Literature DB >> 32919493

Present and Emerging Methodologies in Cryo-EM Single-Particle Analysis.

Mengyu Wu1, Gabriel C Lander2.   

Abstract

Over the past decade, technical and methodological improvements in cryogenic electron microscopy (cryo-EM) single-particle analysis have enabled routine high-resolution structural analyses of biological macromolecules, resulting in a flood of new molecular insights into protracted biological questions. However, despite the tremendous progress and success of the field in recent years, opportunities for improvement remain in various aspects of the cryo-EM single-particle analysis workflow (e.g., sample preparation, image acquisition and processing, and structure validation). Here, we review recent advances that have contributed to the principal methods in cryo-EM and identify persisting challenges and bottlenecks that will require further methodological and hardware development.
Copyright © 2020 Biophysical Society. Published by Elsevier Inc. All rights reserved.

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Year:  2020        PMID: 32919493      PMCID: PMC7567993          DOI: 10.1016/j.bpj.2020.08.027

Source DB:  PubMed          Journal:  Biophys J        ISSN: 0006-3495            Impact factor:   4.033


  78 in total

1.  High-yield monolayer graphene grids for near-atomic resolution cryoelectron microscopy.

Authors:  Yimo Han; Xiao Fan; Haozhe Wang; Fang Zhao; Christopher G Tully; Jing Kong; Nan Yao; Nieng Yan
Journal:  Proc Natl Acad Sci U S A       Date:  2019-12-26       Impact factor: 11.205

2.  A Multi-model Approach to Assessing Local and Global Cryo-EM Map Quality.

Authors:  Mark A Herzik; James S Fraser; Gabriel C Lander
Journal:  Structure       Date:  2018-11-15       Impact factor: 5.006

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.  PROTEINS, INTERFACES, AND CRYO-EM GRIDS.

Authors:  Robert M Glaeser
Journal:  Curr Opin Colloid Interface Sci       Date:  2017-12-22       Impact factor: 6.448

Review 5.  Opinion: hazards faced by macromolecules when confined to thin aqueous films.

Authors:  Robert M Glaeser; Bong-Gyoon Han
Journal:  Biophys Rep       Date:  2016-07-22

6.  Sub-2 Angstrom resolution structure determination using single-particle cryo-EM at 200 keV.

Authors:  Mengyu Wu; Gabriel C Lander; Mark A Herzik
Journal:  J Struct Biol X       Date:  2020-02-28

7.  Benchmarking cryo-EM Single Particle Analysis Workflow.

Authors:  Laura Y Kim; William J Rice; Edward T Eng; Mykhailo Kopylov; Anchi Cheng; Ashleigh M Raczkowski; Kelsey D Jordan; Daija Bobe; Clinton S Potter; Bridget Carragher
Journal:  Front Mol Biosci       Date:  2018-06-04

8.  Characterisation of molecular motions in cryo-EM single-particle data by multi-body refinement in RELION.

Authors:  Takanori Nakane; Dari Kimanius; Erik Lindahl; Sjors Hw Scheres
Journal:  Elife       Date:  2018-06-01       Impact factor: 8.140

9.  A cryo-EM grid preparation device for time-resolved structural studies.

Authors:  Dimitrios Kontziampasis; David P Klebl; Matthew G Iadanza; Charlotte A Scarff; Florian Kopf; Frank Sobott; Diana C F Monteiro; Martin Trebbin; Stephen P Muench; Howard D White
Journal:  IUCrJ       Date:  2019-09-05       Impact factor: 4.769

10.  Structure and drug resistance of the Plasmodium falciparum transporter PfCRT.

Authors:  Jonathan Kim; Yong Zi Tan; Kathryn J Wicht; Satchal K Erramilli; Satish K Dhingra; John Okombo; Jeremie Vendome; Laura M Hagenah; Sabrina I Giacometti; Audrey L Warren; Kamil Nosol; Paul D Roepe; Clinton S Potter; Bridget Carragher; Anthony A Kossiakoff; Matthias Quick; David A Fidock; Filippo Mancia
Journal:  Nature       Date:  2019-11-27       Impact factor: 49.962

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  9 in total

1.  Protein Structural Modeling for Electron Microscopy Maps Using VESPER and MAINMAST.

Authors:  Eman Alnabati; Genki Terashi; Daisuke Kihara
Journal:  Curr Protoc       Date:  2022-07

Review 2.  Emerging Themes in CryoEM─Single Particle Analysis Image Processing.

Authors:  Jose Luis Vilas; Jose Maria Carazo; Carlos Oscar S Sorzano
Journal:  Chem Rev       Date:  2022-07-04       Impact factor: 72.087

3.  Native Mass Spectrometry-Based Screening for Optimal Sample Preparation in Single-Particle Cryo-EM.

Authors:  Paul Dominic B Olinares; Jin Young Kang; Eliza Llewellyn; Courtney Chiu; James Chen; Brandon Malone; Ruth M Saecker; Elizabeth A Campbell; Seth A Darst; Brian T Chait
Journal:  Structure       Date:  2020-11-19       Impact factor: 5.006

Review 4.  Label-free visual proteomics: Coupling MS- and EM-based approaches in structural biology.

Authors:  Oleg Klykov; Mykhailo Kopylov; Bridget Carragher; Albert J R Heck; Alex J Noble; Richard A Scheltema
Journal:  Mol Cell       Date:  2022-01-20       Impact factor: 17.970

Review 5.  Targeting VIP and PACAP Receptor Signaling: New Insights into Designing Drugs for the PACAP Subfamily of Receptors.

Authors:  Jessica Lu; Sarah J Piper; Peishen Zhao; Laurence J Miller; Denise Wootten; Patrick M Sexton
Journal:  Int J Mol Sci       Date:  2022-07-22       Impact factor: 6.208

6.  MarkovFit: Structure Fitting for Protein Complexes in Electron Microscopy Maps Using Markov Random Field.

Authors:  Eman Alnabati; Juan Esquivel-Rodriguez; Genki Terashi; Daisuke Kihara
Journal:  Front Mol Biosci       Date:  2022-07-25

7.  Theoretical 3D electron diffraction electrostatic potential maps of proteins modeled with a multipolar pseudoatom data bank.

Authors:  Marta Kulik; Michał Leszek Chodkiewicz; Paulina Maria Dominiak
Journal:  Acta Crystallogr D Struct Biol       Date:  2022-07-14       Impact factor: 5.699

Review 8.  Simulation and Machine Learning Methods for Ion-Channel Structure Determination, Mechanistic Studies and Drug Design.

Authors:  Zhengdan Zhu; Zhenfeng Deng; Qinrui Wang; Yuhang Wang; Duo Zhang; Ruihan Xu; Lvjun Guo; Han Wen
Journal:  Front Pharmacol       Date:  2022-06-28       Impact factor: 5.988

Review 9.  Recent Advances in Structure, Function, and Pharmacology of Class A Lipid GPCRs: Opportunities and Challenges for Drug Discovery.

Authors:  R N V Krishna Deepak; Ravi Kumar Verma; Yossa Dwi Hartono; Wen Shan Yew; Hao Fan
Journal:  Pharmaceuticals (Basel)       Date:  2021-12-22
  9 in total

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