Copyright: 2004-11-01
• Publisher: WORLD SCIENTIFIC PUB CO INC

Summary

- Summarizes the basic insights into ribosome structure and function- Highly illustrated with simplified drawings and color plates to present all the major steps of protein synthesis- Includes an extensive and up-to-date list of references

Table of Contents

Preface	vii
List of Abbreviations	xv
1 The Basics of Translation	1	(4)
2 Historical Milestones	5	(7)
3 Methods to Study Structure	12	(9)
3.1 Low resolution methods	13	(4)
Assembly	13	(1)
Surface accessibility to enzymes and chemical modifications	13	(1)
Proximity information by chemical and spectroscopic methods	14	(1)
Electron microscopy	15	(1)
Neutron scattering	16	(1)
Tritium bombardment	17	(1)
Mass spectrometry	17	(1)
3.2 High resolution methods	17	(4)
Nuclear magnetic resonance	17	(1)
X-ray diffraction	18	(3)
4 The Message - mRNA	21	(6)
4.1 The genetic code	21	(2)
4.2 Transcription	23	(1)
4.3 Processing of the transcribed RNA	23	(1)
4.4 Reading frame and usage of the genetic code	24	(3)
5 The Adaptor - tRNA	27	(11)
5.1 Structure	27	(3)
5.2 tRNA conformations when bound to the ribosome	30	(1)
5.3 Synthesis	31	(1)
5.4 Codon-anticodon relationships	32	(1)
5.5 Charging - the tRNA synthetases	32	(6)
Classes and subclasses	33	(2)
Amino acid recognition: not a simple matter	35	(1)
Deviations	36	(1)
Editing	37	(1)
6 The Workbench - Ribosomes	38	(9)
6.1 The composition of ribosomes	38	(1)
6.2 rRNA	39	(3)
6.3 Ribosomal proteins	42	(4)
The identification and number of ribosomal proteins	42	(4)
Copy number of ribosomal proteins	46	(1)
6.4 The assembly of ribosomes	46	(1)
7 The Structure of the Ribosome	47	(28)
7.1 Early studies of the structure of ribosomal subunits and ribosomes	47	(2)
7.2 Crystal structures of ribosomes	49	(7)
Some steps in the history of ribosome crystallography	49	(2)
The small subunit	51	(1)
The large subunit	52	(2)
The 70's ribosome	54	(1)
The inter-subunit bridges	54	(2)
7.3 The structures of the ribosomal RNA molecules	56	(2)
7.4 The structures of ribosomal proteins	58	(17)
Relationships between ribosomal proteins	59	(2)
Protein-RNA interactions	61	(2)
Some specific proteins	63	(13)
S1	63	(1)
S12	64	(1)
L1	65	(1)
L10	65	(1)
L12	66	(4)
The P proteins	70	(2)
L22	72	(1)
L25-CTC	72	(3)
8 Ribosomal Sites and Ribosomal States	75	(24)
8.1 The binding of mRNA	76	(2)
The recognition of mRNA	76	(1)
The binding site for mRNA - the decoding site	76	(2)
8.2 The tRNA binding sites	78	(8)
The T-site	80	(2)
The A-site	82	(1)
A tRNA bound to the A-States	83	(1)
The P-site	83	(1)
The E-site	84	(1)
Hybrid tRNA sites	85	(1)
8.3 The peptidyl transfer center (PTC)	86	(2)
8.4 The polypeptide exit tunnel	88	(3)
8.5 The GTPase binding site	91	(2)
8.6 The ribosomal states	93	(6)
Free subunits and translating ribosomes, initiation	93	(1)
The pre- and post-translocation states	94	(1)
The locked and unlocked states	95	(1)
The restrictive and ram states	96	(3)
9 The Catalysts - Translation Factors	99	(60)
9.1 The GTPases	100	(13)
The consensus elements. Nucleotide and Mg²+ binding	105	(2)
Ribosome binding	107	(1)
Which tGTPase should bind?	107	(1)
The induction of GTP hydrolysis - the ribosomal GAP	108	(2)
GTP hydrolysis by tGTPases	110	(2)
Nucleotide exchange	112	(1)
9.2 Initiation factors	113	(6)
IF1	114	(1)
IF2	114	(3)
IF3	117	(2)
Additional initiation factors	119	(1)
9.3 Elongation factors	119	(24)
EF-Tu	119	(9)
Structure	121	(1)
Ternary complexes	122	(1)
Antibiotics targetting EF-Tu	123	(1)
Binding of EF-Tu to the ribosome	124	(2)
GTP hydrolysis by EF-Tu	126	(2)
EF-Ts	128	(2)
SelB	130	(3)
EF-G	133	(18)
Release of inorganic phosphate, Pi	134	(1)
Antibiotics targetting EF-G and EF2	134	(1)
Structure	135	(4)
EF-G bound to the ribosome	139	(2)
GTP hydrolysis and translocation	141	(1)
EF-G mutants	142	(1)
9.4 Release factors	143	(2)
9.5 Ribosome recycling factor (RRF)	145	(2)
9.6 tRNA mimicry	147	(2)
9.7 Additional ribosome-binding GTPases	149	(2)
9.8 Ribosome rescue factors	151	(10)
Tet(O)/Tet(M)	151	(1)
Stringent response	152	(3)
RelBE	155	(1)
tmRNA	155	(1)
Ribosome Modulation Factor RMF	156	(1)
Proteins that respond to temperature stress	157	(4)
Protein Y - pY - RaiA	157	(1)
RbfA	157	(1)
CsdA	158	(1)
10 Inhibitors of Protein Synthesis, Antibiotics, Resistance	159	(16)
10.1 Inhibitors of initiation	161	(1)
Edeine (Ede)	162	(1)
10.2 Interference with decoding. Distortion of fidelity	162	(2)
Streptomycin (Str)	163	(1)
Paramomycin	164	(1)
10.3 Inhibitors of Aminoacyl-tRNA Binding	164	(1)
Tetracycline	164	(1)
10.4 Inhibitors of peptidyl transfer	165	(3)
Puromycin (pur)	166	(1)
Anisomycin	166	(1)
Blasticidin S	167	(1)
Chloramphenicol	167	(1)
Sparsomycin	167	(1)
Virginamycin M	167	(1)
10.5 Inhibitors of the exit tunnel - the macrolides	168	(3)
16-membered lactone rings	169	(1)
15-membered lactone rings	170	(1)
14-membered lactone rings	170	(1)
Macrolide resistance	170	(1)
10.6 Inhibitors of translocation	171	(1)
Hygromycin B (HygB)	171	(1)
Pactamycin (Ptc)	171	(1)
Spectinomycin	172	(1)
10.7 Inhibitors of translation factors	172	(3)
Thiostrepton	172	(1)
Inhibitors binding to EF-Tu	173	(1)
Inhibitors binding to EF-G and EF2	173	(2)
11 The Process - Translation	175	(33)
11.1 The dynamics of translation and the ribosome	175	(1)
11.2 Central assays	176	(1)
11.3 Initiation	177	(4)
11.4 Elongation	181	(23)
Binding of aminoacyl-RNA - decoding	182	(7)
Fidelity related states of the small subunit	182	(1)
The mechanism for decoding	183	(1)
Initial recognition	184	(2)
GTP hydrolysis	186	(2)
Proofreading	188	(1)
Peptidyl transfer	189	(3)
The acceptor ends and hybrid states	192	(3)
The main steps during aminoacyl-tRNA binding and peptidyl transfer	195	(1)
Translocation	195	(3)
Is translocation a spontaneous process inherent in the ribosome?	195	(3)
EF-G catalyzed translocation	198	(4)
Pie relationship between EF-Tu and EF-G	202	(2)
11.5 termination	204	(2)
11.6 Ribosome recycling	206	(2)
12 Protein Folding and Targeting	208	(8)
12.1 Folding of the nascent chain	208	(3)
Trigger factor	209	(1)
DnaK	210	(1)
12.2 Transport of the product	211	(5)
13 Evolution of the Translation Apparatus	216	(7)
13.1 Evolution of codons, tRNAs and tRNA synthetases	217	(1)
13.2 Evolutionary relationship between tRNAs and ribosomal RNAs	218	(1)
13.3 Evolutionary relationship of ribosomal proteins	219	(2)
13.4 The RNA world	221	(2)
Appendix I	223	(6)
Appendix II	229	(2)
References	231	(50)
Index	281