About the 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.
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. A. Simonetti, S. Marzi, A. Myasnikov, J-F. Menetret, and B. 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 2.- 12. 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, andRachel 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-EM.- 32. 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 asa new tool to study the evolution of ribosomal RNA.
