Ribosomes Structure, Function, and Dynamics (eBook)

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 insights2 Venki Ramakrishnan Structural studies on decoding, termination and translocation in the bacterial ribosome3 C. Axel Innis, Gregor Blaha, David Bulkley, and Thomas A. Steitz Structural studies of complexes of the 70S ribosome4 Lasse B. Jenner, Natalia Demeshkina, Gulnara Yusupova, and Marat Yusupov  Interaction of bacterial ribosomes with mRNA and tRNA as studied by X-ray crystallographic analysis5 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 function6 Jack A. Dunkle and Jamie H. D. Cate The packing of ribosomes in crystals and polysomes7 Adam Ben-Shem, Lasse B. Jenner, Gulnara Yusupova, and Marat Yusupov Crystal structure of the eukaryotic 80S ribosome8 Rajendra K. Agrawal, Manjuli R. Sharma, Aymen Yassin, and Linda L. Spremulli  Structure and function of organellar ribosomes9 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 architecture11 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 bias13 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 ribosome14 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 Tu16 Marina V. Rodnina Mechanisms of Decoding and Peptide Bond Formation17 Rodrigo F. Ortiz-Meoz, Shan L. He, Hani S. Zaher, and Rachel Green  Sense and nonsense recognition by the ribosome18 Magnus Johansson, Ka Weng Ieong, Michael Pavlov, and Måns Ehrenberg Rate and accuracy of ribosomal peptidyl transfer19 Aishwarya Devaraj, Sean P. McClory, Daoming Qin, Joshua M. Leisring, and Kurt Fredrick Mutations in 16S rRNA that decrease the fidelity of translation20 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 coin21 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 transfer23 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 ensembles25 Joachim Frank Ribosome dynamics: Progress in the characterization of mRNA-tRNA translocation by cryo-electron microscopy26 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 recycling27 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 Termination29 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 antibiotics31 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