Literature DB >> 22798542

Single-molecule analysis of translational dynamics.

Alexey Petrov1, Jin Chen, Seán O'Leary, Albert Tsai, Joseph D Puglisi.   

Abstract

Decades of extensive biochemical and biophysical research have outlined the mechanism of translation. Rich structural studies have provided detailed snapshots of the translational machinery at all phases of the translation cycle. However, the relationship between structural dynamics, composition, and function remains unknown. The multistep nature of each stage of the translation cycle results in rapid desynchronization of individual ribosomes, thus hindering elucidation of the underlying mechanisms by conventional bulk biophysical and biochemical methods. Single-molecule approaches unsusceptible to these complications have led to the first glances at both compositional and conformational dynamics on the ribosome and their impact on translational control. These experiments provide the necessary link between static structure and mechanism, often providing new perspectives. Here we review recent advances in the field and their relationship to structural and biochemical data.

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Year:  2012        PMID: 22798542      PMCID: PMC3428772          DOI: 10.1101/cshperspect.a011551

Source DB:  PubMed          Journal:  Cold Spring Harb Perspect Biol        ISSN: 1943-0264            Impact factor:   10.005


  68 in total

1.  Allosteric vs. spontaneous exit-site (E-site) tRNA dissociation early in protein synthesis.

Authors:  Chunlai Chen; Benjamin Stevens; Jaskiran Kaur; Zeev Smilansky; Barry S Cooperman; Yale E Goldman
Journal:  Proc Natl Acad Sci U S A       Date:  2011-10-03       Impact factor: 11.205

2.  Multiple elements in the eIF4G1 N-terminus promote assembly of eIF4G1•PABP mRNPs in vivo.

Authors:  Eun-Hee Park; Sarah E Walker; Joseph M Lee; Stefan Rothenburg; Jon R Lorsch; Alan G Hinnebusch
Journal:  EMBO J       Date:  2010-12-07       Impact factor: 11.598

3.  mRNA helicase activity of the ribosome.

Authors:  Seyedtaghi Takyar; Robyn P Hickerson; Harry F Noller
Journal:  Cell       Date:  2005-01-14       Impact factor: 41.582

4.  Structures of the bacterial ribosome at 3.5 A resolution.

Authors:  Barbara S Schuwirth; Maria A Borovinskaya; Cathy W Hau; Wen Zhang; Antón Vila-Sanjurjo; James M Holton; Jamie H Doudna Cate
Journal:  Science       Date:  2005-11-04       Impact factor: 47.728

5.  Quantitative polysome analysis identifies limitations in bacterial cell-free protein synthesis.

Authors:  Kelly A Underwood; James R Swartz; Joseph D Puglisi
Journal:  Biotechnol Bioeng       Date:  2005-08-20       Impact factor: 4.530

6.  How initiation factors tune the rate of initiation of protein synthesis in bacteria.

Authors:  Ayman Antoun; Michael Y Pavlov; Martin Lovmar; Måns Ehrenberg
Journal:  EMBO J       Date:  2006-05-25       Impact factor: 11.598

7.  Translation initiation factor IF2 interacts with the 30 S ribosomal subunit via two separate binding sites.

Authors:  Enrico Caserta; Jerneja Tomsic; Roberto Spurio; Anna La Teana; Cynthia L Pon; Claudio O Gualerzi
Journal:  J Mol Biol       Date:  2006-07-27       Impact factor: 5.469

8.  Structures of the bacterial ribosome in classical and hybrid states of tRNA binding.

Authors:  Jack A Dunkle; Leyi Wang; Michael B Feldman; Arto Pulk; Vincent B Chen; Gary J Kapral; Jonas Noeske; Jane S Richardson; Scott C Blanchard; Jamie H Doudna Cate
Journal:  Science       Date:  2011-05-20       Impact factor: 47.728

9.  Transfer RNA-mediated regulation of ribosome dynamics during protein synthesis.

Authors:  Jingyi Fei; Arianne C Richard; Jonathan E Bronson; Ruben L Gonzalez
Journal:  Nat Struct Mol Biol       Date:  2011-08-21       Impact factor: 15.369

10.  The ribosome uses two active mechanisms to unwind messenger RNA during translation.

Authors:  Xiaohui Qu; Jin-Der Wen; Laura Lancaster; Harry F Noller; Carlos Bustamante; Ignacio Tinoco
Journal:  Nature       Date:  2011-07-06       Impact factor: 49.962

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  21 in total

1.  Synthetic biology: Ribosomal ties that bind.

Authors:  Joseph D Puglisi
Journal:  Nature       Date:  2015-07-29       Impact factor: 49.962

Review 2.  The bright future of single-molecule fluorescence imaging.

Authors:  Manuel F Juette; Daniel S Terry; Michael R Wasserman; Zhou Zhou; Roger B Altman; Qinsi Zheng; Scott C Blanchard
Journal:  Curr Opin Chem Biol       Date:  2014-06-21       Impact factor: 8.822

3.  Analysis of Translation Elongation Dynamics in the Context of an Escherichia coli Cell.

Authors:  Joana Pinto Vieira; Julien Racle; Vassily Hatzimanikatis
Journal:  Biophys J       Date:  2016-05-10       Impact factor: 4.033

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

Review 5.  Principles of translational control: an overview.

Authors:  John W B Hershey; Nahum Sonenberg; Michael B Mathews
Journal:  Cold Spring Harb Perspect Biol       Date:  2012-12-01       Impact factor: 10.005

6.  Bottom-up single-molecule strategy for understanding subunit function of tetrameric β-galactosidase.

Authors:  Xiang Li; Yu Jiang; Shaorong Chong; David R Walt
Journal:  Proc Natl Acad Sci U S A       Date:  2018-07-30       Impact factor: 11.205

7.  Multimodal Measurements of Single-Molecule Dynamics Using FluoRBT.

Authors:  Ivan E Ivanov; Paul Lebel; Florian C Oberstrass; Charles H Starr; Angelica C Parente; Athena Ierokomos; Zev Bryant
Journal:  Biophys J       Date:  2017-12-13       Impact factor: 4.033

Review 8.  Unraveling the dynamics of ribosome translocation.

Authors:  Jin Chen; Albert Tsai; Seán E O'Leary; Alexey Petrov; Joseph D Puglisi
Journal:  Curr Opin Struct Biol       Date:  2012-11-08       Impact factor: 6.809

9.  Real-Time Imaging of Translation on Single mRNA Transcripts in Live Cells.

Authors:  Chong Wang; Boran Han; Ruobo Zhou; Xiaowei Zhuang
Journal:  Cell       Date:  2016-05-05       Impact factor: 41.582

10.  New universal rules of eukaryotic translation initiation fidelity.

Authors:  Hadas Zur; Tamir Tuller
Journal:  PLoS Comput Biol       Date:  2013-07-11       Impact factor: 4.475

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