Literature DB >> 30804214

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

Dmitry Lyumkis1.   

Abstract

Cryogenic electron microscopy (cryo-EM) enables structure determination of macromolecular objects and their assemblies. Although the techniques have been developing for nearly four decades, they have gained widespread attention in recent years due to technical advances on numerous fronts, enabling traditional microscopists to break into the world of molecular structural biology. Many samples can now be routinely analyzed at near-atomic resolution using standard imaging and image analysis techniques. However, numerous challenges to conventional workflows remain, and continued technical advances open entirely novel opportunities for discovery and exploration. Here, I will review some of the main methods surrounding cryo-EM with an emphasis specifically on single-particle analysis, and I will highlight challenges, open questions, and opportunities for methodology development.
© 2019 Lyumkis.

Keywords:  atomic resolution; cryo-electron microscopy; protein structure; protein–protein interaction; single-particle analysis; structural biology

Mesh:

Substances:

Year:  2019        PMID: 30804214      PMCID: PMC6442032          DOI: 10.1074/jbc.REV118.005602

Source DB:  PubMed          Journal:  J Biol Chem        ISSN: 0021-9258            Impact factor:   5.157


  200 in total

Review 1.  Precise beam-tilt alignment and collimation are required to minimize the phase error associated with coma in high-resolution cryo-EM.

Authors:  Robert M Glaeser; Dieter Typke; Peter C Tiemeijer; James Pulokas; Anchi Cheng
Journal:  J Struct Biol       Date:  2010-12-21       Impact factor: 2.867

2.  Finding trimeric HIV-1 envelope glycoproteins in random noise.

Authors:  Marin van Heel
Journal:  Proc Natl Acad Sci U S A       Date:  2013-10-08       Impact factor: 11.205

Review 3.  Expanding the boundaries of cryo-EM with phase plates.

Authors:  Radostin Danev; Wolfgang Baumeister
Journal:  Curr Opin Struct Biol       Date:  2017-07-01       Impact factor: 6.809

4.  MolProbity: More and better reference data for improved all-atom structure validation.

Authors:  Christopher J Williams; Jeffrey J Headd; Nigel W Moriarty; Michael G Prisant; Lizbeth L Videau; Lindsay N Deis; Vishal Verma; Daniel A Keedy; Bradley J Hintze; Vincent B Chen; Swati Jain; Steven M Lewis; W Bryan Arendall; Jack Snoeyink; Paul D Adams; Simon C Lovell; Jane S Richardson; David C Richardson
Journal:  Protein Sci       Date:  2017-11-27       Impact factor: 6.725

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

6.  Breaking Cryo-EM Resolution Barriers to Facilitate Drug Discovery.

Authors:  Alan Merk; Alberto Bartesaghi; Soojay Banerjee; Veronica Falconieri; Prashant Rao; Mindy I Davis; Rajan Pragani; Matthew B Boxer; Lesley A Earl; Jacqueline L S Milne; Sriram Subramaniam
Journal:  Cell       Date:  2016-05-26       Impact factor: 41.582

7.  A practical guide to the use of monolayer purification and affinity grids.

Authors:  Deborah F Kelly; Danijela Dukovski; Thomas Walz
Journal:  Methods Enzymol       Date:  2010       Impact factor: 1.600

8.  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

9.  Overview of the CCP4 suite and current developments.

Authors:  Martyn D Winn; Charles C Ballard; Kevin D Cowtan; Eleanor J Dodson; Paul Emsley; Phil R Evans; Ronan M Keegan; Eugene B Krissinel; Andrew G W Leslie; Airlie McCoy; Stuart J McNicholas; Garib N Murshudov; Navraj S Pannu; Elizabeth A Potterton; Harold R Powell; Randy J Read; Alexei Vagin; Keith S Wilson
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2011-03-18

Review 10.  Approaches to altering particle distributions in cryo-electron microscopy sample preparation.

Authors:  Ieva Drulyte; Rachel M Johnson; Emma L Hesketh; Daniel L Hurdiss; Charlotte A Scarff; Sebastian A Porav; Neil A Ranson; Stephen P Muench; Rebecca F Thompson
Journal:  Acta Crystallogr D Struct Biol       Date:  2018-05-18       Impact factor: 7.652

View more
  84 in total

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

Authors:  Michael A Cianfrocco; Elizabeth H Kellogg
Journal:  J Chem Inf Model       Date:  2020-03-09       Impact factor: 4.956

2.  Transient Transfection and Expression of Eukaryotic Membrane Proteins in Expi293F Cells and Their Screening on a Small Scale: Application for Structural Studies.

Authors:  Ganna O Krasnoselska; Maud Dumoux; Nadisha Gamage; Harish Cheruvara; James Birch; Andrew Quigley; Raymond J Owens
Journal:  Methods Mol Biol       Date:  2021

3.  Image Processing in Cryo-Electron Microscopy of Single Particles: The Power of Combining Methods.

Authors:  Carlos Oscar S Sorzano; Amaya Jiménez-Moreno; David Maluenda; Erney Ramírez-Aportela; Marta Martínez; Ana Cuervo; Robert Melero; Jose Javier Conesa; Ruben Sánchez-García; David Strelak; Jiri Filipovic; Estrella Fernández-Giménez; Federico de Isidro-Gómez; David Herreros; Pablo Conesa; Laura Del Caño; Yunior Fonseca; Jorge Jiménez de la Morena; Jose Ramon Macías; Patricia Losana; Roberto Marabini; Jose-Maria Carazo
Journal:  Methods Mol Biol       Date:  2021

4.  Evaluating Local and Directional Resolution of Cryo-EM Density Maps.

Authors:  Sriram Aiyer; Cheng Zhang; Philp R Baldwin; Dmitry Lyumkis
Journal:  Methods Mol Biol       Date:  2021

Review 5.  Multifaceted HIV integrase functionalities and therapeutic strategies for their inhibition.

Authors:  Alan N Engelman
Journal:  J Biol Chem       Date:  2019-08-29       Impact factor: 5.157

Review 6.  Endoplasmic reticulum quality control in lipoprotein metabolism.

Authors:  Cari M Koerner; Benjamin S Roberts; Saskia B Neher
Journal:  Mol Cell Endocrinol       Date:  2019-08-20       Impact factor: 4.102

7.  Programmable Nanodisc Patterning by DNA Origami.

Authors:  Zhao Zhang; Edwin R Chapman
Journal:  Nano Lett       Date:  2020-07-15       Impact factor: 11.189

8.  High-Throughput Cryo-EM Enabled by User-Free Preprocessing Routines.

Authors:  Yilai Li; Jennifer N Cash; John J G Tesmer; Michael A Cianfrocco
Journal:  Structure       Date:  2020-04-14       Impact factor: 5.006

Review 9.  Development of imaging scaffolds for cryo-electron microscopy.

Authors:  Todd O Yeates; Matthew P Agdanowski; Yuxi Liu
Journal:  Curr Opin Struct Biol       Date:  2020-02-14       Impact factor: 6.809

10.  Deciphering Metabolic Heterogeneity by Single-Cell Analysis.

Authors:  Tom M J Evers; Mazène Hochane; Sander J Tans; Ron M A Heeren; Stefan Semrau; Peter Nemes; Alireza Mashaghi
Journal:  Anal Chem       Date:  2019-10-08       Impact factor: 6.986

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.