Literature DB >> 23640776

Story in a sample-the potential (and limitations) of cryo-electron microscopy applied to molecular machines.

Joachim Frank1.   

Abstract

This article addresses recent developments in cryo-electron microscopy and single-particle reconstruction of macromolecules. With the advent of powerful classification techniques, it is now possible to extract and visualize multiple conformers contained within the same dataset. It is discussed how and to what extent this technique can be used in the study of the dynamics of molecular machines.
Copyright © 2013 Wiley Periodicals, Inc.

Entities:  

Keywords:  conformational states; free-energy landscape; ribosome; single-molecule FRET

Mesh：

Substances：

Year:  2013        PMID： 23640776      PMCID： PMC3785246          DOI： 10.1002/bip.22274

Source DB:  PubMed          Journal:  Biopolymers        ISSN： 0006-3525            Impact factor:   2.505


  30 in total

1.  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

2.  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

3.  Disentangling conformational states of macromolecules in 3D-EM through likelihood optimization.

Authors:  Sjors H W Scheres; Haixiao Gao; Mikel Valle; Gabor T Herman; Paul P B Eggermont; Joachim Frank; Jose-Maria Carazo
Journal:  Nat Methods       Date:  2006-12-10       Impact factor: 28.547

Review 4.  Structural basis for protein synthesis: snapshots of the ribosome in motion.

Authors:  Jonas Noeske; Jamie H D Cate
Journal:  Curr Opin Struct Biol       Date:  2012-08-04       Impact factor: 6.809

5.  Analysis of transient structures by cryo-microscopy combined with rapid mixing of spray droplets.

Authors:  J Berriman; N Unwin
Journal:  Ultramicroscopy       Date:  1994-12       Impact factor: 2.689

Review 6.  Structure and dynamics of a processive Brownian motor: the translating ribosome.

Authors:  Joachim Frank; Ruben L Gonzalez
Journal:  Annu Rev Biochem       Date:  2010       Impact factor: 23.643

Review 7.  Navigating the ribosome's metastable energy landscape.

Authors:  James B Munro; Kevin Y Sanbonmatsu; Christian M T Spahn; Scott C Blanchard
Journal:  Trends Biochem Sci       Date:  2009-08-03       Impact factor: 13.807

8.  Biomolecular dynamics: order-disorder transitions and energy landscapes.

Authors:  Paul C Whitford; Karissa Y Sanbonmatsu; José N Onuchic
Journal:  Rep Prog Phys       Date:  2012-06-28

9.  Electron diffraction analysis of structural changes in the photocycle of bacteriorhodopsin.

Authors:  S Subramaniam; M Gerstein; D Oesterhelt; R Henderson
Journal:  EMBO J       Date:  1993-01       Impact factor: 11.598

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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  8 in total

Review 1.  Two promising future developments of cryo-EM: capturing short-lived states and mapping a continuum of states of a macromolecule.

Authors:  Bo Chen; Joachim Frank
Journal:  Microscopy (Oxf)       Date:  2015-10-31       Impact factor: 1.571

2.  Ion Mobility Spectrometry-Hydrogen Deuterium Exchange Mass Spectrometry of Anions: Part 3. Estimating Surface Area Exposure by Deuterium Uptake.

Authors:  Mahdiar Khakinejad; Samaneh Ghassabi Kondalaji; Gregory C Donohoe; Stephen J Valentine
Journal:  J Am Soc Mass Spectrom       Date:  2015-11-30       Impact factor: 3.109

3.  Covariance Matrix Estimation for the Cryo-EM Heterogeneity Problem.

Authors:  E Katsevich; A Katsevich; A Singer
Journal:  SIAM J Imaging Sci       Date:  2015-01-22       Impact factor: 2.867

Review 4.  Evolution of a dynamic molecular switch.

Authors:  Susan S Taylor; Hiruy S Meharena; Alexandr P Kornev
Journal:  IUBMB Life       Date:  2019-05-06       Impact factor: 3.885

5.  CENP-A arrays are more condensed than canonical arrays at low ionic strength.

Authors:  Christian P Geiss; Dimitra Keramisanou; Nikolina Sekulic; Margot P Scheffer; Ben E Black; Achilleas S Frangakis
Journal:  Biophys J       Date:  2014-02-18       Impact factor: 4.033

6.  Structural snapshots of actively translating human ribosomes.

Authors:  Elmar Behrmann; Justus Loerke; Tatyana V Budkevich; Kaori Yamamoto; Andrea Schmidt; Pawel A Penczek; Matthijn R Vos; Jörg Bürger; Thorsten Mielke; Patrick Scheerer; Christian M T Spahn
Journal:  Cell       Date:  2015-05-07       Impact factor: 41.582

7.  Quantitative Connection between Ensemble Thermodynamics and Single-Molecule Kinetics: A Case Study Using Cryogenic Electron Microscopy and Single-Molecule Fluorescence Resonance Energy Transfer Investigations of the Ribosome.

Authors:  Colin D Kinz Thompson; Ajeet K Sharma; Joachim Frank; Ruben L Gonzalez; Debashish Chowdhury
Journal:  J Phys Chem B       Date:  2015-03-31       Impact factor: 2.991

8.  Continuous changes in structure mapped by manifold embedding of single-particle data in cryo-EM.

Authors:  Joachim Frank; Abbas Ourmazd
Journal:  Methods       Date:  2016-02-13       Impact factor: 4.647
  8 in total

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