Literature DB >> 32078321

What Could Go Wrong? A Practical Guide to Single-Particle Cryo-EM: From Biochemistry to Atomic Models.

Michael A Cianfrocco1, Elizabeth H Kellogg2.   

Abstract

Cryo-electron microscopy (cryo-EM) has enjoyed explosive recent growth due to revolutionary advances in hardware and software, resulting in a steady stream of long-awaited, high-resolution structures with unprecedented atomic detail. With this comes an increased number of microscopes, cryo-EM facilities, and scientists eager to leverage the ability to determine protein structures without crystallization. However, numerous pitfalls and considerations beset the path toward high-resolution structures and are not necessarily obvious from literature surveys. Here, we detail the most common misconceptions when initiating a cryo-EM project and common technical hurdles, as well as their solutions, and we conclude with a vision for the future of this exciting field.

Entities:  

Keywords:  3D reconstruction; Atomic modeling; Microscope instrumentation; Preferred orientation; Sample heterogeneity; Sample preparation; Sample quality assessment; Single-particle cryo-EM

Year:  2020        PMID: 32078321      PMCID: PMC7253330          DOI: 10.1021/acs.jcim.9b01178

Source DB:  PubMed          Journal:  J Chem Inf Model        ISSN: 1549-9596            Impact factor:   4.956


  110 in total

Review 1.  Challenges and opportunities in cryo-EM single-particle analysis.

Authors:  Dmitry Lyumkis
Journal:  J Biol Chem       Date:  2019-02-25       Impact factor: 5.157

2.  goCTF: Geometrically optimized CTF determination for single-particle cryo-EM.

Authors:  Min Su
Journal:  J Struct Biol       Date:  2018-11-26       Impact factor: 2.867

3.  Addressing preferred specimen orientation in single-particle cryo-EM through tilting.

Authors:  Yong Zi Tan; Philip R Baldwin; Joseph H Davis; James R Williamson; Clinton S Potter; Bridget Carragher; Dmitry Lyumkis
Journal:  Nat Methods       Date:  2017-07-03       Impact factor: 28.547

4.  Spotiton: a prototype for an integrated inkjet dispense and vitrification system for cryo-TEM.

Authors:  Tilak Jain; Patrick Sheehan; John Crum; Bridget Carragher; Clinton S Potter
Journal:  J Struct Biol       Date:  2012-05-05       Impact factor: 2.867

5.  Insights into the Distinct Mechanisms of Action of Taxane and Non-Taxane Microtubule Stabilizers from Cryo-EM Structures.

Authors:  Elizabeth H Kellogg; Nisreen M A Hejab; Stuart Howes; Peter Northcote; John H Miller; J Fernando Díaz; Kenneth H Downing; Eva Nogales
Journal:  J Mol Biol       Date:  2017-01-17       Impact factor: 5.469

6.  The structure of the dynactin complex and its interaction with dynein.

Authors:  Linas Urnavicius; Kai Zhang; Aristides G Diamant; Carina Motz; Max A Schlager; Minmin Yu; Nisha A Patel; Carol V Robinson; Andrew P Carter
Journal:  Science       Date:  2015-02-12       Impact factor: 47.728

7.  Structures of transcription pre-initiation complex with TFIIH and Mediator.

Authors:  S Schilbach; M Hantsche; D Tegunov; C Dienemann; C Wigge; H Urlaub; P Cramer
Journal:  Nature       Date:  2017-11-01       Impact factor: 49.962

8.  Microfluidic protein isolation and sample preparation for high-resolution cryo-EM.

Authors:  Claudio Schmidli; Stefan Albiez; Luca Rima; Ricardo Righetto; Inayatulla Mohammed; Paolo Oliva; Lubomir Kovacik; Henning Stahlberg; Thomas Braun
Journal:  Proc Natl Acad Sci U S A       Date:  2019-07-10       Impact factor: 11.205

9.  Architecture of eukaryotic mRNA 3'-end processing machinery.

Authors:  Ana Casañal; Ananthanarayanan Kumar; Chris H Hill; Ashley D Easter; Paul Emsley; Gianluca Degliesposti; Yuliya Gordiyenko; Balaji Santhanam; Jana Wolf; Katrin Wiederhold; Gillian L Dornan; Mark Skehel; Carol V Robinson; Lori A Passmore
Journal:  Science       Date:  2017-10-26       Impact factor: 47.728

10.  Automatically Fixing Errors in Glycoprotein Structures with Rosetta.

Authors:  Brandon Frenz; Sebastian Rämisch; Andrew J Borst; Alexandra C Walls; Jared Adolf-Bryfogle; William R Schief; David Veesler; Frank DiMaio
Journal:  Structure       Date:  2018-10-18       Impact factor: 5.006

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  7 in total

1.  Faces of Contemporary CryoEM Information and Modeling.

Authors:  Giulia Palermo; Yuji Sugita; Willy Wriggers; Rommie E Amaro
Journal:  J Chem Inf Model       Date:  2020-05-26       Impact factor: 4.956

2.  IceBreaker: Software for high-resolution single-particle cryo-EM with non-uniform ice.

Authors:  Mateusz Olek; Kevin Cowtan; Donovan Webb; Yuriy Chaban; Peijun Zhang
Journal:  Structure       Date:  2022-02-11       Impact factor: 5.871

3.  State-dependent sequential allostery exhibited by chaperonin TRiC/CCT revealed by network analysis of Cryo-EM maps.

Authors:  Yan Zhang; James Krieger; Karolina Mikulska-Ruminska; Burak Kaynak; Carlos Oscar S Sorzano; José-María Carazo; Jianhua Xing; Ivet Bahar
Journal:  Prog Biophys Mol Biol       Date:  2020-08-28       Impact factor: 3.667

4.  Molecular Dynamics to Predict Cryo-EM: Capturing Transitions and Short-Lived Conformational States of Biomolecules.

Authors:  Łukasz Nierzwicki; Giulia Palermo
Journal:  Front Mol Biosci       Date:  2021-04-05

5.  Low-energy electron holography imaging of conformational variability of single-antibody molecules from electrospray ion beam deposition.

Authors:  Hannah Ochner; Sven Szilagyi; Sabine Abb; Joseph Gault; Carol V Robinson; Luigi Malavolti; Stephan Rauschenbach; Klaus Kern
Journal:  Proc Natl Acad Sci U S A       Date:  2021-12-21       Impact factor: 11.205

6.  Routine sub-2.5 Å cryo-EM structure determination of GPCRs.

Authors:  Radostin Danev; Matthew Belousoff; Yi-Lynn Liang; Xin Zhang; Fabian Eisenstein; Denise Wootten; Patrick M Sexton
Journal:  Nat Commun       Date:  2021-07-15       Impact factor: 14.919

7.  SARS-CoV-2 3a expression, purification, and reconstitution into lipid nanodiscs.

Authors:  David M Kern; Stephen G Brohawn
Journal:  Methods Enzymol       Date:  2021-01-27       Impact factor: 1.600

  7 in total

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