The Ribosome Cold Spring Harbor Symposia on Quantitative Biology, Volume LXVI

• ISBN13: 9780879696191
• ISBN10: 0879696192
• Edition: 1st
• Format: Hardcover
• Copyright: 2002-05-10
• Publisher: Cold Spring Harbor Laboratory Press
• More Book Details
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Summary

This is the first book to contain the newly published findings on the structure of the ribosome and discuss their meaning for our understanding of how proteins are made and processed inside the cell. With over 60 contributions from the worlds most innovative ribosome biology laboratories, this is the latest volume in the annual series that for over 60 years has provided analysis and interpretation of the most interesting problems in biology.

Table of Contents

Symposium Participants	x
Foreword	xvii
Ribosome Structure
RNA Structure and the Roots of Protein Synthesis	1	(16)
A. Rich
Atomic Structures of the 30S Subunit and Its Complexes with Ligands and Antibiotics	17	(16)
D.E. Brodersen
A.P. Carter
W.M. Clemons Jr.
R.J. Morgan-Warren
F. V. Murphy IV
J.M. Ogle
M.J. Tarry
B.T. Wimberly
V. Ramakrishnan
Progress toward an Understanding of the Structure and Enzymatic Mechanism of the Large Ribosomal Subunit	33	(10)
J.L. Hansen
T.M. Schmeing
D.J. Klein
J.A. Ippolito
N Ban
P. Nissen
B. Freeborn. P.B. Moore
T.A. Steitz
High-resolution Structures of Ribosomal Subunits: Initiation, Inhibition, and Conformational Variability	43	(14)
A. Bashan
I. Agmon
R. Zarivach
F. Schluenzen
J. Harms
M. Pioletti
H. Bartels
M. Gluehmann
H. Hansen
T. Auerbach
R. Franceschi
A. Yonath
Structure of the Ribosome at 5.5 A Resolution and Its Interactions with Functional Ligands	57	(10)
H.F. Noller
M.M. Yusupov
G.Z. Yusupova
A. Baucom
K. Lieberman
L. Lancaster
A. Dollas
K. Fredrick T.N. Earnest
J.H.D. Cate
Ratchet-like Movements between the Two Ribosomal Subunits: Their Implications in Elongation Factor Recognition and tRNA Translocation	67	(10)
J. Frank
R.K. Agrawal
Do Single (Ribosome) Molecules Themselves?	77	(10)
M. van Heel
Ribosome Biochemistry
Correlating the X-ray Structures for Halo-and Thermophilic Ribosomal Subunits with Biochemical Data for the Escherichia Coli Ribosome	87	(14)
P. Sergiev
A. Leonov
S. Dokudovskaya
O. Shpanchenko
O. Dontsova
A. Bogdanov
J. Rinke-Appel
F. Mueller
M. Osswald
K. von Knobluch
R. Brimacombe
Probing Ribosome Structure, and Function by Mutagenesis	101	(8)
S.T. Gregory
M.A. Bayfield
M. O'Connor
J. Thompson
A.E. Dahlberg
Exploring the Mechanism of the Peptidyl Transfer Reaction by Chemical Footprinting	109	(10)
S.A. Strobel
G.W. Muth
L. Chen
Analysis of the Active Site of the Ribosome by Site-directed Mutagenesis	119	(8)
D.F. Kim
K. Semrad
R. Green
Codon Recognition and Decoding: The transorientation Hypothesis	127	(8)
A.B. Simonson
J.A. Lake
Features and Functions of the Ribosomal and E Site	135	(12)
G. Blaha
K.H. Nierhaus
Pseudouridines and Pseudouridine Synthases of the Ribosome	147	(14)
J. Ofengand
A. Malhotra
J. Remme
N.S. Gutgsell
M. Del Campo
S. Jean-Charles
L. Peil
Y. Kaya
The Genetic Code
Formation of Two Classes of tRNA Synthetases in Relation to Editing Functions and Genetic Code	161	(6)
P. Schimmel
L. Ribas de Pouplana
Structural Basis for Amino Acid and tRNA Recognition by Class I Aminoacyl-tRNA synthetases	167	(8)
O. Nureki
S. Fukai
S. Sekine
A. Shimada
T. Terada
T. Nakama
M. Shirouzu
D.G. Vassylyev
S. Yokoyama
Aminoacyl-tRNA Synthesis: A Postgenomic Perspective	175	(10)
C. Stathopoulos
I. Ahel
K. Ali
A. Ambrogelly
H. Becker
S. Bunjan
L. Feng
S. Herring
C. Jacquin-Becker
H. Kobayashi
D. Korencic
N. Mejlhede
B. Min
H. Nakamo
S. Namgoong
C. Polycarpo
G. Raczniak
J. Rinehart
G. Rosas-Sandoval
B. Ruan
J. Sabina. A. Sauerwald
H. Toogood
D. Tambula-Hansen
M. Ibba
D. Soll
tRNA Conformity	185	(10)
A.D. Wolfson
F.J. LaRiviere
J.A. Pleiss
T. Dale
H. Asahara
O.C. Uhlenbeck
Initiator tRNA and Its Role in Initiation of Protein Synthesis	195	(12)
C. Mayer
A. Stortchevoi
C. Kohrer
U. Varshney
U.G. RajBhandary
On Translation by RNAs Alone	207	(10)
M. Yarus
Frameshifting, Recoding, Shunting, IRES
Overriding Standard Decoding: Implications of Recoding for Ribosome Function and Enrichment of Gene Expression	217	(16)
J.F. Atkins
P. V. Baranov
O. Fayet
A.J. Herr
M.T. Howard
LP. Ivanov
S. Matsufuji
W.A. Miller
B. Moore
M.F. Prere
N.M. Wills. J. Zhou
R.F. Gesteland
Structure and Function of the Stimulatory RNAs Involved in Programmed Eukaryotic -1 Ribosomal Frameshifting	233	(16)
I. Brierley
S. Pennell
Programmed +1 Transtational Frameshifting in the Yeast Saccharomyces cerevisiae Results from Disruption of Translational Error Correction	249	(10)
G. Stahl
S. Ben Salem
Z. Li
G. McCarty
A. Raman
M. Shah
P.J. Farabaugh
Preferential Translation of Adenovirus mRNAs in Infected Cells	259	(10)
R. Cuesta
Q. Xi
R.J. Schneider
Shunting and Controlled Reinitiation: The Encounter of Cauliflower Mosaic Virus with the Translational Machinery	269	(8)
T. Hohn
H.-S. Park
O. Guerra-Peraza
L. Stavolone
M.M. Pooggin
K. Kobayashi
L.A. Ryabova
Mechanisms of Internal Ribosome Entry in Translation Initiation	277	(8)
J.S. Kieft
A. Grech
P. Adams
J.A. Doudna
Initiator Met-tRNA-independent Translation Mediated by an Internal Ribosome Entry Site Element in Cricket Paralysis Virus-like Insect Viruses	285	(8)
E. Jan
S.R. Thompson
J.E. Wilson
T.V. Pestova
C.U.T. Hellen
P. Sarnow
Messenger RNA and Translational Control
The mRNA Closed-loop Model: The Function of PABP and PABP-interacting Proteins in mRNA Translation	293	(8)
A. Kahvejian
G. Roy
N. Sonenberg
The mRNA Capping Apparatus as Drug Target and Guide to Eukaryotic Phylogeny	301	(12)
S. Shuman
Nonsense-mediated mRNA Decay: Insights into Mechanism from the Cellular Abundance of Human Upf1, Upf2, Upf3, and Upf3X Proteins	313	(8)
L.E. Maquat
G. Serin
Nonsense-mediated mRNA Decay in Saccharomyces cerevisiae: A Quality Control Mechanism That Degrades Transcripts Harboring Premature Termination Codons	321	(8)
C.I. Gonzalez
W. Wang
S. W. Peltz
Translational Control of 15-Lipoxygenase and msl-2 mRNAs: Single Regulators or Corepressor Assemblies?	329	(8)
F. Gebauer
D.H. Ostareck
A. Ostareck-Lederer
M. Grskovic
M. W. Hentze
PUF Proteins and 3'UTR Regulation in the Caenorhabditis elegans Germ Line	337	(8)
M. Wickens
D. Bernstein
S. Crittenden
C. Luitijens
J. Kimble
Translational Control of Embryonic Cell Division by CPEB and Maskin	345	(8)
I. Groisman
Y.-S. Huang
R. Mendez
Q. Cao
J.D. Richter
Small RNA Regulators of Translation: Mechanisms of Action and Approaches for Identifying New Small RNAs	353	(10)
S. Gottesman
G. Storz
C. Rosenow
N. Majdalani
F. Repoila
K.M. Wassarman
Initiation
Initiation Factors in the Early Events of mRNA Translation in Bacteria	363	(14)
C.O. Gualerzi
G. Brandi
E. Caserta
C. Garofalo
M. Lammi
A. La Teana
D. Petrelli
R. Spurio
J. Tomsic
C.L. Pon
The Translation of Capped mRNAs Has an Absolute Requirement for the Central Domain of eIF4G but Not for the Cap-binding Initiation Factor eIF4E	377	(12)
I.K. Ali
R.J. Jackson
Functions of Eukaryotic Factors in Initiation of Translation	389	(8)
T. V Pestova
C. U. T. Hellen
Interactions of the Eukaryotic Translation Initiation Factor eIF4E	397	(6)
J.D. Gross
K. Matsuo. M. Fletcher
A.B. Sachs
G. Wagner
A Multifactor Complex of eIF1, eIF2, eIF3, eIF5, and tRNAiMet Promotes Initiation Complex Assembly and Couples GTP Hydrolysis to AUG Recognition	403	(14)
K. Asano
L. Phan
L. Valasek
L.W. Schoenfeld
A. Shalev
J. Clayton
K. Nielsen
T.F. Donahue
A.G. Hinnebusch
Universal Translation Initiation Factor IF2/eIF5B	417	(8)
T.E. Dever
A. Roll-Mecak
S.K. Choi
J.H. Lee
C. Cao
B.-S. Shin
S.K. Burley
Elongation and Termination
Structural Studies of Eukaryotic Elongation Factors	425	(14)
G.R. Andersen
J. Nyborg
Translation Elongation Factor 1 Functions in the Yeast Saccharomyces cerevisiae	439	(10)
M. Anand
L. Valente
A. Carr-Schmid
R. Munshi
O. Olarewaju
P.A. Ortiz
T.G. Kinzy
Mechanism of Factor G Function in tRNA Translocation on the Ribosome	449	(10)
W. Wintermeyer
A. Savelsbergh
Y.P. Semenkov
V.l. Katunin
M.V. Rodnina
Modulation of Translation Termination Mechanisms by cis- and trans-Acting Factors	459	(10)
D.M. Janzen
A.P. Geballe
Protein tRNA Mimicry in Translation Termination	469	(8)
Y. Nakamura
M. Uno
T. Toyoda
T. Fujiwara
K. Ito
Regulation of Protein Synthesis
Mitogenic and Nutritional Signals are Transduced into Translational Efficiency of TOP mRNAs	477	(8)
E. Hornstein
H. Tang
O. Meyuhas
Double-stranded RNA-binding Proteins and the Control of Protein Synthesis and Cell Growth	485	(14)
L.M. Parker
I. Fierro-Monti
T. W. Reichman
S. Gunnery
M. B. Mathews
Translational Regulation in the Cellular Response to Biosynthetic Load on the Endoplasmic Reticulum	499	(10)
H.P. Harding
I. Novoa. A. Bertolotti
H. Zeng
F. Urano
C. Jousse
D. Ron
A Novel Stress-response Protein That Binds at the Ribosomal Subunit Interface and Arrests Translation	509	(6)
D.E. Agafonov
V.A. Kolb
A.S. Spirin
The Fourth Step of Protein Synthesis: Disassembly of the Posttermination Complex Is Catalyzed by Elongation Factor G and Ribosome Recycling Factor, a Near-perfect Mimic of tRNA	515	(16)
A. Kaji
M.C. Kiel
G. Hirokawa
A.R. Muto
Y. Inokuchi
H. Kaji
Structure, Function, and Regulation of Free and Membrane-bound Ribosome: The View from Their Substrates and Products	531	(12)
A.E. Johnson
J.-C. Chen
J.J. Flanagan
Y. Miao
Y. Shao
J. Lin
P.E. Bock
The Active 80S Ribosome-Sec61 Complex	543	(12)
R. Beckmann
C.M.T. Spahn
J. Frank
G. Blobel
Ribosome Biogenesis
Ribosomal RNA Genes, RNA Polymerases, Nucleolar Structures, and Synthesis of rRNA in the Yeast Saccharomyces cerevisiae	555	(12)
M. Nomura
Economics of Ribosome Biosynthesis	567	(8)
J.R. Warner
J. Vilardell
J.H. Sohn
Ribosome Biogenesis: Role of Small Nucleolar RNA in Maturation of Eukaryotic rRNA	575	(16)
S.A. Gerbi
A.V. Borovjagin
M. Ezrokhi
T.S. Lange
Thermodynamics and Kinetics of Central Domain Assembly	591	(8)
M.I. Recht
J.R. Williamson
Nuclear Export of the Large Ribosomal Subunit	599	(8)
A.W. Johnson
J.H.-N. Ho
G. Kallstrom
C. Trotta
E. Lund
L. Kahan
J. Dahlberg
J. Hedges
Summary: The Ribosome in the 21st Century: The Post-structural Era	607	(8)
P.B. Moore
Author Index	615	(2)
Subject Index	617