Literature DB >> 19647434

Navigating the ribosome's metastable energy landscape.

James B Munro1, Kevin Y Sanbonmatsu, Christian M T Spahn, Scott C Blanchard.   

Abstract

The molecular mechanisms by which tRNA molecules enter and transit the ribosome during mRNA translation remains elusive. However, recent genetic, biochemical and structural studies offer important new findings into the ordered sequence of events underpinning the translocation process that help place the molecular mechanism within reach. In particular, new structural and kinetic insights have been obtained regarding tRNA movements through 'hybrid state' configurations. These dynamic views reveal that the macromolecular ribosome particle, like many smaller proteins, has an intrinsic capacity to reversibly sample an ensemble of similarly stable native states. Such perspectives suggest that substrates, factors and environmental cues contribute to translation regulation by helping the dynamic system navigate through a highly complex and metastable energy landscape.

Entities:  

Mesh:

Substances:

Year:  2009        PMID: 19647434      PMCID: PMC2914510          DOI: 10.1016/j.tibs.2009.04.004

Source DB:  PubMed          Journal:  Trends Biochem Sci        ISSN: 0968-0004            Impact factor:   13.807


  83 in total

1.  Simultaneous, coincident optical trapping and single-molecule fluorescence.

Authors:  Matthew J Lang; Polly M Fordyce; Anita M Engh; Keir C Neuman; Steven M Block
Journal:  Nat Methods       Date:  2004-10-21       Impact factor: 28.547

Review 2.  Regulation of translation via mRNA structure in prokaryotes and eukaryotes.

Authors:  Marilyn Kozak
Journal:  Gene       Date:  2005-10-05       Impact factor: 3.688

Review 3.  Translation initiation: structures, mechanisms and evolution.

Authors:  Assen Marintchev; Gerhard Wagner
Journal:  Q Rev Biophys       Date:  2004 Aug-Nov       Impact factor: 5.318

4.  Sequence of steps in ribosome recycling as defined by kinetic analysis.

Authors:  Frank Peske; Marina V Rodnina; Wolfgang Wintermeyer
Journal:  Mol Cell       Date:  2005-05-13       Impact factor: 17.970

Review 5.  Structural insights into translational fidelity.

Authors:  James M Ogle; V Ramakrishnan
Journal:  Annu Rev Biochem       Date:  2005       Impact factor: 23.643

6.  Arrangement of tRNAs in pre- and posttranslocational ribosomes revealed by electron cryomicroscopy.

Authors:  H Stark; E V Orlova; J Rinke-Appel; N Jünke; F Mueller; M Rodnina; W Wintermeyer; R Brimacombe; M van Heel
Journal:  Cell       Date:  1997-01-10       Impact factor: 41.582

7.  Contribution of 16S rRNA nucleotides forming the 30S subunit A and P sites to translation in Escherichia coli.

Authors:  Nimo M Abdi; Kurt Fredrick
Journal:  RNA       Date:  2005-09-21       Impact factor: 4.942

8.  A base pair between tRNA and 23S rRNA in the peptidyl transferase centre of the ribosome.

Authors:  R R Samaha; R Green; H F Noller
Journal:  Nature       Date:  1995-09-28       Impact factor: 49.962

9.  Effect of buffer conditions on the position of tRNA on the 70 S ribosome as visualized by cryoelectron microscopy.

Authors:  R K Agrawal; P Penczek; R A Grassucci; N Burkhardt; K H Nierhaus; J Frank
Journal:  J Biol Chem       Date:  1999-03-26       Impact factor: 5.157

10.  Deacylated tRNA is released from the E site upon A site occupation but before GTP is hydrolyzed by EF-Tu.

Authors:  George Dinos; Dimitrios L Kalpaxis; Daniel N Wilson; Knud H Nierhaus
Journal:  Nucleic Acids Res       Date:  2005-09-15       Impact factor: 16.971

View more
  73 in total

1.  Insights into the molecular determinants of EF-G catalyzed translocation.

Authors:  Leyi Wang; Roger B Altman; Scott C Blanchard
Journal:  RNA       Date:  2011-10-27       Impact factor: 4.942

2.  Crystal structure of release factor RF3 trapped in the GTP state on a rotated conformation of the ribosome.

Authors:  Jie Zhou; Laura Lancaster; Sergei Trakhanov; Harry F Noller
Journal:  RNA       Date:  2011-12-20       Impact factor: 4.942

3.  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

4.  Structural insights into initial and intermediate steps of the ribosome-recycling process.

Authors:  Takeshi Yokoyama; Tanvir R Shaikh; Nobuhiro Iwakura; Hideko Kaji; Akira Kaji; Rajendra K Agrawal
Journal:  EMBO J       Date:  2012-03-02       Impact factor: 11.598

5.  Structural characterization of mRNA-tRNA translocation intermediates.

Authors:  Xabier Agirrezabala; Hstau Y Liao; Eduard Schreiner; Jie Fu; Rodrigo F Ortiz-Meoz; Klaus Schulten; Rachel Green; Joachim Frank
Journal:  Proc Natl Acad Sci U S A       Date:  2012-03-30       Impact factor: 11.205

Review 6.  Origin and evolution of the ribosome.

Authors:  George E Fox
Journal:  Cold Spring Harb Perspect Biol       Date:  2010-06-09       Impact factor: 10.005

7.  Single-molecule study of ribosome hierarchic dynamics at the peptidyl transferase center.

Authors:  Mediha Esra Altuntop; Cindy Tu Ly; Yuhong Wang
Journal:  Biophys J       Date:  2010-11-03       Impact factor: 4.033

8.  The Ribosome Comes Alive.

Authors:  Joachim Frank
Journal:  Isr J Chem       Date:  2010-06-18       Impact factor: 3.333

Review 9.  EF-G and EF4: translocation and back-translocation on the bacterial ribosome.

Authors:  Hiroshi Yamamoto; Yan Qin; John Achenbach; Chengmin Li; Jaroslaw Kijek; Christian M T Spahn; Knud H Nierhaus
Journal:  Nat Rev Microbiol       Date:  2013-12-23       Impact factor: 60.633

10.  Allosteric control of the ribosome by small-molecule antibiotics.

Authors:  Leyi Wang; Arto Pulk; Michael R Wasserman; Michael B Feldman; Roger B Altman; Jamie H Doudna Cate; Scott C Blanchard
Journal:  Nat Struct Mol Biol       Date:  2012-08-19       Impact factor: 15.369

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.