Literature DB >> 28138066

The translation elongation cycle-capturing multiple states by cryo-electron microscopy.

Joachim Frank1,2,3.   

Abstract

During the work cycle of elongation, the ribosome, a molecular machine of vast complexity, exists in a large number of states distinguished by constellation of its subunits, its subunit domains and binding partners. Single-particle cryogenic electron microscopy (cryo-EM), developed over the past 40 years, is uniquely suited to determine the structure of molecular machines in their native states. With the emergence, 10 years ago, of unsupervised clustering techniques in the analysis of single-particle data, it has been possible to determine multiple structures from a sample containing ribosomes equilibrating in different thermally accessible states. In addition, recent advances in detector technology have made it possible to reach near-atomic resolution for some of these states. With these capabilities, single-particle cryo-EM has been at the forefront of exploring ribosome dynamics during its functional cycle, along with single-molecule fluorescence resonance energy transfer and molecular dynamics computations, offering insights into molecular architecture uniquely honed by evolution to capitalize on thermal energy in the ambient environment.This article is part of the themed issue 'Perspectives on the ribosome'.
© 2017 The Author(s).

Keywords:  free-energy landscape; mRNA–tRNA translocation; molecular machines; single-particle reconstruction

Mesh:

Year:  2017        PMID: 28138066      PMCID: PMC5311924          DOI: 10.1098/rstb.2016.0180

Source DB:  PubMed          Journal:  Philos Trans R Soc Lond B Biol Sci        ISSN: 0962-8436            Impact factor:   6.237


  99 in total

1.  The complete atomic structure of the large ribosomal subunit at 2.4 A resolution.

Authors:  N Ban; P Nissen; J Hansen; P B Moore; T A Steitz
Journal:  Science       Date:  2000-08-11       Impact factor: 47.728

2.  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

3.  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

4.  Visualization of elongation factor G on the Escherichia coli 70S ribosome: the mechanism of translocation.

Authors:  R K Agrawal; P Penczek; R A Grassucci; J Frank
Journal:  Proc Natl Acad Sci U S A       Date:  1998-05-26       Impact factor: 11.205

5.  Motif detection in quantum noise-limited electron micrographs by cross-correlation.

Authors:  W O Saxton; J Frank
Journal:  Ultramicroscopy       Date:  1977-04       Impact factor: 2.689

6.  Trajectories of the ribosome as a Brownian nanomachine.

Authors:  Ali Dashti; Peter Schwander; Robert Langlois; Russell Fung; Wen Li; Ahmad Hosseinizadeh; Hstau Y Liao; Jesper Pallesen; Gyanesh Sharma; Vera A Stupina; Anne E Simon; Jonathan D Dinman; Joachim Frank; Abbas Ourmazd
Journal:  Proc Natl Acad Sci U S A       Date:  2014-11-24       Impact factor: 11.205

7.  Dynamic contact network between ribosomal subunits enables rapid large-scale rotation during spontaneous translocation.

Authors:  Lars V Bock; Christian Blau; Andrea C Vaiana; Helmut Grubmüller
Journal:  Nucleic Acids Res       Date:  2015-06-24       Impact factor: 16.971

8.  Direct visualization of A-, P-, and E-site transfer RNAs in the Escherichia coli ribosome.

Authors:  R K Agrawal; P Penczek; R A Grassucci; Y Li; A Leith; K H Nierhaus; J Frank
Journal:  Science       Date:  1996-02-16       Impact factor: 47.728

9.  Contribution of intersubunit bridges to the energy barrier of ribosomal translocation.

Authors:  Qi Liu; Kurt Fredrick
Journal:  Nucleic Acids Res       Date:  2012-11-17       Impact factor: 16.971

10.  High-resolution cryo-electron microscopy structure of the Trypanosoma brucei ribosome.

Authors:  Yaser Hashem; Amedee des Georges; Jie Fu; Sarah N Buss; Fabrice Jossinet; Amy Jobe; Qin Zhang; Hstau Y Liao; Robert A Grassucci; Chandrajit Bajaj; Eric Westhof; Susan Madison-Antenucci; Joachim Frank
Journal:  Nature       Date:  2013-02-10       Impact factor: 49.962

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  9 in total

Review 1.  Relating Structure and Dynamics in RNA Biology.

Authors:  Kevin P Larsen; Junhong Choi; Arjun Prabhakar; Elisabetta Viani Puglisi; Joseph D Puglisi
Journal:  Cold Spring Harb Perspect Biol       Date:  2019-07-01       Impact factor: 10.005

2.  Perspectives on the ribosome.

Authors:  Thomas A Steitz; Peter B Moore
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2017-03-19       Impact factor: 6.237

Review 3.  New Insights into Ribosome Structure and Function.

Authors:  Amy Jobe; Zheng Liu; Cristina Gutierrez-Vargas; Joachim Frank
Journal:  Cold Spring Harb Perspect Biol       Date:  2019-01-02       Impact factor: 10.005

Review 4.  Challenges and approaches to predicting RNA with multiple functional structures.

Authors:  Susan J Schroeder
Journal:  RNA       Date:  2018-08-24       Impact factor: 4.942

5.  Alternative conformations and motions adopted by 30S ribosomal subunits visualized by cryo-electron microscopy.

Authors:  Dushyant Jahagirdar; Vikash Jha; Kaustuv Basu; Josue Gomez-Blanco; Javier Vargas; Joaquin Ortega
Journal:  RNA       Date:  2020-09-28       Impact factor: 4.942

6.  Protein identification from electron cryomicroscopy maps by automated model building and side-chain matching.

Authors:  Thomas C Terwilliger; Oleg V Sobolev; Pavel V Afonine; Paul D Adams; Chi Min Ho; Xiaorun Li; Z Hong Zhou
Journal:  Acta Crystallogr D Struct Biol       Date:  2021-03-30       Impact factor: 5.699

7.  High-resolution structures of a thermophilic eukaryotic 80S ribosome reveal atomistic details of translocation.

Authors:  Miglė Kišonaitė; Klemens Wild; Karine Lapouge; Thomas Ruppert; Irmgard Sinning
Journal:  Nat Commun       Date:  2022-01-25       Impact factor: 17.694

8.  Direct measurements of mRNA translation kinetics in living cells.

Authors:  Mikhail Metelev; Erik Lundin; Ivan L Volkov; Arvid H Gynnå; Johan Elf; Magnus Johansson
Journal:  Nat Commun       Date:  2022-04-06       Impact factor: 14.919

Review 9.  Mechanical Forces and Their Effect on the Ribosome and Protein Translation Machinery.

Authors:  Lisa J Simpson; John S Reader; Ellie Tzima
Journal:  Cells       Date:  2020-03-07       Impact factor: 6.600

  9 in total

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