Literature DB >> 21256733

Dynamics of the translational machinery.

Alexey Petrov1, Guy Kornberg, Seán O'Leary, Albert Tsai, Sotaro Uemura, Joseph D Puglisi.   

Abstract

The recent growth in single molecule studies of translation has provided an insight into the molecular mechanism of ribosomal function. Single molecule fluorescence approaches allowed direct observation of the structural rearrangements occurring during translation and revealed dynamic motions of the ribosome and its ligands. These studies demonstrated how ligand binding affects dynamics of the ribosome, and the role of the conformational sampling in large-scale rearrangements intrinsic to translation elongation. The application of time-resolved cryo-electron microscopy revealed new conformational intermediates during back-translocation providing an insight into ribosomal dynamics from an alternative perspective. Recent developments permitted examination of conformational and compositional dynamics of the ribosome in real-time through multiple cycles of elongation at the single molecule level. The zero-mode waveguide approach allowed direct observation of the compositional dynamics of tRNA occupancy on the elongating ribosome. The emergence of single molecule in vivo techniques provided insights into the mechanism and regulation of translation at the organismal level.
Copyright © 2010 Elsevier Ltd. All rights reserved.

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Year:  2011        PMID: 21256733      PMCID: PMC3826783          DOI: 10.1016/j.sbi.2010.11.007

Source DB:  PubMed          Journal:  Curr Opin Struct Biol        ISSN: 0959-440X            Impact factor:   6.809


  47 in total

1.  Ribosome dynamics and tRNA movement by time-resolved electron cryomicroscopy.

Authors:  Niels Fischer; Andrey L Konevega; Wolfgang Wintermeyer; Marina V Rodnina; Holger Stark
Journal:  Nature       Date:  2010-07-15       Impact factor: 49.962

2.  Accommodation of aminoacyl-tRNA into the ribosome involves reversible excursions along multiple pathways.

Authors:  Paul C Whitford; Peter Geggier; Roger B Altman; Scott C Blanchard; José N Onuchic; Karissa Y Sanbonmatsu
Journal:  RNA       Date:  2010-04-28       Impact factor: 4.942

3.  Conformational sampling of aminoacyl-tRNA during selection on the bacterial ribosome.

Authors:  Peter Geggier; Richa Dave; Michael B Feldman; Daniel S Terry; Roger B Altman; James B Munro; Scott C Blanchard
Journal:  J Mol Biol       Date:  2010-04-29       Impact factor: 5.469

4.  Visualizing ribosome biogenesis: parallel assembly pathways for the 30S subunit.

Authors:  Anke M Mulder; Craig Yoshioka; Andrea H Beck; Anne E Bunner; Ronald A Milligan; Clinton S Potter; Bridget Carragher; James R Williamson
Journal:  Science       Date:  2010-10-29       Impact factor: 47.728

5.  A fast dynamic mode of the EF-G-bound ribosome.

Authors:  James B Munro; Roger B Altman; Chang-Shung Tung; Kevin Y Sanbonmatsu; Scott C Blanchard
Journal:  EMBO J       Date:  2009-12-24       Impact factor: 11.598

6.  Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells.

Authors:  Yuichi Taniguchi; Paul J Choi; Gene-Wei Li; Huiyi Chen; Mohan Babu; Jeremy Hearn; Andrew Emili; X Sunney Xie
Journal:  Science       Date:  2010-07-30       Impact factor: 47.728

7.  Site-specific labeling of Saccharomyces cerevisiae ribosomes for single-molecule manipulations.

Authors:  Alexey Petrov; Joseph D Puglisi
Journal:  Nucleic Acids Res       Date:  2010-05-25       Impact factor: 16.971

8.  The mechanism for activation of GTP hydrolysis on the ribosome.

Authors:  Rebecca M Voorhees; T Martin Schmeing; Ann C Kelley; V Ramakrishnan
Journal:  Science       Date:  2010-11-05       Impact factor: 47.728

9.  Following the intersubunit conformation of the ribosome during translation in real time.

Authors:  Colin Echeverría Aitken; Joseph D Puglisi
Journal:  Nat Struct Mol Biol       Date:  2010-06-20       Impact factor: 15.369

10.  Real-time tRNA transit on single translating ribosomes at codon resolution.

Authors:  Sotaro Uemura; Colin Echeverría Aitken; Jonas Korlach; Benjamin A Flusberg; Stephen W Turner; Joseph D Puglisi
Journal:  Nature       Date:  2010-04-15       Impact factor: 49.962

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  29 in total

1.  Excited states of ribosome translocation revealed through integrative molecular modeling.

Authors:  Paul C Whitford; Aqeel Ahmed; Yanan Yu; Scott P Hennelly; Florence Tama; Christian M T Spahn; José N Onuchic; Karissa Y Sanbonmatsu
Journal:  Proc Natl Acad Sci U S A       Date:  2011-11-11       Impact factor: 11.205

2.  Simulating movement of tRNA through the ribosome during hybrid-state formation.

Authors:  Paul C Whitford; Karissa Y Sanbonmatsu
Journal:  J Chem Phys       Date:  2013-09-28       Impact factor: 3.488

Review 3.  Approaches for measuring the dynamics of RNA-protein interactions.

Authors:  Donny D Licatalosi; Xuan Ye; Eckhard Jankowsky
Journal:  Wiley Interdiscip Rev RNA       Date:  2019-08-20       Impact factor: 9.957

Review 4.  Probing the mechanisms of translation with force.

Authors:  Christian M Kaiser; Ignacio Tinoco
Journal:  Chem Rev       Date:  2014-01-09       Impact factor: 60.622

5.  Capturing transition paths and transition states for conformational rearrangements in the ribosome.

Authors:  Jeffrey K Noel; Jorge Chahine; Vitor B P Leite; Paul Charles Whitford
Journal:  Biophys J       Date:  2014-12-16       Impact factor: 4.033

6.  The ribosome's energy landscape: Recent insights from computation.

Authors:  Paul Charles Whitford
Journal:  Biophys Rev       Date:  2015-01-18

7.  Rotation of the head of the 30S ribosomal subunit during mRNA translocation.

Authors:  Zhuojun Guo; Harry F Noller
Journal:  Proc Natl Acad Sci U S A       Date:  2012-11-27       Impact factor: 11.205

8.  Model of ribosome translation and mRNA unwinding.

Authors:  Ping Xie
Journal:  Eur Biophys J       Date:  2012-12-25       Impact factor: 1.733

Review 9.  Studying genomic processes at the single-molecule level: introducing the tools and applications.

Authors:  David Dulin; Jan Lipfert; M Charl Moolman; Nynke H Dekker
Journal:  Nat Rev Genet       Date:  2012-10-30       Impact factor: 53.242

10.  Ribosome profiling reveals sequence-independent post-initiation pausing as a signature of translation.

Authors:  Yan Han; Xiangwei Gao; Botao Liu; Ji Wan; Xingqian Zhang; Shu-Bing Qian
Journal:  Cell Res       Date:  2014-06-06       Impact factor: 25.617

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