Description
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. Dr. Marina V. RodninaProf. Dr. Wolfgang WintermeyerMPI for Biophysical Chemistry, Dept. of Physical Biochemistry, Goettingen, GermanyDr. Rachel GreenDept. of Molecular Biology and Genetics, Investigator, Howard Hughes Medical Institute,Johns Hopkins University School of Medicine, Baltimore, MD, USA 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-Franois Menetret, and Bruno Klaholz Insights into translation initiation and termination complexes and into the polysome architecture 11 Michael Pavlov, Suparna Sanyal, and Mns 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 Echeverra 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 Mns 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, Dborah 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. Bttger 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 Vzquez-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
