1
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Collier CP, Bolmatov D, Elkins JG, Katsaras J. Nanoscopic lipid domains determined by microscopy and neutron scattering. Methods 2024; 223:127-135. [PMID: 38331125 DOI: 10.1016/j.ymeth.2024.01.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 01/22/2024] [Accepted: 01/26/2024] [Indexed: 02/10/2024] Open
Abstract
Biological membranes are highly complex supramolecular assemblies, which play central roles in biology. However, their complexity makes them challenging to study their nanoscale structures. To overcome this challenge, model membranes assembled using reduced sets of membrane-associated biomolecules have been found to be both excellent and tractable proxies for biological membranes. Due to their relative simplicity, they have been studied using a range of biophysical characterization techniques. In this review article, we will briefly detail the use of fluorescence and electron microscopies, and X-ray and neutron scattering techniques used over the past few decades to study the nanostructure of biological membranes.
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Affiliation(s)
- Charles P Collier
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Dima Bolmatov
- Department of Physics and Astronomy, University of Tennessee, Knoxville, TN, USA; Shull Wollan Center, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - James G Elkins
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - John Katsaras
- Department of Physics and Astronomy, University of Tennessee, Knoxville, TN, USA; Shull Wollan Center, Oak Ridge National Laboratory, Oak Ridge, TN, USA; Neutron Scattering Division, Oak Ridge National Laboratorry, Oak Ridege, TN, USA
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2
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Vénien-Bryan C, Fernandes CAH. Overview of Membrane Protein Sample Preparation for Single-Particle Cryo-Electron Microscopy Analysis. Int J Mol Sci 2023; 24:14785. [PMID: 37834233 PMCID: PMC10573263 DOI: 10.3390/ijms241914785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 09/21/2023] [Accepted: 09/28/2023] [Indexed: 10/15/2023] Open
Abstract
Single-particle cryo-electron microscopy (cryo-EM SPA) has recently emerged as an exceptionally well-suited technique for determining the structure of membrane proteins (MPs). Indeed, in recent years, huge increase in the number of MPs solved via cryo-EM SPA at a resolution better than 3.0 Å in the Protein Data Bank (PDB) has been observed. However, sample preparation remains a significant challenge in the field. Here, we evaluated the MPs solved using cryo-EM SPA deposited in the PDB in the last two years at a resolution below 3.0 Å. The most critical parameters for sample preparation are as follows: (i) the surfactant used for protein extraction from the membrane, (ii) the surfactant, amphiphiles, nanodiscs or other molecules present in the vitrification step, (iii) the vitrification method employed, and (iv) the type of grids used. The aim is not to provide a definitive answer on the optimal sample conditions for cryo-EM SPA of MPs but rather assess the current trends in the MP structural biology community towards obtaining high-resolution cryo-EM structures.
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Affiliation(s)
| | - Carlos A. H. Fernandes
- Unité Mixte de Recherche (UMR) 7590, Centre National de la Recherche Scientifique (CNRS), Muséum National d’Histoire Naturelle, Institut de Recherche pour le Développement (IRD), Institut de Minéralogie, Physique des Matériaux et de Cosmochimie (IMPMC), Sorbonne Université, 75005 Paris, France;
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3
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Chua EYD, Neselu K, Wang B, Rice WJ, Potter CS, Carragher B. Measuring the Effect of Ice Thickness and Microscope Configuration on Resolution in Single Particle Cryo-EM. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2023; 29:1040. [PMID: 37613233 DOI: 10.1093/micmic/ozad067.531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/25/2023]
Affiliation(s)
- Eugene Y D Chua
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Kasahun Neselu
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Bing Wang
- Cryo-Electron Microscopy Core, New York University Grossman School of Medicine, New York, NYUSA
| | - William J Rice
- Cryo-Electron Microscopy Core, New York University Grossman School of Medicine, New York, NYUSA
- Department of Cell Biology, New York University Grossman School of Medicine, New York, NY, USA
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4
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Chang SYS, Dijkman PM, Wiessing SA, Kudryashev M. Determining the structure of the bacterial voltage-gated sodium channel NaChBac embedded in liposomes by cryo electron tomography and subtomogram averaging. Sci Rep 2023; 13:11523. [PMID: 37460541 PMCID: PMC10352297 DOI: 10.1038/s41598-023-38027-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Accepted: 06/30/2023] [Indexed: 07/20/2023] Open
Abstract
Voltage-gated sodium channels shape action potentials that propagate signals along cells. When the membrane potential reaches a certain threshold, the channels open and allow sodium ions to flow through the membrane depolarizing it, followed by the deactivation of the channels. Opening and closing of the channels is important for cellular signalling and regulates various physiological processes in muscles, heart and brain. Mechanistic insights into the voltage-gated channels are difficult to achieve as the proteins are typically extracted from membranes for structural analysis which results in the loss of the transmembrane potential that regulates their activity. Here, we report the structural analysis of a bacterial voltage-gated sodium channel, NaChBac, reconstituted in liposomes under an electrochemical gradient by cryo electron tomography and subtomogram averaging. We show that the small channel, most of the residues of which are embedded in the membrane, can be localized using a genetically fused GFP. GFP can aid the initial alignment to an average resulting in a correct structure, but does not help for the final refinement. At a moderate resolution of ˜16 Å the structure of NaChBac in an unrestricted membrane bilayer is 10% wider than the structure of the purified protein previously solved in nanodiscs, suggesting the potential movement of the peripheral voltage-sensing domains. Our study explores the limits of structural analysis of membrane proteins in membranes.
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Affiliation(s)
- Shih-Ying Scott Chang
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), In Situ Structural Biology, Berlin, Germany
- Max Planck Institute of Biophysics, Frankfurt on Main, Germany
- Buchmann Institute for Molecular Life Sciences, Goethe University of Frankfurt on Main, Frankfurt on Main, Germany
| | - Patricia M Dijkman
- Max Planck Institute of Biophysics, Frankfurt on Main, Germany
- Buchmann Institute for Molecular Life Sciences, Goethe University of Frankfurt on Main, Frankfurt on Main, Germany
| | | | - Misha Kudryashev
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), In Situ Structural Biology, Berlin, Germany.
- Max Planck Institute of Biophysics, Frankfurt on Main, Germany.
- Buchmann Institute for Molecular Life Sciences, Goethe University of Frankfurt on Main, Frankfurt on Main, Germany.
- Institute of Medical Physics and Biophysics, Charité-Universitätsmedizin Berlin, Berlin, Germany.
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5
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Bohmer M, Bhullar AS, Weitao T, Zhang L, Lee JH, Guo P. Revolving hexameric ATPases as asymmetric motors to translocate double-stranded DNA genome along one strand. iScience 2023; 26:106922. [PMID: 37305704 PMCID: PMC10250835 DOI: 10.1016/j.isci.2023.106922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023] Open
Abstract
DsDNA translocation through nanoscale pores is generally accomplished by ATPase biomotors. The discovery of the revolving dsDNA translocation mechanism, as opposed to rotation, in bacteriophage phi29 elucidated how ATPase motors move dsDNA. Revolution-driven, hexameric dsDNA motors have been reported in herpesvirus, bacterial FtsK, Streptomyces TraB, and T7 phage. This review explores the common relationship between their structure and mechanisms. Commonalities include moving along the 5'→3' strand, inchworm sequential action leading to an asymmetrical structure, channel chirality, channel size, and 3-step channel gating for controlling motion direction. The revolving mechanism and contact with one of the dsDNA strands addresses the historic controversy of dsDNA packaging using nicked, gapped, hybrid, or chemically modified DNA. These controversies surrounding dsDNA packaging activity using modified materials can be answered by whether the modification was introduced into the 3'→5' or 5'→3' strand. Perspectives concerning solutions to the controversy of motor structure and stoichiometry are also discussed.
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Affiliation(s)
- Margaret Bohmer
- Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, OH, USA
- College of Pharmacy, Division of Pharmaceutics and Pharmacology, The Ohio State University, Columbus, OH, USA
- College of Medicine, Dorothy M. Davis Heart and Lung Research Institute and James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Abhjeet S. Bhullar
- Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, OH, USA
- College of Pharmacy, Division of Pharmaceutics and Pharmacology, The Ohio State University, Columbus, OH, USA
- College of Medicine, Dorothy M. Davis Heart and Lung Research Institute and James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
- Interdisciplinary Biophysics Graduate Program, College of Art and Science, The Ohio State University, Columbus, OH 43210, USA
| | - Tao Weitao
- Center for the Genetics of Host Defense UT Southwestern Medical Center, Dallas, TX, USA
| | - Long Zhang
- Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, OH, USA
- College of Pharmacy, Division of Pharmaceutics and Pharmacology, The Ohio State University, Columbus, OH, USA
- College of Medicine, Dorothy M. Davis Heart and Lung Research Institute and James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Jing-Huei Lee
- Department of Biomedical Engineering, College of Engineering and Applied Science, University of Cincinnati, Cincinnati, OH, USA
| | - Peixuan Guo
- Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, OH, USA
- College of Pharmacy, Division of Pharmaceutics and Pharmacology, The Ohio State University, Columbus, OH, USA
- College of Medicine, Dorothy M. Davis Heart and Lung Research Institute and James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
- Interdisciplinary Biophysics Graduate Program, College of Art and Science, The Ohio State University, Columbus, OH 43210, USA
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6
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Cheng H, Zheng L, Liu N, Huang C, Xu J, Lu Y, Cui X, Xu K, Hou Y, Tang J, Zhang Z, Li J, Ni X, Chen Y, Peng H, Wang HW. Dual-Affinity Graphene Sheets for High-Resolution Cryo-Electron Microscopy. J Am Chem Soc 2023; 145:8073-8081. [PMID: 37011903 PMCID: PMC10103130 DOI: 10.1021/jacs.3c00659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
Abstract
With the development of cryo-electron microscopy (cryo-EM), high-resolution structures of macromolecules can be reconstructed by the single particle method efficiently. However, challenges may still persist during the specimen preparation stage. Specifically, proteins tend to adsorb at the air-water interface and exhibit a preferred orientation in vitreous ice. To overcome these challenges, we have explored dual-affinity graphene (DAG) modified with two different affinity ligands as a supporting material for cryo-EM sample preparation. The ligands can bind to distinct sites on the corresponding tagged particles, which in turn generates various orientation distributions of particles and prevents the adsorption of protein particles onto the air-water interface. As expected, the DAG exhibited high binding specificity and affinity to target macromolecules, resulting in more balanced particle Euler angular distributions compared to single functionalized graphene on two different protein cases, including the SARS -CoV-2 spike glycoprotein. We anticipate that the DAG grids will enable facile and efficient three-dimensional (3D) reconstruction for cryo-EM structural determination, providing a robust and general technique for future studies.
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Affiliation(s)
- Hang Cheng
- Ministry of Education Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing 100084, China
- Joint Graduate Program of Peking-Tsinghua-NIBS, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Shuimu BioSciences Ltd., Beijing 102206, China
| | - Liming Zheng
- Center for Nanochemistry, Beijing Science and Engineering Center for Nanocarbons, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Nan Liu
- Ministry of Education Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing 100084, China
- Beijing Frontier Research Center for Biological Structures, Tsinghua University, Beijing 100084, China
| | - Congyuan Huang
- Ministry of Education Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jie Xu
- Ministry of Education Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Ye Lu
- Ministry of Education Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xiaoya Cui
- Ministry of Education Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing 100084, China
- Beijing Frontier Research Center for Biological Structures, Tsinghua University, Beijing 100084, China
| | - Kui Xu
- Ministry of Education Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yuan Hou
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing 100190, China
| | - Junchuan Tang
- Center for Nanochemistry, Beijing Science and Engineering Center for Nanocarbons, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Zhong Zhang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing 100190, China
| | - Jing Li
- Shuimu BioSciences Ltd., Beijing 102206, China
| | - Xiaodan Ni
- Shuimu BioSciences Ltd., Beijing 102206, China
| | - Yanan Chen
- School of Materials Science and Engineering, Tianjin University, Tianjin 300072, China
| | - Hailin Peng
- Center for Nanochemistry, Beijing Science and Engineering Center for Nanocarbons, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
- Beijing Graphene Institute (BGI), Beijing 100095, China
| | - Hong-Wei Wang
- Ministry of Education Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing 100084, China
- Joint Graduate Program of Peking-Tsinghua-NIBS, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Beijing Frontier Research Center for Biological Structures, Tsinghua University, Beijing 100084, China
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7
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Neselu K, Wang B, Rice WJ, Potter CS, Carragher B, Chua EY. Measuring the effects of ice thickness on resolution in single particle cryo-EM. J Struct Biol X 2023; 7:100085. [PMID: 36742017 PMCID: PMC9894782 DOI: 10.1016/j.yjsbx.2023.100085] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 01/10/2023] [Accepted: 01/23/2023] [Indexed: 01/25/2023] Open
Abstract
Ice thickness is a critical parameter in single particle cryo-EM - too thin ice can break during imaging or exclude the sample of interest, while ice that is too thick contributes to more inelastic scattering that precludes obtaining high resolution reconstructions. Here we present the practical effects of ice thickness on resolution, and the influence of energy filters, accelerating voltage, or detector mode. We collected apoferritin data with a wide range of ice thicknesses on three microscopes with different instrumentation and settings. We show that on a 300 kV microscope, using a 20 eV energy filter slit has a greater effect on improving resolution in thicker ice; that operating at 300 kV instead of 200 kV accelerating voltage provides significant resolution improvements at an ice thickness above 150 nm; and that on a 200 kV microscope using a detector operating in super resolution mode enables good reconstructions for up to 200 nm ice thickness, while collecting in counting instead of linear mode leads to improvements in resolution for ice of 50-150 nm thickness. Our findings can serve as a guide for users seeking to optimize data collection or sample preparation routines for both single particle and in situ cryo-EM. We note that most in situ data collection is done on samples in a range of ice thickness above 150 nm so these results may be especially relevant to that community.
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Affiliation(s)
- Kasahun Neselu
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Bing Wang
- Cryo-Electron Microscopy Core, New York University Grossman School of Medicine, New York, NY, USA
| | - William J. Rice
- Cryo-Electron Microscopy Core, New York University Grossman School of Medicine, New York, NY, USA,Department of Cell Biology, New York University Grossman School of Medicine, New York, NY, USA
| | - Clinton S. Potter
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Bridget Carragher
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA,Corresponding authors.
| | - Eugene Y.D. Chua
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA,Corresponding authors.
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8
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Hall M, Schexnaydre E, Holmlund C, Carroni M. Protein Structural Analysis by Cryogenic Electron Microscopy. Methods Mol Biol 2023; 2652:439-463. [PMID: 37093490 DOI: 10.1007/978-1-0716-3147-8_24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Cryogenic electron microscopy (cryo-EM) is constantly developing and growing as a major technique for structure determination of protein complexes. Here, we detail the first steps of any cryo-EM project: specimen preparation and data collection. Step by step, a list of material needed is provided and the sequence of actions to carry out is given. We hope that these protocols will be useful to all people getting started with cryo-EM.
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Affiliation(s)
- Michael Hall
- SciLifeLab Cryo-EM Facility, Department of Chemistry, Umeå University, Umeå, Sweden.
| | - Erin Schexnaydre
- SciLifeLab Cryo-EM Facility, Department of Chemistry, Umeå University, Umeå, Sweden
| | - Camilla Holmlund
- SciLifeLab Cryo-EM Facility, Department of Chemistry, Umeå University, Umeå, Sweden
| | - Marta Carroni
- SciLifeLab Cryo-EM Facility, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden.
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9
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Fan H, Sun F. Developing Graphene Grids for Cryoelectron Microscopy. Front Mol Biosci 2022; 9:937253. [PMID: 35911962 PMCID: PMC9326159 DOI: 10.3389/fmolb.2022.937253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 05/31/2022] [Indexed: 11/13/2022] Open
Abstract
Cryogenic electron microscopy (cryo-EM) single particle analysis has become one of the major techniques used to study high-resolution 3D structures of biological macromolecules. Specimens are generally prepared in a thin layer of vitrified ice using a holey carbon grid. However, the sample quality using this type of grid is not always ideal for high-resolution imaging even when the specimens in the test tube behave ideally. Various problems occur during a vitrification procedure, including poor/nonuniform distribution of particles, preferred orientation of particles, specimen denaturation/degradation, high background from thick ice, and beam-induced motion, which have become important bottlenecks in high-resolution structural studies using cryo-EM in many projects. In recent years, grids with support films made of graphene and its derivatives have been developed to efficiently solve these problems. Here, the various advantages of graphene grids over conventional holey carbon film grids, functionalization of graphene support films, production methods of graphene grids, and origins of pristine graphene contamination are reviewed and discussed.
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Affiliation(s)
- Hongcheng Fan
- National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Fei Sun
- National Key Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- Center for Biological Imaging, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- Bioland Laboratory, Guangzhou, China
- *Correspondence: Fei Sun,
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10
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DeVore K, Chiu PL. Probing Structural Perturbation of Biomolecules by Extracting Cryo-EM Data Heterogeneity. Biomolecules 2022; 12:biom12050628. [PMID: 35625556 PMCID: PMC9138638 DOI: 10.3390/biom12050628] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 04/15/2022] [Accepted: 04/18/2022] [Indexed: 02/04/2023] Open
Abstract
Single-particle cryogenic electron microscopy (cryo-EM) has become an indispensable tool to probe high-resolution structural detail of biomolecules. It enables direct visualization of the biomolecules and opens a possibility for averaging molecular images to reconstruct a three-dimensional Coulomb potential density map. Newly developed algorithms for data analysis allow for the extraction of structural heterogeneity from a massive and low signal-to-noise-ratio (SNR) cryo-EM dataset, expanding our understanding of multiple conformational states, or further implications in dynamics, of the target biomolecule. This review provides an overview that briefly describes the workflow of single-particle cryo-EM, including imaging and data processing, and new methods developed for analyzing the data heterogeneity to understand the structural variability of biomolecules.
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11
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Bock LV, Grubmüller H. Effects of cryo-EM cooling on structural ensembles. Nat Commun 2022; 13:1709. [PMID: 35361752 PMCID: PMC8971465 DOI: 10.1038/s41467-022-29332-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 03/10/2022] [Indexed: 01/01/2023] Open
Abstract
Structure determination by cryo electron microscopy (cryo-EM) provides information on structural heterogeneity and ensembles at atomic resolution. To obtain cryo-EM images of macromolecules, the samples are first rapidly cooled down to cryogenic temperatures. To what extent the structural ensemble is perturbed during cooling is currently unknown. Here, to quantify the effects of cooling, we combined continuum model calculations of the temperature drop, molecular dynamics simulations of a ribosome complex before and during cooling with kinetic models. Our results suggest that three effects markedly contribute to the narrowing of the structural ensembles: thermal contraction, reduced thermal motion within local potential wells, and the equilibration into lower free-energy conformations by overcoming separating free-energy barriers. During cooling, barrier heights below 10 kJ/mol were found to be overcome, which is expected to reduce B-factors in ensembles imaged by cryo-EM. Our approach now enables the quantification of the heterogeneity of room-temperature ensembles from cryo-EM structures. The rapid temperature drop during plunge-freezing affects the structural ensembles obtained by cryo-EM. To quantify the extent of perturbation, Bock and Grubmüller combined continuum calculations, MD simulations, and kinetic models.
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Affiliation(s)
- Lars V Bock
- Theoretical and Computational Biophysics Department, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
| | - Helmut Grubmüller
- Theoretical and Computational Biophysics Department, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
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12
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OUP accepted manuscript. Microscopy (Oxf) 2022; 71:i60-i65. [DOI: 10.1093/jmicro/dfab059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 12/19/2021] [Accepted: 01/14/2022] [Indexed: 11/13/2022] Open
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13
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Kang MH, Park J, Kang S, Jeon S, Lee M, Shim JY, Lee J, Jeon TJ, Ahn MK, Lee SM, Kwon O, Kim BH, Meyerson JR, Lee MJ, Lim KI, Roh SH, Lee WC, Park J. Graphene Oxide-Supported Microwell Grids for Preparing Cryo-EM Samples with Controlled Ice Thickness. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2021; 33:e2102991. [PMID: 34510585 DOI: 10.1002/adma.202102991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 08/11/2021] [Indexed: 06/13/2023]
Abstract
Cryogenic-electron microscopy (cryo-EM) is the preferred method to determine 3D structures of proteins and to study diverse material systems that intrinsically have radiation or air sensitivity. Current cryo-EM sample preparation methods provide limited control over the sample quality, which limits the efficiency and high throughput of 3D structure analysis. This is partly because it is difficult to control the thickness of the vitreous ice that embeds specimens, in the range of nanoscale, depending on the size and type of materials of interest. Thus, there is a need for fine regulation of the thickness of vitreous ice to deliver consistent high signal-to-noise ratios for low-contrast biological specimens. Herein, an advanced silicon-chip-based device is developed which has a regular array of micropatterned holes with a graphene oxide (GO) window on freestanding silicon nitride (Six Ny ). Accurately regulated depths of micropatterned holes enable precise control of vitreous ice thickness. Furthermore, GO window with affinity for biomolecules can facilitate concentration of the sample molecules at a higher level. Incorporation of micropatterned chips with a GO window enhances cryo-EM imaging for various nanoscale biological samples including human immunodeficiency viral particles, groEL tetradecamers, apoferritin octahedral, aldolase homotetramer complexes, and tau filaments, as well as inorganic materials.
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Affiliation(s)
- Min-Ho Kang
- School of Chemical and Biological Engineering, and Institute of Chemical Processes (ICP), Seoul National University, Seoul, 08826, Republic of Korea
- Center for Nanoparticle Research, Institute of Basic Science (IBS), Seoul, 08826, Republic of Korea
| | - Junsun Park
- School of Biological Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Sungsu Kang
- School of Chemical and Biological Engineering, and Institute of Chemical Processes (ICP), Seoul National University, Seoul, 08826, Republic of Korea
- Center for Nanoparticle Research, Institute of Basic Science (IBS), Seoul, 08826, Republic of Korea
| | - Sungho Jeon
- Department of Mechanical Engineering, BK21FOUR ERICA-ACE Center, Hanyang University, Ansan, Gyeonggi, 15588, Republic of Korea
| | - Minyoung Lee
- School of Chemical and Biological Engineering, and Institute of Chemical Processes (ICP), Seoul National University, Seoul, 08826, Republic of Korea
- Center for Nanoparticle Research, Institute of Basic Science (IBS), Seoul, 08826, Republic of Korea
| | - Ji-Yeon Shim
- Department of Chemical and Biological Engineering, Sookmyung Women's University, Seoul, 04310, Republic of Korea
| | - Jeeyoung Lee
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
| | - Tae Jin Jeon
- National Instrumentation Center for Environmental Management, Seoul National University, Seoul, 08826, Republic of Korea
| | - Min Kyung Ahn
- Department of Materials Science and Engineering, Seoul National University, Seoul, 08826, Republic of Korea
- Biomedical Implant Convergence Research Lab, Advanced Institutes of Convergence Technology, Suwon, 16229, Republic of Korea
| | - Sung Mi Lee
- Department of Materials Science and Engineering, Seoul National University, Seoul, 08826, Republic of Korea
- Biomedical Implant Convergence Research Lab, Advanced Institutes of Convergence Technology, Suwon, 16229, Republic of Korea
| | - Ohkyung Kwon
- National Instrumentation Center for Environmental Management, Seoul National University, Seoul, 08826, Republic of Korea
| | - Byung Hyo Kim
- Department of Organic Materials and Fiber Engineering, Soongsil University, Seoul, 06978, Republic of Korea
| | - Joel R Meyerson
- Department of Physiology and Biophysics, Weill Cornell Medical College of Cornell University, New York, NY, 10065, USA
| | - Min Jae Lee
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, 03080, Republic of Korea
| | - Kwang-Il Lim
- Department of Chemical and Biological Engineering, Sookmyung Women's University, Seoul, 04310, Republic of Korea
| | - Soung-Hun Roh
- School of Biological Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Won Chul Lee
- Department of Mechanical Engineering, BK21FOUR ERICA-ACE Center, Hanyang University, Ansan, Gyeonggi, 15588, Republic of Korea
| | - Jungwon Park
- School of Chemical and Biological Engineering, and Institute of Chemical Processes (ICP), Seoul National University, Seoul, 08826, Republic of Korea
- Center for Nanoparticle Research, Institute of Basic Science (IBS), Seoul, 08826, Republic of Korea
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14
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Rheinberger J, Oostergetel G, Resch GP, Paulino C. Optimized cryo-EM data-acquisition workflow by sample-thickness determination. Acta Crystallogr D Struct Biol 2021; 77:565-571. [PMID: 33950013 PMCID: PMC8098475 DOI: 10.1107/s205979832100334x] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 03/29/2021] [Indexed: 12/19/2022] Open
Abstract
Sample thickness is a known key parameter in cryo-electron microscopy (cryo-EM) and can affect the amount of high-resolution information retained in the image. Yet, common data-acquisition approaches in single-particle cryo-EM do not take it into account. Here, it is demonstrated how the sample thickness can be determined before data acquisition, allowing the identification of optimal regions and the restriction of automated data collection to images with preserved high-resolution details. This quality-over-quantity approach almost entirely eliminates the time- and storage-consuming collection of suboptimal images, which are discarded after a recorded session or during early image processing due to a lack of high-resolution information. It maximizes the data-collection efficiency and lowers the electron-microscopy time required per data set. This strategy is especially useful if the speed of data collection is restricted by the microscope hardware and software, or if microscope access time, data transfer, data storage and computational power are a bottleneck.
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Affiliation(s)
- Jan Rheinberger
- Department of Structural Biology and Membrane Enzymology at the Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Gert Oostergetel
- Department of Structural Biology and Membrane Enzymology at the Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Guenter P. Resch
- Nexperion e.U. – Solutions for Electron Microscopy, Vienna, Austria
| | - Cristina Paulino
- Department of Structural Biology and Membrane Enzymology at the Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
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15
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Parent LR, Gnanasekaran K, Korpanty J, Gianneschi NC. 100th Anniversary of Macromolecular Science Viewpoint: Polymeric Materials by In Situ Liquid-Phase Transmission Electron Microscopy. ACS Macro Lett 2021; 10:14-38. [PMID: 35548998 DOI: 10.1021/acsmacrolett.0c00595] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
A century ago, Hermann Staudinger proposed the macromolecular theory of polymers, and now, as we enter the second century of polymer science, we face a different set of opportunities and challenges for the development of functional soft matter. Indeed, many fundamental questions remain open, relating to physical structures and mechanisms of phase transformations at the molecular and nanoscale. In this Viewpoint, we describe efforts to develop a dynamic, in situ microscopy tool suited to the study of polymeric materials at the nanoscale that allows for direct observation of discrete structures and processes in solution, as a complement to light, neutron, and X-ray scattering methods. Liquid-phase transmission electron microscopy (LPTEM) is a nascent in situ imaging technique for characterizing and examining solvated nanomaterials in real time. Though still under development, LPTEM has been shown to be capable of several modes of imaging: (1) imaging static solvated materials analogous to cryo-TEM, (2) videography of nanomaterials in motion, (3) observing solutions or nanomaterials undergoing physical and chemical transformations, including synthesis, assembly, and phase transitions, and (4) observing electron beam-induced chemical-materials processes. Herein, we describe opportunities and limitations of LPTEM for polymer science. We review the basic experimental platform of LPTEM and describe the origin of electron beam effects that go hand in hand with the imaging process. These electron beam effects cause perturbation and damage to the sample and solvent that can manifest as artefacts in images and videos. We describe sample-specific experimental guidelines and outline approaches to mitigate, characterize, and quantify beam damaging effects. Altogether, we seek to provide an overview of this nascent field in the context of its potential to contribute to the advancement of polymer science.
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Affiliation(s)
- Lucas R. Parent
- Innovation Partnership Building, The University of Connecticut, Storrs, Connecticut 06269, United States
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16
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Haberfehlner G, Hoefler SF, Rath T, Trimmel G, Kothleitner G, Hofer F. Benefits of direct electron detection and PCA for EELS investigation of organic photovoltaics materials. Micron 2020; 140:102981. [PMID: 33202362 DOI: 10.1016/j.micron.2020.102981] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 10/21/2020] [Accepted: 10/21/2020] [Indexed: 10/23/2022]
Abstract
Electron energy-loss spectroscopy (EELS) is a powerful tool for imaging chemical variations at the nanoscale. Here, we investigate a polymer/organic small molecule-blend used as absorber layer in an organic solar cell and employ EELS for distinguishing polymer donor and small molecule acceptor domains in the nanostructured blend based on elemental maps of light elements, such as nitrogen, sulfur or fluorine. Especially for beam sensitive samples, the electron dose needs to be limited, therefore optimized acquisition and data processing strategies are required. We compare data acquired on a post-column energy filter with a direct electron detection camera to data from a conventional CCD camera on the same filter and we investigate the impact of statistical data processing methods (principal components analysis, PCA) on acquired spectra and elemental maps extracted from spectrum images. Our work shows, that the quality of spectra on a direct electron detection camera is far superior to conventional CCD imaging, and thereby allows clear identification of ionization edges and the fine structure of these edges. For the quality of the elemental maps, the application of PCA is essential to allow a clear separation between the donor and acceptor phase in the bulk heterojunction absorber layer of a non-fullerene organic solar cell.
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Affiliation(s)
- Georg Haberfehlner
- Institute of Electron Microscopy and Nanoanalysis, NAWI Graz, Graz University of Technology, Steyrergasse 17, 8010, Graz, Austria.
| | - Sebastian F Hoefler
- Institute for Chemistry and Technology of Materials (ICTM), NAWI Graz, Graz University of Technology, Stremayrgasse 9, 8010, Graz, Austria
| | - Thomas Rath
- Institute for Chemistry and Technology of Materials (ICTM), NAWI Graz, Graz University of Technology, Stremayrgasse 9, 8010, Graz, Austria
| | - Gregor Trimmel
- Institute for Chemistry and Technology of Materials (ICTM), NAWI Graz, Graz University of Technology, Stremayrgasse 9, 8010, Graz, Austria
| | - Gerald Kothleitner
- Institute of Electron Microscopy and Nanoanalysis, NAWI Graz, Graz University of Technology, Steyrergasse 17, 8010, Graz, Austria; Graz Centre for Electron Microscopy, Steyrergasse 17, Graz, 8010, Austria
| | - Ferdinand Hofer
- Institute of Electron Microscopy and Nanoanalysis, NAWI Graz, Graz University of Technology, Steyrergasse 17, 8010, Graz, Austria; Graz Centre for Electron Microscopy, Steyrergasse 17, Graz, 8010, Austria
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17
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Nguyen C, Gonen T. Beyond protein structure determination with MicroED. Curr Opin Struct Biol 2020; 64:51-58. [PMID: 32610218 PMCID: PMC7321661 DOI: 10.1016/j.sbi.2020.05.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 05/22/2020] [Accepted: 05/22/2020] [Indexed: 12/14/2022]
Abstract
Microcrystal electron diffraction (MicroED) was first coined and developed in 2013 at the Janelia Research Campus as a new modality in electron cryomicroscopy (cryoEM). Since then, MicroED has not only made important contributions in pushing the resolution limits of cryoEM protein structure characterization but also of peptides, small-organic and inorganic molecules, and natural-products that have resisted structure determination by other methods. This review showcases important recent developments in MicroED, highlighting the importance of the technique in fields of studies beyond protein structure determination where MicroED is beginning to have paradigm shifting roles.
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Affiliation(s)
- Chi Nguyen
- Department of Biological Chemistry, University of California Los Angeles, 615 Charles E Young Drive South, Los Angeles, CA90095, United States
| | - Tamir Gonen
- Department of Biological Chemistry, University of California Los Angeles, 615 Charles E Young Drive South, Los Angeles, CA90095, United States; Department of Physiology, University of California Los Angeles, 615 Charles E Young Drive South, Los Angeles, CA90095, United States; Howard Hughes Medical Institute, University of California Los Angeles, Los Angeles, CA90095, United States.
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18
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Yao R, Qian J, Huang Q. Deep-learning with synthetic data enables automated picking of cryo-EM particle images of biological macromolecules. Bioinformatics 2020; 36:1252-1259. [PMID: 31584618 DOI: 10.1093/bioinformatics/btz728] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 08/28/2019] [Accepted: 09/26/2019] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION Single-particle cryo-electron microscopy (cryo-EM) has become a powerful technique for determining 3D structures of biological macromolecules at near-atomic resolution. However, this approach requires picking huge numbers of macromolecular particle images from thousands of low-contrast, high-noisy electron micrographs. Although machine-learning methods were developed to get rid of this bottleneck, it still lacks universal methods that could automatically picking the noisy cryo-EM particles of various macromolecules. RESULTS Here, we present a deep-learning segmentation model that employs fully convolutional networks trained with synthetic data of known 3D structures, called PARSED (PARticle SEgmentation Detector). Without using any experimental information, PARSED could automatically segment the cryo-EM particles in a whole micrograph at a time, enabling faster particle picking than previous template/feature-matching and particle-classification methods. Applications to six large public cryo-EM datasets clearly validated its universal ability to pick macromolecular particles of various sizes. Thus, our deep-learning method could break the particle-picking bottleneck in the single-particle analysis, and thereby accelerates the high-resolution structure determination by cryo-EM. AVAILABILITY AND IMPLEMENTATION The PARSED package and user manual for noncommercial use are available as Supplementary Material (in the compressed file: parsed_v1.zip). SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Ruijie Yao
- State Key Laboratory of Genetic Engineering, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Jiaqiang Qian
- State Key Laboratory of Genetic Engineering, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Qiang Huang
- State Key Laboratory of Genetic Engineering, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai 200438, China.,Multiscale Research Institute of Complex Systems, Fudan University, Shanghai 201203, China
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19
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Ortiz S, Stanisic L, Rodriguez BA, Rampp M, Hummer G, Cossio P. Validation tests for cryo-EM maps using an independent particle set. J Struct Biol X 2020; 4:100032. [PMID: 32743544 PMCID: PMC7385033 DOI: 10.1016/j.yjsbx.2020.100032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Cryo-electron microscopy (cryo-EM) has revolutionized structural biology by providing 3D density maps of biomolecules at near-atomic resolution. However, map validation is still an open issue. Despite several efforts from the community, it is possible to overfit 3D maps to noisy data. Here, we develop a novel methodology that uses a small independent particle set (not used during the 3D refinement) to validate the maps. The main idea is to monitor how the map probability evolves over the control set during the 3D refinement. The method is complementary to the gold-standard procedure, which generates two reconstructions at each iteration. We low-pass filter the two reconstructions for different frequency cutoffs, and we calculate the probability of each filtered map given the control set. For high-quality maps, the probability should increase as a function of the frequency cutoff and the refinement iteration. We also compute the similarity between the densities of probability distributions of the two reconstructions. As higher frequencies are included, the distributions become more dissimilar. We optimized the BioEM package to perform these calculations, and tested it over systems ranging from quality data to pure noise. Our results show that with our methodology, it possible to discriminate datasets that are constructed from noise particles. We conclude that validation against a control particle set provides a powerful tool to assess the quality of cryo-EM maps.
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Affiliation(s)
- Sebastian Ortiz
- Biophysics of Tropical Diseases, Max Planck Tandem Group, University of Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia
| | - Luka Stanisic
- Max Planck Computing and Data Facility, 85748 Garching, Germany
| | - Boris A Rodriguez
- Grupo de Fósica Atómica y Molecular, Instituto de Física, Facultad de Ciencias Exactas y Naturales, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia
| | - Markus Rampp
- Max Planck Computing and Data Facility, 85748 Garching, Germany
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
- Institute of Biophysics, Goethe University, 60438 Frankfurt am Main, Germany
| | - Pilar Cossio
- Biophysics of Tropical Diseases, Max Planck Tandem Group, University of Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
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20
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Abstract
Cross-validation is used to determine the validity of a model on unseen data by assessing if the model is overfitted to noise. It is widely used in many fields, from artificial intelligence to structural biology in X-ray crystallography and nuclear magnetic resonance. Although there are concerns of map overfitting in cryo-electron microscopy (cryo-EM), cross-validation is rarely used. The problem is that establishing a performance metric of the maps over unseen data (given by 2D-projection images) is difficult due to the low signal-to-noise ratios in the individual particles. Here, I present recent advances for cryo-EM map reconstruction. I highlight that the gold-standard procedure can fail to detect map overfitting in certain cases, showing the necessity of assessing the map quality on unbiased data. Finally, I describe the challenges and advantages of developing a robust cross-validation methodology for cryo-EM.
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Affiliation(s)
- Pilar Cossio
- Biophysics of Tropical Diseases, Max Planck Tandem Group, University of Antioquia UdeA, Calle 70 No. 52-21, Medellin, Colombia.,Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
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21
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Benjin X, Ling L. Developments, applications, and prospects of cryo-electron microscopy. Protein Sci 2019; 29:872-882. [PMID: 31854478 PMCID: PMC7096719 DOI: 10.1002/pro.3805] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 12/12/2019] [Accepted: 12/16/2019] [Indexed: 12/30/2022]
Abstract
Cryo‐electron microscopy (cryo‐EM) is a structural biological method that is used to determine the 3D structures of biomacromolecules. After years of development, cryo‐EM has made great achievements, which has led to a revolution in structural biology. In this article, the principle, characteristics, history, current situation, workflow, and common problems of cryo‐EM are systematically reviewed. In addition, the new development direction of cryo‐EM—cryo‐electron tomography (cryo‐ET), is discussed in detail. Also, cryo‐EM is prospected from the following aspects: the structural analysis of small proteins, the improvement of resolution and efficiency, and the relationship between cryo‐EM and drug development. This review is dedicated to giving readers a comprehensive understanding of the development and application of cryo‐EM, and to bringing them new insights.
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Affiliation(s)
- Xu Benjin
- Laboratory Medicine Department in Fenyang College of Shanxi Medical University, Shanxi, Fenyang, China
| | - Liu Ling
- Laboratory Medicine Department in Fenyang College of Shanxi Medical University, Shanxi, Fenyang, China
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22
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Shorter J, Southworth DR. Spiraling in Control: Structures and Mechanisms of the Hsp104 Disaggregase. Cold Spring Harb Perspect Biol 2019; 11:cshperspect.a034033. [PMID: 30745294 DOI: 10.1101/cshperspect.a034033] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Hsp104 is a hexameric AAA+ ATPase and protein disaggregase found in yeast, which couples ATP hydrolysis to the dissolution of diverse polypeptides trapped in toxic preamyloid oligomers, phase-transitioned gels, disordered aggregates, amyloids, and prions. Hsp104 shows plasticity in disaggregating diverse substrates, but how its hexameric architecture operates as a molecular machine has remained unclear. Here, we highlight structural advances made via cryoelectron microscopy (cryo-EM) that enhance our mechanistic understanding of Hsp104 and other related AAA+ translocases. Hsp104 hexamers are dynamic and adopt open "lock-washer" spiral states and closed ring structures that envelope polypeptide substrate inside the axial channel. ATP hydrolysis-driven conformational changes at the spiral seam ratchet substrate deeper into the channel. Remarkably, this mode of polypeptide translocation is reminiscent of models for how hexameric helicases unwind DNA and RNA duplexes. Thus, Hsp104 likely adapts elements of a deeply rooted, ring-translocase mechanism to the specialized task of protein disaggregation.
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Affiliation(s)
- James Shorter
- Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Daniel R Southworth
- Department of Biochemistry and Biophysics; and the Institute for Neurodegenerative Diseases, University of California San Francisco, San Francisco, California 94158
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23
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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.
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Affiliation(s)
- Dmitry Lyumkis
- From the Laboratory of Genetics and Helmsley Center for Genomic Medicine, The Salk Institute for Biological Studies, La Jolla, California 92037
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24
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Rice WJ, Cheng A, Noble AJ, Eng ET, Kim LY, Carragher B, Potter CS. Routine determination of ice thickness for cryo-EM grids. J Struct Biol 2018; 204:38-44. [PMID: 29981485 PMCID: PMC6119488 DOI: 10.1016/j.jsb.2018.06.007] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Revised: 06/11/2018] [Accepted: 06/27/2018] [Indexed: 12/12/2022]
Abstract
Recent advances in instrumentation and automation have made cryo-EM a popular method for producing near-atomic resolution structures of a variety of proteins and complexes. Sample preparation is still a limiting factor in collecting high quality data. Thickness of the vitreous ice in which the particles are embedded is one of the many variables that need to be optimized for collection of the highest quality data. Here we present two methods, using either an energy filter or scattering outside the objective aperture, to measure ice thickness for potentially every image collected. Unlike geometrical or tomographic methods, these can be implemented directly in the single particle collection workflow without interrupting or significantly slowing down data collection. We describe the methods as implemented into the Leginon/Appion data collection workflow, along with some examples from test cases. Routine monitoring of ice thickness should prove helpful for optimizing sample preparation, data collection, and data processing.
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Affiliation(s)
- William J. Rice
- National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, United States
| | - Anchi Cheng
- National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, United States
| | - Alex J. Noble
- National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, United States
| | - Edward T. Eng
- National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, United States
| | - Laura Y. Kim
- National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, United States
| | - Bridget Carragher
- National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, United States
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Clinton S. Potter
- National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, United States
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
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25
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Oshima A. Structure of an innexin gap junction channel and cryo-EM sample preparation. Microscopy (Oxf) 2018; 66:371-379. [PMID: 29036409 PMCID: PMC6084585 DOI: 10.1093/jmicro/dfx035] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 08/31/2017] [Indexed: 01/05/2023] Open
Abstract
Gap junction channels are essential for mediating intercellular communication in most multicellular organisms. Two gene families encode gap junction channels, innexin and connexin. Although the sequence similarity between these two families based on bioinformatics is not conclusively determined, the gap junction channels encoded by these two gene families are structurally and functionally analogous. We recently reported an atomic structure of an invertebrate innexin gap junction channel using single-particle cryo-electron microscopy. Our findings revealed that connexin and innexin families share several structural properties with regard to their monomeric and oligomeric structures, while simultaneously suggesting a diversity of gap junction channels in nature. This review summarizes cutting-edge progress toward determining an innexin gap junction channel structure, as well as essential tips for preparing cryo-electron microscopy samples for high-resolution structural analysis of an innexin gap junction channel.
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Affiliation(s)
- Atsunori Oshima
- Cellular and Structural Physiology Institute (CeSPI), Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan.,Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
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26
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Gallagher JR, McCraw DM, Torian U, Gulati NM, Myers ML, Conlon MT, Harris AK. Characterization of Hemagglutinin Antigens on Influenza Virus and within Vaccines Using Electron Microscopy. Vaccines (Basel) 2018; 6:E31. [PMID: 29799445 PMCID: PMC6027289 DOI: 10.3390/vaccines6020031] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Revised: 05/11/2018] [Accepted: 05/21/2018] [Indexed: 01/08/2023] Open
Abstract
Influenza viruses affect millions of people worldwide on an annual basis. Although vaccines are available, influenza still causes significant human mortality and morbidity. Vaccines target the major influenza surface glycoprotein hemagglutinin (HA). However, circulating HA subtypes undergo continual variation in their dominant epitopes, requiring vaccines to be updated annually. A goal of next-generation influenza vaccine research is to produce broader protective immunity against the different types, subtypes, and strains of influenza viruses. One emerging strategy is to focus the immune response away from variable epitopes, and instead target the conserved stem region of HA. To increase the display and immunogenicity of the HA stem, nanoparticles are being developed to display epitopes in a controlled spatial arrangement to improve immunogenicity and elicit protective immune responses. Engineering of these nanoparticles requires structure-guided design to optimize the fidelity and valency of antigen presentation. Here, we review electron microscopy applied to study the 3D structures of influenza viruses and different vaccine antigens. Structure-guided information from electron microscopy should be integrated into pipelines for the development of both more efficacious seasonal and universal influenza vaccine antigens. The lessons learned from influenza vaccine electron microscopic research could aid in the development of novel vaccines for other pathogens.
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Affiliation(s)
- John R Gallagher
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 50 South Drive, Room 6351, Bethesda, MD 20892, USA.
| | - Dustin M McCraw
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 50 South Drive, Room 6351, Bethesda, MD 20892, USA.
| | - Udana Torian
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 50 South Drive, Room 6351, Bethesda, MD 20892, USA.
| | - Neetu M Gulati
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 50 South Drive, Room 6351, Bethesda, MD 20892, USA.
| | - Mallory L Myers
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 50 South Drive, Room 6351, Bethesda, MD 20892, USA.
| | - Michael T Conlon
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 50 South Drive, Room 6351, Bethesda, MD 20892, USA.
| | - Audray K Harris
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 50 South Drive, Room 6351, Bethesda, MD 20892, USA.
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27
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28
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Madej MG, Ziegler CM. Dawning of a new era in TRP channel structural biology by cryo-electron microscopy. Pflugers Arch 2018; 470:213-225. [PMID: 29344776 DOI: 10.1007/s00424-018-2107-2] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 01/03/2018] [Indexed: 12/20/2022]
Abstract
Cryo-electron microscopy (cryo-EM) permits the determination of atomic protein structures by averaging large numbers of individual projection images recorded at cryogenic temperatures-a method termed single-particle analysis. The cryo-preservation traps proteins within a thin glass-like ice layer, making literally a freeze image of proteins in solution. Projections of randomly adopted orientations are merged to reconstruct a 3D density map. While atomic resolution for highly symmetric viruses was achieved already in 2009, the development of new sensitive and fast electron detectors has enabled cryo-EM for smaller and asymmetrical proteins including fragile membrane proteins. As one of the most important structural biology methods at present, cryo-EM was awarded in October 2017 with the Nobel Prize in Chemistry. The molecular understanding of Transient-Receptor-Potential (TRP) channels has been boosted tremendously by cryo-EM single-particle analysis. Several near-atomic and atomic structures gave important mechanistic insights, e.g., into ion permeation and selectivity, gating, as well as into the activation of this enigmatic and medically important membrane protein family by various chemical and physical stimuli. Lastly, these structures have set the starting point for the rational design of TRP channel-targeted therapeutics to counteract life-threatening channelopathies. Here, we attempt a brief introduction to the method, review the latest advances in cryo-EM structure determination of TRP channels, and discuss molecular insights into the channel function based on the wealth of TRP channel cryo-EM structures.
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Affiliation(s)
- M Gregor Madej
- Department of Structural Biology, Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstrasse 31, D-93053, Regensburg, Germany
| | - Christine M Ziegler
- Department of Structural Biology, Institute of Biophysics and Physical Biochemistry, University of Regensburg, Universitätsstrasse 31, D-93053, Regensburg, Germany.
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B Kumar R, Zhu L, Hebert H, Jegerschöld C. Method to Visualize and Analyze Membrane Interacting Proteins by Transmission Electron Microscopy. J Vis Exp 2017. [PMID: 28287545 DOI: 10.3791/55148] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Monotopic proteins exert their function when attached to a membrane surface, and such interactions depend on the specific lipid composition and on the availability of enough area to perform the function. Nanodiscs are used to provide a membrane surface of controlled size and lipid content. In the absence of bound extrinsic proteins, sodium phosphotungstate-stained nanodiscs appear as stacks of coins when viewed from the side by transmission electron microscopy (TEM). This protocol is therefore designed to intentionally promote stacking; consequently, the prevention of stacking can be interpreted as the binding of the membrane-binding protein to the nanodisc. In a further step, the TEM images of the protein-nanodisc complexes can be processed with standard single-particle methods to yield low-resolution structures as a basis for higher resolution cryoEM work. Furthermore, the nanodiscs provide samples suitable for either TEM or non-denaturing gel electrophoresis. To illustrate the method, Ca2+-induced binding of 5-lipoxygenase on nanodiscs is presented.
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Affiliation(s)
| | - Lin Zhu
- School of Technology and Health, KTH Royal Institute of Technology
| | - Hans Hebert
- Department of Biosciences and Nutrition, Karolinska Institutet; School of Technology and Health, KTH Royal Institute of Technology
| | - Caroline Jegerschöld
- Department of Biosciences and Nutrition, Karolinska Institutet; School of Technology and Health, KTH Royal Institute of Technology; ;
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30
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Structural Study of Heterogeneous Biological Samples by Cryoelectron Microscopy and Image Processing. BIOMED RESEARCH INTERNATIONAL 2017; 2017:1032432. [PMID: 28191458 PMCID: PMC5274696 DOI: 10.1155/2017/1032432] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 11/23/2016] [Indexed: 11/18/2022]
Abstract
In living organisms, biological macromolecules are intrinsically flexible and naturally exist in multiple conformations. Modern electron microscopy, especially at liquid nitrogen temperatures (cryo-EM), is able to visualise biocomplexes in nearly native conditions and in multiple conformational states. The advances made during the last decade in electronic technology and software development have led to the revelation of structural variations in complexes and also improved the resolution of EM structures. Nowadays, structural studies based on single particle analysis (SPA) suggests several approaches for the separation of different conformational states and therefore disclosure of the mechanisms for functioning of complexes. The task of resolving different states requires the examination of large datasets, sophisticated programs, and significant computing power. Some methods are based on analysis of two-dimensional images, while others are based on three-dimensional studies. In this review, we describe the basic principles implemented in the various techniques that are currently used in the analysis of structural conformations and provide some examples of successful applications of these methods in structural studies of biologically significant complexes.
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31
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Walls A, Tortorici MA, Bosch B, Frenz B, Rottier PJM, DiMaio F, Rey FA, Veesler D. Crucial steps in the structure determination of a coronavirus spike glycoprotein using cryo-electron microscopy. Protein Sci 2017; 26:113-121. [PMID: 27667334 PMCID: PMC5192993 DOI: 10.1002/pro.3048] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 09/21/2016] [Accepted: 09/22/2016] [Indexed: 12/21/2022]
Abstract
The tremendous pandemic potential of coronaviruses was demonstrated twice in the last 15 years by two global outbreaks of deadly pneumonia. Entry of coronaviruses into cells is mediated by the transmembrane spike glycoprotein S, which forms a trimer carrying receptor-binding and membrane fusion functions. Despite their biomedical importance, coronavirus S glycoproteins have proven difficult targets for structural characterization, precluding high-resolution studies of the biologically relevant trimer. Recent technological developments in single particle cryo-electron microscopy allowed us to determine the first structure of a coronavirus S glycoprotein trimer which provided a framework to understand the mechanisms of viral entry and suggested potential inhibition strategies for this family of viruses. Here, we describe the key factors that enabled this breakthrough.
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Affiliation(s)
- Alexandra Walls
- Department of BiochemistryUniversity of WashingtonSeattleWashington98195
| | - M. Alejandra Tortorici
- Institut Pasteur, Département de Virologie, Unité de Virologie StructuraleParisFrance
- CNRS UMR 3569 VirologieParisFrance
| | - Berend‐Jan Bosch
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary MedicineUtrecht University3584 CL UtrechtThe Netherlands
| | - Brandon Frenz
- Department of BiochemistryUniversity of WashingtonSeattleWashington98195
| | - Peter J. M. Rottier
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary MedicineUtrecht University3584 CL UtrechtThe Netherlands
| | - Frank DiMaio
- Department of BiochemistryUniversity of WashingtonSeattleWashington98195
| | - Felix A. Rey
- Institut Pasteur, Département de Virologie, Unité de Virologie StructuraleParisFrance
- CNRS UMR 3569 VirologieParisFrance
| | - David Veesler
- Department of BiochemistryUniversity of WashingtonSeattleWashington98195
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