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Schreiber MT, Maigné A, Beleggia M, Shibata S, Wolf M. Temporal dynamics of charge buildup in cryo-electron microscopy. J Struct Biol X 2022; 7:100081. [PMID: 36632442 PMCID: PMC9826809 DOI: 10.1016/j.yjsbx.2022.100081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
It is well known that insulating samples can accumulate electric charges from exposure to an electron beam. How the accumulation of charge affects imaging parameters and sample stability in transmission electron microscopy is poorly understood. To quantify these effects, it is important to know how the charge is distributed within the sample and how it builds up over time. In the present study, we determine the spatial distribution and temporal dynamics of charge accumulation on vitreous ice samples with embedded proteins through a combination of modeling and Fresnel diffraction experiments. Our data reveal a rapid evolution of the charge state on ice upon initial exposure to the electron beam accompanied by charge gradients at the interfaces between ice and carbon films. We demonstrate that ice film movement and charge state variations occur upon electron beam exposure and are dose-rate dependent. Both affect the image defocus through a combination of sample height changes and lensing effects. Our results may be used as a guide to improve sample preparation, data collection, and data processing for imaging of dose-sensitive samples.
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Affiliation(s)
- Makoto Tokoro Schreiber
- Molecular Cryo-Electron Microscopy Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa, Japan
| | - Alan Maigné
- Molecular Cryo-Electron Microscopy Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa, Japan
| | - Marco Beleggia
- DTU Nanolab, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Satoshi Shibata
- Molecular Cryo-Electron Microscopy Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa, Japan
| | - Matthias Wolf
- Molecular Cryo-Electron Microscopy Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa, Japan,Institute of Biological Chemistry, Academia Sinica, Nankang, Taipei 115, Taiwan,Corresponding author at: Molecular Cryo-Electron Microscopy Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa, Japan.
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Valencia L, de la Mata M, Herrera M, Delgado F, Hernández-Saz J, Molina S. Induced damage during STEM-EELS analyses on acrylic-based materials for Stereolithography. Polym Degrad Stab 2022. [DOI: 10.1016/j.polymdegradstab.2022.110044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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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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Abstract
CryoEM has become the method of choice for determining the structure of large macromolecular complexes in multiple conformations, at resolutions where unambiguous atomic models can be built. Two effects that have limited progress in single-particle cryoEM are (i) beam-induced movement during image acquisition and (ii) protein adsorption and denaturation at the air-water interface during specimen preparation. While beam-induced movement now appears to have been resolved by all-gold specimen support grids with very small holes, surface effects at the air-water interface are a persistent problem. Strategies to overcome these effects include the use of alternative support films and new techniques for specimen deposition. We examine the future potential of recording perfect images of biological samples for routine structure determination at atomic resolution.
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D'Imprima E, Floris D, Joppe M, Sánchez R, Grininger M, Kühlbrandt W. Protein denaturation at the air-water interface and how to prevent it. eLife 2019; 8:42747. [PMID: 30932812 PMCID: PMC6443348 DOI: 10.7554/elife.42747] [Citation(s) in RCA: 160] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 02/27/2019] [Indexed: 12/19/2022] Open
Abstract
Electron cryo-microscopy analyzes the structure of proteins and protein complexes in vitrified solution. Proteins tend to adsorb to the air-water interface in unsupported films of aqueous solution, which can result in partial or complete denaturation. We investigated the structure of yeast fatty acid synthase at the air-water interface by electron cryo-tomography and single-particle image processing. Around 90% of complexes adsorbed to the air-water interface are partly denatured. We show that the unfolded regions face the air-water interface. Denaturation by contact with air may happen at any stage of specimen preparation. Denaturation at the air-water interface is completely avoided when the complex is plunge-frozen on a substrate of hydrophilized graphene.
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Affiliation(s)
- Edoardo D'Imprima
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt, Germany
| | - Davide Floris
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt, Germany
| | - Mirko Joppe
- Buchmann Institute for Molecular Life Sciences, Institute of Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt, Germany
| | - Ricardo Sánchez
- Sofja Kovalevskaja Group, Max Planck Institute of Biophysics, Frankfurt, Germany
| | - Martin Grininger
- Buchmann Institute for Molecular Life Sciences, Institute of Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt, Germany
| | - Werner Kühlbrandt
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt, Germany
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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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Li J, Zheng C, Liu B, Chou T, Kim Y, Qiu S, Li J, Yan W, Fu J. Controlled graphene encapsulation: a nanoscale shield for characterising single bacterial cells in liquid. NANOTECHNOLOGY 2018; 29:365705. [PMID: 29889049 DOI: 10.1088/1361-6528/aacba7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
High-resolution single-cell imaging in their native or near-native state has received considerable interest for decades. In this research, we present an innovative approach that can be employed to study both morphological and nano-mechanical properties of hydrated single bacterial cells. The proposed strategy is to encapsulate wet cells with monolayer graphene with a newly developed water membrane approach, followed by imaging with both electron microscopy (EM) and atomic force microscopy (AFM). A computational framework was developed to provide additional insights, with the detailed nanoindentation process on graphene modelled based on the finite element method. The model was first validated by calibration with polymer materials of known properties, and the contribution of graphene was then studied and corrected to determine the actual moduli of the encapsulated hydrated sample. Application of the proposed approach was performed on hydrated bacterial cells (Klebsiella pneumoniae) to correlate the structural and mechanical information. EM and energy-dispersive x-ray spectroscopy imaging confirmed that the cells in their near-native stage can be studied inside the miniaturised environment enabled with graphene encapsulation. The actual moduli of the encapsulated hydrated cells were determined based on the developed computational model in parallel, with results comparable with those acquired with wet AFM. It is expected that the successful establishment of controlled graphene encapsulation offers a new route for probing liquid/live cells with scanning probe microscopy, as well as correlative imaging of hydrated samples for both biological and material sciences.
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Affiliation(s)
- Jiayao Li
- Department of Mechanical and Aerospace Engineering, Monash University, Clayton, VIC 3800, Australia
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Hettler S, Kano E, Dries M, Gerthsen D, Pfaffmann L, Bruns M, Beleggia M, Malac M. Charging of carbon thin films in scanning and phase-plate transmission electron microscopy. Ultramicroscopy 2018; 184:252-266. [DOI: 10.1016/j.ultramic.2017.09.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 09/08/2017] [Accepted: 09/26/2017] [Indexed: 01/29/2023]
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Yamashita M, Leyden MR, Adaniya H, Cheung MP, Hirai T, Qi Y, Shintake T. Graphene specimen support technique for low voltage STEM imaging. Microscopy (Oxf) 2017; 66:261-271. [PMID: 28453814 DOI: 10.1093/jmicro/dfx014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 04/13/2017] [Indexed: 06/07/2023] Open
Abstract
The scanning transmission electron microscopy (STEM) mode of today's field emission scanning electron microscopes enables sub-nanometer resolution imaging. Graphene is a single-atom thick, electrically conductive material, making it an excellent specimen support for the low voltage STEM imaging of nanometer-sized objects such as viruses. Here we present low voltage STEM images of bacteriophage T4 recorded on highly cleaned graphene films. The results show that ultrathin graphene support films markedly improve image signal at low accelerating voltages. Staining with a low atomic number methylamine vanadate stain combined with the graphene support film enables the clear visualization of the fine structure of the T4 tail by the low voltage STEM technique. Despite the advantages of graphene support films, difficulties are often encountered in placing hydrophilic biological samples on hydrophobic graphene electron microscopy grids. We employed a spin sedimentation sample loading method to overcome this problem.
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Affiliation(s)
- Masao Yamashita
- Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa 904-0495, Japan
| | - Matthew Ryan Leyden
- Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa 904-0495, Japan
| | - Hidehito Adaniya
- Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa 904-0495, Japan
| | - Martin Philip Cheung
- Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa 904-0495, Japan
| | - Teruhisa Hirai
- Cellular and Structural Physiology Institute, Nagoya University, Chikusa-ku, Furo-cho, Nagoya 464-8601, Japan
| | - Yabing Qi
- Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa 904-0495, Japan
| | - Tsumoru Shintake
- Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa 904-0495, Japan
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Abstract
AbstractThere has been enormous progress during the last few years in the determination of three-dimensional biological structures by single particle electron cryomicroscopy (cryoEM), allowing maps to be obtained with higher resolution and from fewer images than required previously. This is due principally to the introduction of a new type of direct electron detector that has 2- to 3-fold higher detective quantum efficiency than available previously, and to the improvement of the computational algorithms for image processing. In spite of the great strides that have been made, quantitative analysis shows that there are still significant gains to be made provided that the problems associated with image degradation can be solved, possibly by minimising beam-induced specimen movement and charge build up during imaging. If this can be achieved, it should be possible to obtain near atomic resolution structures of smaller single particles, using fewer images and resolving more conformational states than at present, thus realising the full potential of the method. The recent popularity of cryoEM for molecular structure determination also highlights the need for lower cost microscopes, so we encourage development of an inexpensive, 100 keV electron cryomicroscope with a high-brightness field emission gun to make the method accessible to individual groups or institutions that cannot afford the investment and running costs of a state-of-the-art 300 keV installation. A key requisite for successful high-resolution structure determination by cryoEM includes interpretation of images and optimising the biochemistry and grid preparation to obtain nicely distributed macromolecules of interest. We thus include in this review a gallery of cryoEM micrographs that shows illustrative examples of single particle images of large and small macromolecular complexes.
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Russo CJ, Passmore LA. Progress towards an optimal specimen support for electron cryomicroscopy. Curr Opin Struct Biol 2016; 37:81-9. [PMID: 26774849 PMCID: PMC4863039 DOI: 10.1016/j.sbi.2015.12.007] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 12/21/2015] [Accepted: 12/21/2015] [Indexed: 01/04/2023]
Abstract
Physical principles of electron scattering govern the design of specimen supports. Radiation-induced motion causes loss of resolution in electron micrographs. Specimen supports can now be designed to reduce specimen motion. Tailored surfaces in the support allow control of particle distribution and orientation. Future developments in support technology will further improve image quality.
The physical principles of electron–specimen interaction govern the design of specimen supports for electron cryomicroscopy (cryo-EM). Supports are constructed to suspend biological samples within the vacuum of the electron microscope in a way that maximises image contrast. Although the problem of specimen motion during imaging has been known since cryo-EM was first developed, the role of the support in this movement has only been recently identified. Here we review the key technological advances in specimen supports for cryo-EM. This includes the use of graphene as a surface for the adsorption of proteins and the design of an ultrastable, all-gold substrate that reduces the motion of molecules during electron irradiation. We discuss the implications of these and other recent improvements in specimen supports on resolution, and place them in the context of important developments in structure determination by cryo-EM.
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Affiliation(s)
- Christopher J Russo
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
| | - Lori A Passmore
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
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13
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How cryo-EM is revolutionizing structural biology. Trends Biochem Sci 2015; 40:49-57. [DOI: 10.1016/j.tibs.2014.10.005] [Citation(s) in RCA: 570] [Impact Index Per Article: 63.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Revised: 10/10/2014] [Accepted: 10/16/2014] [Indexed: 02/06/2023]
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Russo CJ, Passmore LA. Controlling protein adsorption on graphene for cryo-EM using low-energy hydrogen plasmas. Nat Methods 2014; 11:649-52. [PMID: 24747813 PMCID: PMC4141966 DOI: 10.1038/nmeth.2931] [Citation(s) in RCA: 119] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Accepted: 02/28/2014] [Indexed: 12/24/2022]
Abstract
Despite its many favorable properties as a sample support for biological electron microscopy, graphene is not widely used because its hydrophobicity precludes reliable protein deposition. We describe a method to modify graphene with a low-energy hydrogen plasma, which reduces hydrophobicity without degrading the graphene lattice. Use of plasma-treated graphene enables better control of protein distribution in ice for electron cryo-microscopy and improves image quality by reducing radiation-induced sample motion.
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Affiliation(s)
| | - Lori A Passmore
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
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