Literature DB >> 19223173

Single-molecule observations of ribosome function.

Scott C Blanchard1.   

Abstract

Single-molecule investigations promise to greatly advance our understanding of basic and regulated ribosome functions during the process of translation. Here, recent progress towards directly imaging the elemental translation elongation steps using fluorescence resonance energy transfer (FRET)-based imaging methods is discussed, which provide striking evidence of the highly dynamic nature of the ribosome. In this view, global rates and fidelities of protein synthesis reactions may be regulated by interactions of the ribosome with mRNA, tRNA, translation factors and potentially many other cellular ligands that modify intrinsic conformational equilibria in the translating particle. Future investigations probing this model must aim to visualize translation processes from multiple structural and kinetic perspectives simultaneously, to provide direct correlations between factor binding and conformational events.

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Year:  2009        PMID: 19223173      PMCID: PMC2673810          DOI: 10.1016/j.sbi.2009.01.002

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


  50 in total

1.  Locking and unlocking of ribosomal motions.

Authors:  Mikel Valle; Andrey Zavialov; Jayati Sengupta; Urmila Rawat; Måns Ehrenberg; Joachim Frank
Journal:  Cell       Date:  2003-07-11       Impact factor: 41.582

2.  Conformational heterogeneity in RNA polymerase observed by single-pair FRET microscopy.

Authors:  Oana Coban; Don C Lamb; Evgeny Zaychikov; Hermann Heumann; G Ulrich Nienhaus
Journal:  Biophys J       Date:  2006-03-31       Impact factor: 4.033

Review 3.  A structural understanding of the dynamic ribosome machine.

Authors:  Thomas A Steitz
Journal:  Nat Rev Mol Cell Biol       Date:  2008-03       Impact factor: 94.444

4.  Dissecting the multistep reaction pathway of an RNA enzyme by single-molecule kinetic "fingerprinting".

Authors:  Shixin Liu; Gregory Bokinsky; Nils G Walter; Xiaowei Zhuang
Journal:  Proc Natl Acad Sci U S A       Date:  2007-05-11       Impact factor: 11.205

Review 5.  Advances in single-molecule fluorescence methods for molecular biology.

Authors:  Chirlmin Joo; Hamza Balci; Yuji Ishitsuka; Chittanon Buranachai; Taekjip Ha
Journal:  Annu Rev Biochem       Date:  2008       Impact factor: 23.643

Review 6.  A practical guide to single-molecule FRET.

Authors:  Rahul Roy; Sungchul Hohng; Taekjip Ha
Journal:  Nat Methods       Date:  2008-06       Impact factor: 28.547

Review 7.  Translation at the single-molecule level.

Authors:  R Andrew Marshall; Colin Echeverría Aitken; Magdalena Dorywalska; Joseph D Puglisi
Journal:  Annu Rev Biochem       Date:  2008       Impact factor: 23.643

8.  Coupling of ribosomal L1 stalk and tRNA dynamics during translation elongation.

Authors:  Jingyi Fei; Pallav Kosuri; Daniel D MacDougall; Ruben L Gonzalez
Journal:  Mol Cell       Date:  2008-05-09       Impact factor: 17.970

9.  Single-molecule experiments in biological physics: methods and applications.

Authors:  F Ritort
Journal:  J Phys Condens Matter       Date:  2006-07-25       Impact factor: 2.333

Review 10.  A new view of protein synthesis: mapping the free energy landscape of the ribosome using single-molecule FRET.

Authors:  James B Munro; Andrea Vaiana; Kevin Y Sanbonmatsu; Scott C Blanchard
Journal:  Biopolymers       Date:  2008-07       Impact factor: 2.505

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  38 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.  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

3.  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

4.  Integrating molecular dynamics simulations with chemical probing experiments using SHAPE-FIT.

Authors:  Serdal Kirmizialtin; Scott P Hennelly; Alexander Schug; Jose N Onuchic; Karissa Y Sanbonmatsu
Journal:  Methods Enzymol       Date:  2015-02-07       Impact factor: 1.600

5.  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 6.  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

Review 7.  Biological mechanisms, one molecule at a time.

Authors:  Ignacio Tinoco; Ruben L Gonzalez
Journal:  Genes Dev       Date:  2011-06-15       Impact factor: 11.361

8.  Cryoelectron microscopy structures of the ribosome complex in intermediate states during tRNA translocation.

Authors:  Jie Fu; James B Munro; Scott C Blanchard; Joachim Frank
Journal:  Proc Natl Acad Sci U S A       Date:  2011-03-07       Impact factor: 11.205

9.  Conformational flexibility of viral RNA switches studied by FRET.

Authors:  Mark A Boerneke; Thomas Hermann
Journal:  Methods       Date:  2015-09-14       Impact factor: 3.608

10.  Comparative proteomic analysis of silkworm fat body after knocking out fibroin heavy chain gene: a novel insight into cross-talk between tissues.

Authors:  Quanmei Chen; Zhengang Ma; Xin Wang; Zhiqing Li; Yan Zhang; Sanyuan Ma; Ping Zhao; Qingyou Xia
Journal:  Funct Integr Genomics       Date:  2015-08-18       Impact factor: 3.410

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