Ribosomes. Structure, Function, and Dynamics

About this book

The ribosome is a macromolecular machine that synthesizes proteins with a high degree of speed and accuracy. Our present understanding of its structure, function and dynamics is the result of six decades of research. This book collects over 40 articles based on the talks presented at the 2010 Ribosome Meeting, held in Orvieto, Italy, covering all facets of the structure and function of the ribosome. New high-resolution crystal structures of functional ribosome complexes and cryo-EM structures of translating ribosomes are presented, while partial reactions of translation are examined in structural and mechanistic detail, featuring translocation as a most dynamic process. Mechanisms of initiation, both in bacterial and eukaryotic systems, translation termination, and novel details of the functions of the respective factors are described. Structure and interactions of the nascent peptide within, and emerging from, the ribosomal peptide exit tunnel are addressed in several articles. Structural and single-molecule studies reveal a picture of the ribosome exhibiting the energy landscape of a processive Brownian machine. The collection provides up-to-date reviews which will serve as a source of essential information for years to come.

Content Level » Research

Related subjects » Biophysics & Biological Physics - Human Genetics

Table of contents

Section I: Ribosome structure

1 Anat Bashan and Ada Yonath
Ribosome crystallography: From early evolution to contemporary medical insights
2 Venki Ramakrishnan
Structural studies on decoding, termination and translocation in the bacterial ribosome
3 C. Axel Innis, Gregor Blaha, David Bulkley, and Thomas A. Steitz
Structural studies of complexes of the 70S ribosome
4 Lasse B. Jenner, Natalia Demeshkina, Gulnara Yusupova, and Marat Yusupov
Interaction of bacterial ribosomes with mRNA and tRNA as studied by X-ray crystallographic analysis
5 Steven T. Gregory, Hasan Demirci, Jennifer F. Carr, Riccardo Belardinelli, Jill R. Thompson, Dale Cameron, Daniel Rodriguez-Correa, Frank Murphy, Venki Ramakrishnan, Gerwald Jogl and Albert E. Dahlberg
Genetic and crystallographic approaches to investigating ribosome structure and function
6 Jack A. Dunkle and Jamie H. D. Cate
The packing of ribosomes in crystals and polysomes
7 Adam Ben-Shem, Lasse B. Jenner, Gulnara Yusupova, and Marat Yusupov
Crystal structure of the eukaryotic 80S ribosome
8 Rajendra K. Agrawal, Manjuli R. Sharma, Aymen Yassin, and Linda L. Spremulli
Structure and function of organellar ribosomes
9 Petr Sergiev, Anna Golovina, Irina Prokhorova, Olga Sergeeva, Ilya Osterman , Mikhail Nesterchuk, Dmitry Burakovsky, Alexey Bogdanov, and Olga Dontsova
Modifications of ribosomal RNA: From enzymes to function

Section II: Recruiting the ribosome for translation

10 Angelita Simonetti, Stefano Marzi, Alexander G. Myasnikov, Jean-François Menetret, and Bruno Klaholz
Insights into translation initiation and termination complexes and into the polysome architecture
11 Michael Pavlov, Suparna Sanyal, and Måns Ehrenberg
Initiation of bacterial protein synthesis with wild type and novel mutants of initiation factor 212 Claudio O. Gualerzi, Anna Maria Giuliodori, Anna Brandi, Fabio DI Pietro, Lolita Piersimoni, Attilio Fabbretti, and Cynthia L. Pon
Translation initiation at the root of the cold-shock translational bias
13 Sarah F. Mitchell, Sarah E. Walker, Vaishnavi Rajagopal, Colin Echeverría Aitken, and Jon R. Lorsch
Recruiting knotty partners: The roles of translation initiation factors in mRNA recruitment to the eukaryotic ribosome
14 Andrey V. Pisarev, Maxim A. Skabkin, Vera P. Pisareva, Olga V. Skabkina, Christopher U. T. Hellen, and Tatyana V. Pestova
The mechanism of ribosomal recycling in eukaryotes

Section III: Decoding, fidelity, and peptidyl transfer

15 Jared M. Schrader, Margaret E. Saks, and Olke C. Uhlenbeck
The specific interaction between aminoacyl-tRNAs and elongation factor Tu
16 Marina V. Rodnina
Mechanisms of Decoding and Peptide Bond Formation
17 Rodrigo F. Ortiz-Meoz, Shan L. He, Hani S. Zaher, and Rachel Green
Sense and nonsense recognition by the ribosome
18 Magnus Johansson, Ka Weng Ieong, Michael Pavlov, and Måns Ehrenberg
Rate and accuracy of ribosomal peptidyl transfer
19 Aishwarya Devaraj, Sean P. McClory, Daoming Qin, Joshua M. Leisring, and Kurt Fredrick
Mutations in 16S rRNA that decrease the fidelity of translation
20 Rashid Akbergenov, Dmitry Shcherbakov, Tanja Matt, Stefan Duscha, Martin Meyer, Déborah Perez Fernandez, Rashmi Pathak, Shinde Harish, Iwona Kudyba, Srinivas R. Dubbaka, Sandrina Silva, Maria del Carmen Ruiz Ruiz, Sumantha Salian, Andrea Vasella, and Erik C. Böttger
Decoding and deafness: Two sides of a coin
21 Biswajoy Roy-Chaudhuri, Narayanaswamy Kirthi, Teresa Kelley, and Gloria M. Culver
Ribosomal protein S5, ribosomal biogenesis and translational fidelity

Section IV: Elongation and ribosome dynamics
22 Daniel D. MacDougall and Ruben L. Gonzalez, Jr.
Exploring the structural dynamics of the translational machinery using single-molecule fluorescence resonance energy transfer
23 Sotaro Uemura and Joseph D. Puglisi
Real-time monitoring of single molecule translation
24 Paul C. Whitford, Roger B. Altman, Peter Geggier, Daniel S. Terry, James B. Munro, Jose' N. Onuchic, Christian M. T. Spahn, Karissa Y. Sanbonmatsu, and Scott C. Blanchard
Dynamic views of ribosome function: Energy landscapes and ensembles
25 Joachim Frank
Ribosome dynamics: Progress in the characterization of mRNA-tRNA translocation by cryo-electron microscopy
26 Wolfgang Wintermeyer, Andreas Savelsbergh, Andrey L. Konevega, Frank Peske, Vladimir I. Katunin, Yuri P. Semenkov, Niels Fischer, Holger Stark, and Marina V. Rodnina
Elongation factor G in translocation and ribosome recycling
27 Barry S. Cooperman, Yale E. Goldman, Chunlai Chen, Ian Farrell, Jaskarin Kaur, Hanqing Liu, Wie Liu, Gabriel Rosenblum, Zeev Smilansky, Benjamin Stevens, and Haibo Zhang
Mechanism and dynamics of the elongation cycle
28 Harry F. Noller, Dmitri N. Ermolenko, Andrei Kortostelev, Martin Laurberg, Jianyu Zhu, Haruichi Asahara, Laura Lancaster, Lucas Horan. Alexander Hirschi, John Paul Donahue, Sergei Trahanov, Clint Spiegel, Robyn Hickerson, Peter Cornish, and Taekjip Ha
Studies on the Mechanisms of Translocation and Termination
29 David Healey, Mickey Miller, Christopher Woolstenhulme, and Allen Buskirk
The mechanism by which tmRNA rescues stalled ribosomes

Section V: Nascent peptide and tunnel interactions

30 Nora Vázquez-Laslop, Haripriya Ramu, and Alexander Mankin
Nascent peptide-mediated ribosome stalling promoted by antibiotics
31 Daniel N. Wilson, Shashi Bhushan, Thomas Becker, and Roland Beckmann
Nascent polypeptide chains within the ribosomal tunnel analyzed by cryo-EM32 Daniel Boehringer and Nenad Ban
Mechanistic insight into co-translational protein processing, folding, targeting, and membrane insertion

Section VI: Evolution

33 Sergey V. Steinberg and Konstantin Bokov
Molecular palaeontology as a new tool to study the evolution of ribosomal RNA