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Küçükoğlu B, Mohammed I, Guerrero-Ferreira RC, Ribet SM, Varnavides G, Leidl ML, Lau K, Nazarov S, Myasnikov A, Kube M, Radecke J, Sachse C, Müller-Caspary K, Ophus C, Stahlberg H. Low-dose cryo-electron ptychography of proteins at sub-nanometer resolution. Nat Commun 2024; 15:8062. [PMID: 39277607 PMCID: PMC11401879 DOI: 10.1038/s41467-024-52403-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Accepted: 09/05/2024] [Indexed: 09/17/2024] Open
Abstract
Cryo-transmission electron microscopy (cryo-EM) of frozen hydrated specimens is an efficient method for the structural analysis of purified biological molecules. However, cryo-EM and cryo-electron tomography are limited by the low signal-to-noise ratio (SNR) of recorded images, making detection of smaller particles challenging. For dose-resilient samples often studied in the physical sciences, electron ptychography - a coherent diffractive imaging technique using 4D scanning transmission electron microscopy (4D-STEM) - has recently demonstrated excellent SNR and resolution down to tens of picometers for thin specimens imaged at room temperature. Here we apply 4D-STEM and ptychographic data analysis to frozen hydrated proteins, reaching sub-nanometer resolution 3D reconstructions. We employ low-dose cryo-EM with an aberration-corrected, convergent electron beam to collect 4D-STEM data for our reconstructions. The high frame rate of the electron detector allows us to record large datasets of electron diffraction patterns with substantial overlaps between the interaction volumes of adjacent scan positions, from which the scattering potentials of the samples are iteratively reconstructed. The reconstructed micrographs show strong SNR enabling the reconstruction of the structure of apoferritin protein at up to 5.8 Å resolution. We also show structural analysis of the Phi92 capsid and sheath, tobacco mosaic virus, and bacteriorhodopsin at slightly lower resolutions.
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Affiliation(s)
- Berk Küçükoğlu
- Laboratory of Biological Electron Microscopy, Institute of Physics, School of Basic Sciences, EPFL, and Department of Fundamental Microbiology, Faculty of Biology and Medicine, UNIL, Rte. de la Sorge, 1015, Lausanne, Switzerland
| | - Inayathulla Mohammed
- Laboratory of Biological Electron Microscopy, Institute of Physics, School of Basic Sciences, EPFL, and Department of Fundamental Microbiology, Faculty of Biology and Medicine, UNIL, Rte. de la Sorge, 1015, Lausanne, Switzerland
| | - Ricardo C Guerrero-Ferreira
- Laboratory of Biological Electron Microscopy, Institute of Physics, School of Basic Sciences, EPFL, and Department of Fundamental Microbiology, Faculty of Biology and Medicine, UNIL, Rte. de la Sorge, 1015, Lausanne, Switzerland
- Robert P. Apkarian Integrated Electron Microscopy Core, Emory University School of Medicine, 1521 Dickey Drive NE, Atlanta, GA, 30322, USA
| | - Stephanie M Ribet
- National Center for Electron Microscopy (NCEM), Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Georgios Varnavides
- National Center for Electron Microscopy (NCEM), Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Miller Institute for Basic Research in Science, University of California, Berkeley, CA, 94720, USA
| | - Max Leo Leidl
- Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons (ER-C-3): Structural Biology, Jülich, Germany
- Department of Chemistry and Centre for NanoScience, Ludwig-Maximilians-Universität München, Butenandstr. 11, 81377, München, Germany
| | - Kelvin Lau
- Protein Production and Structure Core Facility (PTPSP), School of Life Sciences, EPFL, Rte Cantonale, 1015, Lausanne, Switzerland
| | - Sergey Nazarov
- Dubochet Center for Imaging Lausanne, EPFL and UNIL, EPFL VPA DCI-Lausanne, 1015, Lausanne, Switzerland
| | - Alexander Myasnikov
- Dubochet Center for Imaging Lausanne, EPFL and UNIL, EPFL VPA DCI-Lausanne, 1015, Lausanne, Switzerland
| | - Massimo Kube
- Laboratory of Biological Electron Microscopy, Institute of Physics, School of Basic Sciences, EPFL, and Department of Fundamental Microbiology, Faculty of Biology and Medicine, UNIL, Rte. de la Sorge, 1015, Lausanne, Switzerland
| | - Julika Radecke
- Laboratory of Biological Electron Microscopy, Institute of Physics, School of Basic Sciences, EPFL, and Department of Fundamental Microbiology, Faculty of Biology and Medicine, UNIL, Rte. de la Sorge, 1015, Lausanne, Switzerland
| | - Carsten Sachse
- Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons (ER-C-3): Structural Biology, Jülich, Germany
- Department of Biology, Heinrich Heine University, Düsseldorf, Germany
| | - Knut Müller-Caspary
- Department of Chemistry and Centre for NanoScience, Ludwig-Maximilians-Universität München, Butenandstr. 11, 81377, München, Germany
| | - Colin Ophus
- National Center for Electron Microscopy (NCEM), Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Henning Stahlberg
- Laboratory of Biological Electron Microscopy, Institute of Physics, School of Basic Sciences, EPFL, and Department of Fundamental Microbiology, Faculty of Biology and Medicine, UNIL, Rte. de la Sorge, 1015, Lausanne, Switzerland.
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Cebi E, Lee J, Subramani VK, Bak N, Oh C, Kim KK. Cryo-electron microscopy-based drug design. Front Mol Biosci 2024; 11:1342179. [PMID: 38501110 PMCID: PMC10945328 DOI: 10.3389/fmolb.2024.1342179] [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] [Received: 11/21/2023] [Accepted: 01/31/2024] [Indexed: 03/20/2024] Open
Abstract
Structure-based drug design (SBDD) has gained popularity owing to its ability to develop more potent drugs compared to conventional drug-discovery methods. The success of SBDD relies heavily on obtaining the three-dimensional structures of drug targets. X-ray crystallography is the primary method used for solving structures and aiding the SBDD workflow; however, it is not suitable for all targets. With the resolution revolution, enabling routine high-resolution reconstruction of structures, cryogenic electron microscopy (cryo-EM) has emerged as a promising alternative and has attracted increasing attention in SBDD. Cryo-EM offers various advantages over X-ray crystallography and can potentially replace X-ray crystallography in SBDD. To fully utilize cryo-EM in drug discovery, understanding the strengths and weaknesses of this technique and noting the key advancements in the field are crucial. This review provides an overview of the general workflow of cryo-EM in SBDD and highlights technical innovations that enable its application in drug design. Furthermore, the most recent achievements in the cryo-EM methodology for drug discovery are discussed, demonstrating the potential of this technique for advancing drug development. By understanding the capabilities and advancements of cryo-EM, researchers can leverage the benefits of designing more effective drugs. This review concludes with a discussion of the future perspectives of cryo-EM-based SBDD, emphasizing the role of this technique in driving innovations in drug discovery and development. The integration of cryo-EM into the drug design process holds great promise for accelerating the discovery of new and improved therapeutic agents to combat various diseases.
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Affiliation(s)
| | | | | | | | - Changsuk Oh
- Department of Precision Medicine, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
| | - Kyeong Kyu Kim
- Department of Precision Medicine, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
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Flannigan DJ, VandenBussche EJ. Pulsed-beam transmission electron microscopy and radiation damage. Micron 2023; 172:103501. [PMID: 37390662 DOI: 10.1016/j.micron.2023.103501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 06/20/2023] [Accepted: 06/21/2023] [Indexed: 07/02/2023]
Abstract
We review the use of pulsed electron-beams in transmission electron microscopes (TEMs) for the purpose of mitigating specimen damage. We begin by placing the importance of TEMs with respect to materials characterization into proper context, and we provide a brief overview of established methods for reducing or eliminating the deleterious effects of beam-induced damage. We then introduce the concept of pulsed-beam TEM, and we briefly describe the basic methods and instrument configurations used to create so-called temporally structured electron beams. Following a brief overview of the use of high-dose-rate pulsed-electron beams in cancer radiation therapy, we review historical speculations and more recent compelling but mostly anecdotal findings of a pulsed-beam TEM damage effect. This is followed by an in-depth technical review of recent works seeking to establish cause-and-effect relationships, to conclusively uncover the presence of an effect, and to explore the practicality of the approach. These studies, in particular, provide the most compelling evidence to date that using a pulsed electron beam in the TEM is indeed a viable way to mitigate damage. Throughout, we point out current gaps in understanding, and we conclude with a brief perspective of current needs and future directions.
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Affiliation(s)
- David J Flannigan
- Department of Chemical Engineering and Materials Science, University of Minnesota, 421 Washington Avenue SE, Minneapolis, MN 55455, USA; Minnesota Institute for Ultrafast Science, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Elisah J VandenBussche
- Department of Chemical Engineering and Materials Science, University of Minnesota, 421 Washington Avenue SE, Minneapolis, MN 55455, USA; Minnesota Institute for Ultrafast Science, University of Minnesota, Minneapolis, MN 55455, USA
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Biran I, Houben L, Weissman H, Hildebrand M, Kronik L, Rybtchinski B. Real-Space Crystal Structure Analysis by Low-Dose Focal-Series TEM Imaging of Organic Materials with Near-Atomic Resolution. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2022; 34:e2202088. [PMID: 35451121 DOI: 10.1002/adma.202202088] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 04/17/2022] [Indexed: 06/14/2023]
Abstract
Structural analysis of beam-sensitive materials by transmission electron microscopy (TEM) represents a significant challenge, as high-resolution TEM (HRTEM) requires high electron doses that limit its applicability to stable inorganic materials. Beam-sensitive materials, e.g., organic crystals, must be imaged under low dose conditions, leading to problematic contrast interpretation and loss of fine structural details. Here, HRTEM imaging of organic crystalline materials with near-atomic resolution of up to 1.6 Å is described, which enables real-space studies of crystal structures, as well as observation of co-existing polymorphs, crystal defects, and atoms. This is made possible by a low-dose focal-series reconstruction methodology, which provides HRTEM images where contrast reflects true object structure and can be performed on contemporary cryo-EM instruments available to many research institutions. Copper phthalocyanine (CuPc), a perchlorinated analogue of CuPc, and indigo crystalline films are imaged. In the case of indigo crystals, co-existing polymorphs and individual atoms (carbonyl oxygen) can be observed. In the case of CuPc, several polymorphs are observed, including a new one, for which the crystal structure is found based on direct in-focus imaging, accomplishing real-space crystal structure elucidation. Such direct analysis can be transformative for structure studies of organic materials.
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Affiliation(s)
- Idan Biran
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Lothar Houben
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Haim Weissman
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Mariana Hildebrand
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Leeor Kronik
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Boris Rybtchinski
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot, 7610001, Israel
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Allione M, Limongi T, Marini M, Torre B, Zhang P, Moretti M, Perozziello G, Candeloro P, Napione L, Pirri CF, Di Fabrizio E. Micro/Nanopatterned Superhydrophobic Surfaces Fabrication for Biomolecules and Biomaterials Manipulation and Analysis. MICROMACHINES 2021; 12:1501. [PMID: 34945349 PMCID: PMC8708205 DOI: 10.3390/mi12121501] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/19/2021] [Accepted: 11/25/2021] [Indexed: 01/04/2023]
Abstract
Superhydrophobic surfaces display an extraordinary repulsion to water and water-based solutions. This effect emerges from the interplay of intrinsic hydrophobicity of the surface and its morphology. These surfaces have been established for a long time and have been studied for decades. The increasing interest in recent years has been focused towards applications in many different fields and, in particular, biomedical applications. In this paper, we review the progress achieved in the last years in the fabrication of regularly patterned superhydrophobic surfaces in many different materials and their exploitation for the manipulation and characterization of biomaterial, with particular emphasis on the issues affecting the yields of the fabrication processes and the quality of the manufactured devices.
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Affiliation(s)
- Marco Allione
- Center for Sustainable Future Technologies @POLITO, Istituto Italiano di Tecnologia, Via Livorno 60, 10144 Turin, Italy;
- Dipartimento di Scienza Applicata e Tecnologia (DISAT), Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Turin, Italy; (M.M.); (B.T.); (L.N.); (E.D.F.)
| | - Tania Limongi
- Dipartimento di Scienza Applicata e Tecnologia (DISAT), Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Turin, Italy; (M.M.); (B.T.); (L.N.); (E.D.F.)
| | - Monica Marini
- Dipartimento di Scienza Applicata e Tecnologia (DISAT), Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Turin, Italy; (M.M.); (B.T.); (L.N.); (E.D.F.)
| | - Bruno Torre
- Dipartimento di Scienza Applicata e Tecnologia (DISAT), Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Turin, Italy; (M.M.); (B.T.); (L.N.); (E.D.F.)
| | - Peng Zhang
- Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; (P.Z.); (M.M.)
| | - Manola Moretti
- Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; (P.Z.); (M.M.)
| | - Gerardo Perozziello
- BioNEM Laboratory, Department of Experimental and Clinical Medicine, Campus S. Venuta, Magna Graecia University, Germaneto, Viale Europa, 88100 Catanzaro, Italy; (G.P.); (P.C.)
| | - Patrizio Candeloro
- BioNEM Laboratory, Department of Experimental and Clinical Medicine, Campus S. Venuta, Magna Graecia University, Germaneto, Viale Europa, 88100 Catanzaro, Italy; (G.P.); (P.C.)
| | - Lucia Napione
- Dipartimento di Scienza Applicata e Tecnologia (DISAT), Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Turin, Italy; (M.M.); (B.T.); (L.N.); (E.D.F.)
| | - Candido Fabrizio Pirri
- Center for Sustainable Future Technologies @POLITO, Istituto Italiano di Tecnologia, Via Livorno 60, 10144 Turin, Italy;
- Dipartimento di Scienza Applicata e Tecnologia (DISAT), Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Turin, Italy; (M.M.); (B.T.); (L.N.); (E.D.F.)
| | - Enzo Di Fabrizio
- Dipartimento di Scienza Applicata e Tecnologia (DISAT), Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Turin, Italy; (M.M.); (B.T.); (L.N.); (E.D.F.)
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黄 新, 李 莎, 高 嵩. [Progress in filters for denoising cryo-electron microscopy images]. BEIJING DA XUE XUE BAO. YI XUE BAN = JOURNAL OF PEKING UNIVERSITY. HEALTH SCIENCES 2021; 53:425-433. [PMID: 33879921 PMCID: PMC8072428 DOI: 10.19723/j.issn.1671-167x.2021.02.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Indexed: 06/12/2023]
Abstract
Cryo-electron microscopy (cryo-EM) imaging has the unique potential to bridge the gap between cellular and molecular biology. Therefore, cryo-EM three-dimensional (3D) reconstruction has been rapidly developed in recent several years and applied widely in life science research to reveal the structures of large macromolecular assemblies and cellular complexes, which is critical to understanding their functions at all scales. Although the technical breakthrough in recent years, for example, the introduction of the direct detection device (DDD) camera and the development of cryo-EM software tools, made the three cryo-EM pioneers share the 2017 Nobel Prize, several bottleneck problems still exist that hamper the further increase of the resolution of single-particle reconstruction and hold back the application of in situ subnanometer structure determination by cryo-tomography. Radiation damage is still the key limiting factor in cryo-EM. In order to minimize the radiation damage and preserve as much resolution as possible, the imaging conditions of a low dose and weak contrast make cryo-EM images extremely noisy with very low signal-to-noise ratios (SNR), generally about 0.1. The high noise will obscure the fine details in cryo-EM images or reconstructed maps. Thus, a method to reduce the level of noise and improve the resolution has become an important issue. In this paper, we systematically reviewed and compared some robust filters in the cryo-EM field of two aspects, single-particle analysis (SPA) and cryo-electron tomography (cryo-ET), and especially studied their applications, such as, 3D reconstruction, visualization, structural analysis, and interpretation. Conventional approaches to noise reduction in cryo-EM imaging include the use of Gaussian, median, and bilateral filters, among other means. A Gaussian filter selects an appropriate filter kernel to conduct spatial convolution with a noisy image. Although noise with larger standard deviations in cryo-EM images can be suppressed and satisfactory performance is achieved in certain cases, this filter also blurs the images and over-smooths small-scale image features. This is especially detrimental when precise quantitative information needs to be extracted. Unlike a Gaussian filter, a median filter is based on the order statistics of the image and selects the median intensity in a window of the adjacent pixels to denoise the image. Although this filter is robust to outliers, it suffers from aliasing problems that possibly result in incorrect information for cryo-EM structure interpretation. A bilateral filter is a nonlinear filter that performs spatial weighted averaging and is more selective in the pixels allowing to contribute to the weighted sum, excluding the high frequency noise from the smoothing process. Thus, this filter can be used to smooth out noise while maintaining the edge details, which is similar to an anisotropic diffusion filter, and distinct from a Gaussian filter but its utility will be limited when the SNR of a cryo-EM image is very low. Generally, spatial filtering methods have the disadvantage of losing image resolution when reducing noise. A wavelet transform can exploit the wavelet's natural ability to separate a signal from noise at multiple image scales to allow for joint resolution in both the spatial and frequency domains, and thus has the potential to outperform existing methods. The modified wavelet shrinkage filter we developed can offer a remarkable improvement in image quality with a good compromise between detail preservation and noise smoothing. We expect that our review study on different filters can provide benefits to cryo-EM applications and the interpretation of biological structures.
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Affiliation(s)
- 新瑞 黄
- 北京大学基础医学院生物化学与生物物理学系,北京 100191Department of Biochemistry and Biophysics, Peking University School of Basic Medical Sciences, Beijing 100191, China
| | - 莎 李
- 北京大学医学部医学技术研究院,北京 100191Institute of Medical Technology, Peking University Health Science Center, Beijing 100191, China
| | - 嵩 高
- 北京大学医学部医学技术研究院,北京 100191Institute of Medical Technology, Peking University Health Science Center, Beijing 100191, China
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Scherr J, Tang Z, Küllmer M, Balser S, Scholz AS, Winter A, Parey K, Rittner A, Grininger M, Zickermann V, Rhinow D, Terfort A, Turchanin A. Smart Molecular Nanosheets for Advanced Preparation of Biological Samples in Electron Cryo-Microscopy. ACS NANO 2020; 14:9972-9978. [PMID: 32589396 DOI: 10.1021/acsnano.0c03052] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Transmission electron cryo-microscopy (cryoEM) of vitrified biological specimens is a powerful tool for structural biology. Current preparation of vitrified biological samples starts off with sample isolation and purification, followed by the fixation in a freestanding layer of amorphous ice. Here, we demonstrate that ultrathin (∼10 nm) smart molecular nanosheets having specific biorecognition sites embedded in a biorepulsive layer covalently bound to a mechanically stable carbon nanomembrane allow for a much simpler isolation and structural analysis. We characterize in detail the engineering of these nanosheets and their biorecognition properties employing complementary methods such as X-ray photoelectron and infrared spectroscopy, atomic force microscopy as well as surface plasmon resonance measurements. The desired functionality of the developed nanosheets is demonstrated by in situ selection of a His-tagged protein from a mixture and its subsequent structural analysis by cryoEM.
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Affiliation(s)
- Julian Scherr
- Department of Chemistry, University of Frankfurt, Max-von-Laue-Str. 7, 60438 Frankfurt, Germany
| | - Zian Tang
- Institute of Physical Chemistry, Friedrich Schiller University Jena, Lessingstr. 10, 07743 Jena, Germany
| | - Maria Küllmer
- Institute of Physical Chemistry, Friedrich Schiller University Jena, Lessingstr. 10, 07743 Jena, Germany
| | - Sebastian Balser
- Department of Chemistry, University of Frankfurt, Max-von-Laue-Str. 7, 60438 Frankfurt, Germany
| | - Alexander Stefan Scholz
- Department of Chemistry, University of Frankfurt, Max-von-Laue-Str. 7, 60438 Frankfurt, Germany
| | - Andreas Winter
- Institute of Physical Chemistry, Friedrich Schiller University Jena, Lessingstr. 10, 07743 Jena, Germany
| | - Kristian Parey
- Department of Structural Biology, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438 Frankfurt, Germany
| | - Alexander Rittner
- Institute of Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, University of Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt, Germany
| | - Martin Grininger
- Institute of Organic Chemistry and Chemical Biology, Buchmann Institute for Molecular Life Sciences, University of Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt, Germany
| | - Volker Zickermann
- Institute of Biochemistry II, Medical School, University of Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt, Germany
| | - Daniel Rhinow
- Department of Structural Biology, Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, 60438 Frankfurt, Germany
| | - Andreas Terfort
- Department of Chemistry, University of Frankfurt, Max-von-Laue-Str. 7, 60438 Frankfurt, Germany
| | - Andrey Turchanin
- Institute of Physical Chemistry, Friedrich Schiller University Jena, Lessingstr. 10, 07743 Jena, Germany
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Graham UM, Dozier AK, Oberdörster G, Yokel RA, Molina R, Brain JD, Pinto JM, Weuve J, Bennett DA. Tissue Specific Fate of Nanomaterials by Advanced Analytical Imaging Techniques - A Review. Chem Res Toxicol 2020; 33:1145-1162. [PMID: 32349469 PMCID: PMC7774012 DOI: 10.1021/acs.chemrestox.0c00072] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
A variety of imaging and analytical methods have been developed to study nanoparticles in cells. Each has its benefits, limitations, and varying degrees of expense and difficulties in implementation. High-resolution analytical scanning transmission electron microscopy (HRSTEM) has the unique ability to image local cellular environments adjacent to a nanoparticle at near atomic resolution and apply analytical tools to these environments such as energy dispersive spectroscopy and electron energy loss spectroscopy. These tools can be used to analyze particle location, translocation and potential reformation, ion dispersion, and in vivo synthesis of second-generation nanoparticles. Such analyses can provide in depth understanding of tissue-particle interactions and effects that are caused by the environmental "invader" nanoparticles. Analytical imaging can also distinguish phases that form due to the transformation of "invader" nanoparticles in contrast to those that are triggered by a response mechanism, including the commonly observed iron biomineralization in the form of ferritin nanoparticles. The analyses can distinguish ion species, crystal phases, and valence of parent nanoparticles and reformed or in vivo synthesized phases throughout the tissue. This article will briefly review the plethora of methods that have been developed over the last 20 years with an emphasis on the state-of-the-art techniques used to image and analyze nanoparticles in cells and highlight the sample preparation necessary for biological thin section observation in a HRSTEM. Specific applications that provide visual and chemical mapping of the local cellular environments surrounding parent nanoparticles and second-generation phases are demonstrated, which will help to identify novel nanoparticle-produced adverse effects and their associated mechanisms.
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Affiliation(s)
- Uschi M Graham
- Centers for Disease Control and Prevention, National Institute for Occupational Safety and Health, 5555 Ridge Avenue, Cincinnati, Ohio 45213, United States
- Pharmaceutical Sciences, University of Kentucky, 789 South Limestone, Lexington, Kentucky 40506, United States
| | - Alan K Dozier
- Centers for Disease Control and Prevention, National Institute for Occupational Safety and Health, 5555 Ridge Avenue, Cincinnati, Ohio 45213, United States
| | - Günter Oberdörster
- School of Medicine and Dentistry, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, New York 14642, United States
| | - Robert A Yokel
- Pharmaceutical Sciences, University of Kentucky, 789 South Limestone, Lexington, Kentucky 40506, United States
| | - Ramon Molina
- Harvard T.H. Chan School of Public Health, 677 Huntington Ave, Boston, Massachusetts 02115, United States
| | - Joseph D Brain
- Harvard T.H. Chan School of Public Health, 677 Huntington Ave, Boston, Massachusetts 02115, United States
| | - Jayant M Pinto
- Department of Surgery, The University of Chicago Medicine, 5841 S. Maryland Avenue, Chicago, Illinois 60637, United States
| | - Jennifer Weuve
- School of Public Health, Department of Epidemiology, Boston University, 715 Albany Street, The Talbot Building, T3E & T4E, Boston, Massachusetts 02118, United States
| | - David A Bennett
- Department of Neurological Sciences, Rush University Medical Center, 1725 W. Harrison Street, Suite 1118, Chicago, Illinois 60612, United States
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VandenBussche EJ, Flannigan DJ. Reducing Radiation Damage in Soft Matter with Femtosecond-Timed Single-Electron Packets. NANO LETTERS 2019; 19:6687-6694. [PMID: 31433192 DOI: 10.1021/acs.nanolett.9b03074] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Despite the development of a myriad of mitigation methods, radiation damage continues to be a major limiting factor in transmission electron microscopy. Intriguing results have been reported using pulsed-laser driven and chopped electron beams for modulated dose delivery, but the underlying relationships and effects remain unclear. Indeed, delivering precisely timed single-electron packets to the specimen has yet to be systematically explored, and no direct comparisons to conventional methods within a common parameter space have been made. Here, using a model linear saturated hydrocarbon (n-hexatriacontane, C36H74), we show that precisely timed delivery of each electron to the specimen, with a well-defined and uniform time between arrival, leads to a repeatable reduction in damage compared to conventional ultralow-dose methods for the same dose rate and the same accumulated dose. Using a femtosecond pulsed laser to confine the probability of electron emission to a 300 fs temporal window, we find damage to be sensitively dependent on the time between electron arrival (controlled with the laser repetition rate) and on the number of electrons per packet (controlled with the laser-pulse energy). Relative arrival times of 5, 20, and 100 μs were tested for electron packets comprised of, on average, 1, 5, and 20 electrons. In general, damage increased with decreasing time between electrons and, more substantially, with increasing electron number. Further, we find that improvements relative to conventional methods vanish once a threshold number of electrons per packet is reached. The results indicate that precise electron-by-electron dose delivery leads to a repeatable reduction in irreversible structural damage, and the systematic studies indicate this arises from control of the time between sequential electrons arriving within the same damage radius, all else being equal.
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Affiliation(s)
- Elisah J VandenBussche
- Department of Chemical Engineering and Materials Science , University of Minnesota , 421 Washington Avenue SE , Minneapolis , Minnesota 55455 , United States
| | - David J Flannigan
- Department of Chemical Engineering and Materials Science , University of Minnesota , 421 Washington Avenue SE , Minneapolis , Minnesota 55455 , United States
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Mitra AK. Visualization of biological macromolecules at near-atomic resolution: cryo-electron microscopy comes of age. Acta Crystallogr F Struct Biol Commun 2019; 75:3-11. [PMID: 30605120 PMCID: PMC6317457 DOI: 10.1107/s2053230x18015133] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 10/26/2018] [Indexed: 11/11/2022] Open
Abstract
Structural biology is going through a revolution as a result of transformational advances in the field of cryo-electron microscopy (cryo-EM) driven by the development of direct electron detectors and ultrastable electron microscopes. High-resolution cryo-EM images of isolated biomolecules (single particles) suspended in a thin layer of vitrified buffer are subjected to powerful image-processing algorithms, enabling near-atomic resolution structures to be determined in unprecedented numbers. Prior to these advances, electron crystallography of two-dimensional crystals and helical assemblies of proteins had established the feasibility of atomic resolution structure determination using cryo-EM. Atomic resolution single-particle analysis, without the need for crystals, now promises to resolve problems in structural biology that were intractable just a few years ago.
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MESH Headings
- Algorithms
- Bibliometrics
- Cryoelectron Microscopy/history
- Cryoelectron Microscopy/instrumentation
- Cryoelectron Microscopy/methods
- Crystallography, X-Ray/history
- Crystallography, X-Ray/instrumentation
- Crystallography, X-Ray/methods
- Equipment Design/history
- History, 20th Century
- History, 21st Century
- Humans
- Image Processing, Computer-Assisted/statistics & numerical data
- Imaging, Three-Dimensional/instrumentation
- Imaging, Three-Dimensional/methods
- Macromolecular Substances/chemistry
- Macromolecular Substances/ultrastructure
- Microscopy, Electron, Transmission/history
- Microscopy, Electron, Transmission/instrumentation
- Microscopy, Electron, Transmission/methods
- Specimen Handling/instrumentation
- Specimen Handling/methods
- Vitrification
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Affiliation(s)
- Alok K. Mitra
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
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12
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Khelfa A, Byun C, Nelayah J, Wang G, Ricolleau C, Alloyeau D. Structural analysis of single nanoparticles in liquid by low-dose STEM nanodiffraction. Micron 2018; 116:30-35. [PMID: 30265881 DOI: 10.1016/j.micron.2018.09.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 09/11/2018] [Accepted: 09/14/2018] [Indexed: 11/26/2022]
Abstract
Liquid-cell TEM has enabled an interdisciplinary community of scientists to carry out atomic- / nano-scale studies of solid/liquid interfaces. Nevertheless, the restricted resolution of TEM in liquid media and the necessity to reduce the electron dose to avoid harmful radiolytic effects induced by the beam have limited the use of high resolution imaging to study the atomic structure of nanomaterials in liquid. Here we show that STEM nanodiffraction can be exploited in liquid-cell TEM experiments to overcome these two limitations. We evidence that this technique allows quick analysis of the structure of single gold nanoparticles whatever their zone axis orientation, which substantially increases the percentage of analysable nanostructures with respect to HRTEM investigations. Moreover, STEM nanodiffraction can also be used in very low dose conditions. The electron dose irradiating the analyzed nanostructures during data acquisition can be reduced by almost four orders of magnitude compared to conventional HRTEM analysis. Finally, dynamical analyses in reciprocal space are used to provide new insights into the shape-dependent rotation of nanocrystals in the liquid-cell.
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Affiliation(s)
- Abdelali Khelfa
- Laboratoire Matériaux et Phénomènes Quantiques, Université Paris Diderot - CNRS, Paris, France
| | - Caroline Byun
- Laboratoire Matériaux et Phénomènes Quantiques, Université Paris Diderot - CNRS, Paris, France
| | - Jaysen Nelayah
- Laboratoire Matériaux et Phénomènes Quantiques, Université Paris Diderot - CNRS, Paris, France
| | - Guillaume Wang
- Laboratoire Matériaux et Phénomènes Quantiques, Université Paris Diderot - CNRS, Paris, France
| | - Christian Ricolleau
- Laboratoire Matériaux et Phénomènes Quantiques, Université Paris Diderot - CNRS, Paris, France
| | - Damien Alloyeau
- Laboratoire Matériaux et Phénomènes Quantiques, Université Paris Diderot - CNRS, Paris, France.
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13
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Polidori C, Pastor A, Jorge A, Pertusa J. Ultrastructural Alterations of Midgut Epithelium, But Not Greater Wing Fluctuating Asymmetry, in Paper Wasps (Polistes dominula) from Urban Environments. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2018; 24:183-192. [PMID: 29560839 DOI: 10.1017/s1431927618000107] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Polistes paper wasps can be used to monitor trace metal contaminants, but the effects of pollution on the health of these insects are still unknown. We evaluated, in a south-eastern area of Spain, whether workers of Polistes dominula collected at urban and rural sites differ in health of midgut tissue and in fluctuating asymmetry, an estimate of developmental noise. We found that wasps collected at the urban sites had abundant lead (Pb)-containing spherites, which were less visible in wasps from the rural sites. Evident ultrastructural alterations in the epithelium of the midgut of the wasps collected at the urban sites included broken and disorganized microvilli, a high amount and density of heterochromatin in the nucleus of epithelial cells, cytoplasmic vacuolization and mitochondrial disruptions. Altogether, these findings suggest a negative effect on the transmembrane transport and a less efficient transcription. On the contrary, a healthy epithelium was observed in wasps from the rural sites. These differences may be preliminarily linked with levels of lead pollution, given that wasps from urban sites had double the Pb concentrations of wasps from rural sites. Level of fluctuating asymmetry was unrelated to wasp origin, thus suggesting no link between developmental noise and Pb-driven pollution.
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Affiliation(s)
- Carlo Polidori
- 1Instituto de Ciencias Ambientales (ICAM),Universidad de Castilla-La Mancha,Avenida Carlos III,s/n,45071 Toledo,Spain
| | - Agustín Pastor
- 2Departament de Química Analítica,Universitat de València,C/ Dr Moliner 50,ES-46100,Burjassot,Valencia,Spain
| | - Alberto Jorge
- 3Laboratorio de Microscopia,Museo Nacional de Ciencias Naturales (CSIC),C/ José Gutiérrez Abascal 2,ES-28006,Madrid,Spain
| | - José Pertusa
- 4Departament de Biologia Funcional i Antropologia Física,Universitat de València,C/ Dr Moliner 50,ES-46100,Burjassot,Valencia,Spain
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14
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Near-Atomic Resolution Structure Determination in Over-Focus with Volta Phase Plate by Cs-Corrected Cryo-EM. Structure 2017; 25:1623-1630.e3. [DOI: 10.1016/j.str.2017.08.008] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 07/25/2017] [Accepted: 08/15/2017] [Indexed: 11/21/2022]
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15
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Firlar E, Çınar S, Kashyap S, Akinc M, Prozorov T. Direct Visualization of the Hydration Layer on Alumina Nanoparticles with the Fluid Cell STEM in situ. Sci Rep 2015; 5:9830. [PMID: 25996055 PMCID: PMC4440531 DOI: 10.1038/srep09830] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2014] [Accepted: 03/20/2015] [Indexed: 11/21/2022] Open
Abstract
Rheological behavior of aqueous suspensions containing nanometer-sized powders is of relevance to many branches of industry. Unusually high viscosities observed for suspensions of nanoparticles compared to those of micron size powders cannot be explained by current viscosity models. Formation of so-called hydration layer on alumina nanoparticles in water was hypothesized, but never observed experimentally. We report here on the direct visualization of aqueous suspensions of alumina with the fluid cell in situ. We observe the hydration layer formed over the particle aggregates and show that such hydrated aggregates constitute new particle assemblies and affect the flow behavior of the suspensions. We discuss how these hydrated nanoclusters alter the effective solid content and the viscosity of nanostructured suspensions. Our findings elucidate the source of high viscosity observed for nanoparticle suspensions and are of direct relevance to many industrial sectors including materials, food, cosmetics, pharmaceutical among others employing colloidal slurries with nanometer-scale particles.
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Affiliation(s)
- Emre Firlar
- Division of Materials Science and Engineering, US DOE Ames Laboratory, Ames, IA, 50011, USA
| | - Simge Çınar
- Department of Materials Science and Engineering, Iowa State University, Ames, IA, 50011, USA
| | - Sanjay Kashyap
- Division of Materials Science and Engineering, US DOE Ames Laboratory, Ames, IA, 50011, USA
| | - Mufit Akinc
- 1] Division of Materials Science and Engineering, US DOE Ames Laboratory, Ames, IA, 50011, USA [2] Department of Materials Science and Engineering, Iowa State University, Ames, IA, 50011, USA
| | - Tanya Prozorov
- Division of Materials Science and Engineering, US DOE Ames Laboratory, Ames, IA, 50011, USA
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17
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Polyamide–POSS hybrid membranes for seawater desalination: Effect of POSS inclusion on membrane properties. J Memb Sci 2014. [DOI: 10.1016/j.memsci.2014.03.004] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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18
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Proetto MT, Rush AM, Chien MP, Abellan Baeza P, Patterson JP, Thompson MP, Olson NH, Moore CE, Rheingold AL, Andolina C, Millstone J, Howell SB, Browning ND, Evans JE, Gianneschi NC. Dynamics of soft nanomaterials captured by transmission electron microscopy in liquid water. J Am Chem Soc 2014; 136:1162-5. [PMID: 24422495 DOI: 10.1021/ja408513m] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this paper we present in situ transmission electron microscopy of synthetic polymeric nanoparticles with emphasis on capturing motion in a solvated, aqueous state. The nanoparticles studied were obtained from the direct polymerization of a Pt(II)-containing monomer. The resulting structures provided sufficient contrast for facile imaging in situ. We contend that this technique will quickly become essential in the characterization of analogous systems, especially where dynamics are of interest in the solvated state. We describe the preparation of the synthetic micellar nanoparticles together with their characterization and motion in liquid water with comparison to conventional electron microscopy analyses.
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Affiliation(s)
- Maria T Proetto
- Department of Chemistry & Biochemistry and ⊥Moores Cancer Center, University of California, San Diego , La Jolla, California 92093, United States
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19
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Browning ND, Aydin C, Lu J, Kulkarni A, Okamoto NL, Ortalan V, Reed BW, Uzun A, Gates BC. QuantitativeZ-Contrast Imaging of Supported Metal Complexes and Clusters-A Gateway to Understanding Catalysis on the Atomic Scale. ChemCatChem 2013. [DOI: 10.1002/cctc.201200872] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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20
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Wu JS, Kim AM, Bleher R, Myers BD, Marvin RG, Inada H, Nakamura K, Zhang XF, Roth E, Li SY, Woodruff TK, O'Halloran TV, Dravid VP. Imaging and elemental mapping of biological specimens with a dual-EDS dedicated scanning transmission electron microscope. Ultramicroscopy 2013; 128:24-31. [PMID: 23500508 DOI: 10.1016/j.ultramic.2013.01.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Revised: 01/22/2013] [Accepted: 01/24/2013] [Indexed: 11/30/2022]
Abstract
A dedicated analytical scanning transmission electron microscope (STEM) with dual energy dispersive spectroscopy (EDS) detectors has been designed for complementary high performance imaging as well as high sensitivity elemental analysis and mapping of biological structures. The performance of this new design, based on a Hitachi HD-2300A model, was evaluated using a variety of biological specimens. With three imaging detectors, both the surface and internal structure of cells can be examined simultaneously. The whole-cell elemental mapping, especially of heavier metal species that have low cross-section for electron energy loss spectroscopy (EELS), can be faithfully obtained. Optimization of STEM imaging conditions is applied to thick sections as well as thin sections of biological cells under low-dose conditions at room and cryogenic temperatures. Such multimodal capabilities applied to soft/biological structures usher a new era for analytical studies in biological systems.
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Affiliation(s)
- J S Wu
- Northwestern University Atomic and Nanoscale Characterization Experimental (NUANCE) Center, Northwestern University, Evanston, IL 60208, USA.
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21
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Evans JE, Browning ND. Enabling direct nanoscale observations of biological reactions with dynamic TEM. Microscopy (Oxf) 2013; 62:147-56. [PMID: 23315566 DOI: 10.1093/jmicro/dfs081] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Biological processes occur on a wide range of spatial and temporal scales: from femtoseconds to hours and from angstroms to meters. Many new biological insights can be expected from a better understanding of the processes that occur on these very fast and very small scales. In this regard, new instruments that use fast X-ray or electron pulses are expected to reveal novel mechanistic details for macromolecular protein dynamics. To ensure that any observed conformational change is physiologically relevant and not constrained by 3D crystal packing, it would be preferable for experiments to utilize small protein samples such as single particles or 2D crystals that mimic the target protein's native environment. These samples are not typically amenable to X-ray analysis, but transmission electron microscopy has imaged such sample geometries for over 40 years using both direct imaging and diffraction modes. While conventional transmission electron microscopes (TEM) have visualized biological samples with atomic resolution in an arrested or frozen state, the recent development of the dynamic TEM (DTEM) extends electron microscopy into a dynamic regime using pump-probe imaging. A new second-generation DTEM, which is currently being constructed, has the potential to observe live biological processes with unprecedented spatiotemporal resolution by using pulsed electron packets to probe the sample on micro- and nanosecond timescales. This article reviews the experimental parameters necessary for coupling DTEM with in situ liquid microscopy to enable direct imaging of protein conformational dynamics in a fully hydrated environment and visualize reactions propagating in real time.
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Affiliation(s)
- James E Evans
- Pacific Northwest National Laboratory, Environmental Molecular Sciences Laboratory, 3335 Innovation Boulevard, Richland, WA 99354, USA.
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22
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Newcomb CJ, Moyer TJ, Lee SS, Stupp SI. Advances in cryogenic transmission electron microscopy for the characterization of dynamic self-assembling nanostructures. Curr Opin Colloid Interface Sci 2012. [PMID: 23204913 DOI: 10.1016/j.cocis.2012.09.004] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Elucidating the structural information of nanoscale materials in their solvent-exposed state is crucial, as a result, cryogenic transmission electron microscopy (cryo-TEM) has become an increasingly popular technique in the materials science, chemistry, and biology communities. Cryo-TEM provides a method to directly visualize the specimen structure in a solution-state through a thin film of vitrified solvent. This technique complements X-ray, neutron, and light scattering methods that probe the statistical average of all species present; furthermore, cryo-TEM can be used to observe changes in structure over time. In the area of self-assembly, this tool has been particularly powerful for the characterization of natural and synthetic small molecule assemblies, as well as hybrid organic-inorganic composites. In this review, we discuss recent advances in cryogenic TEM in the context of self-assembling systems with emphasis on characterization of transitions observed in response to external stimuli.
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Affiliation(s)
- Christina J Newcomb
- Department of Materials Science and Engineering Northwestern University, Evanston, IL, USA
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23
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Tiemeijer P, Bischoff M, Freitag B, Kisielowski C. Using a monochromator to improve the resolution in TEM to below 0.5Å. Part II: Application to focal series reconstruction. Ultramicroscopy 2012; 118:35-43. [DOI: 10.1016/j.ultramic.2012.03.019] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2008] [Revised: 03/29/2012] [Accepted: 03/30/2012] [Indexed: 10/28/2022]
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24
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The Application of Scanning Transmission Electron Microscopy (STEM) to the Study of Nanoscale Systems. MODELING NANOSCALE IMAGING IN ELECTRON MICROSCOPY 2012. [DOI: 10.1007/978-1-4614-2191-7_2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
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25
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26
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27
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Buban JP, Ramasse Q, Gipson B, Browning ND, Stahlberg H. High-resolution low-dose scanning transmission electron microscopy. JOURNAL OF ELECTRON MICROSCOPY 2009; 59:103-12. [PMID: 19915208 PMCID: PMC2857930 DOI: 10.1093/jmicro/dfp052] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2009] [Accepted: 09/24/2009] [Indexed: 05/24/2023]
Abstract
During the past two decades instrumentation in scanning transmission electron microscopy (STEM) has pushed toward higher intensity electron probes to increase the signal-to-noise ratio of recorded images. While this is suitable for robust specimens, biological specimens require a much reduced electron dose for high-resolution imaging. We describe here protocols for low-dose STEM image recording with a conventional field-emission gun STEM, while maintaining the high-resolution capability of the instrument. Our findings show that a combination of reduced pixel dwell time and reduced gun current can achieve radiation doses comparable to low-dose TEM.
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MESH Headings
- Electrons
- Image Processing, Computer-Assisted
- Imaging, Three-Dimensional
- Microscopy, Electron, Scanning Transmission/instrumentation
- Microscopy, Electron, Scanning Transmission/methods
- Microscopy, Electron, Transmission/instrumentation
- Microscopy, Electron, Transmission/methods
- Oxides/chemistry
- Proteins/chemistry
- Strontium/chemistry
- Titanium/chemistry
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Affiliation(s)
- James P Buban
- Department of Molecular and Cellular Biology, College of Biological Sciences, University of California at Davis, 1 Shields Ave, Davis, CA, USA.
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28
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Abstract
Single-particle electron microscopy (EM) can provide structural information for a large variety of biological molecules, ranging from small proteins to large macromolecular assemblies, without the need to produce crystals. The year 2008 has become a landmark year for single-particle EM as for the first time density maps have been produced at a resolution that made it possible to trace protein backbones or even to build atomic models. In this review, we highlight some of the recent successes achieved by single-particle EM and describe the individual steps involved in producing a density map by this technique. We also discuss some of the remaining challenges and areas, in which further advances would have a great impact on the results that can be achieved by single-particle EM.
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Affiliation(s)
- Yifan Cheng
- The W.M. Keck Advanced Microscopy Laboratory, Department of Biochemistry and Biophysics, University of California-San Francisco, CA 94158, USA.
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29
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Abstract
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The objective of molecular electron microscopy (EM) is to use electron
microscopes to visualize the structure of biological molecules. This
Review provides a brief overview of the methods used in molecular
EM, their respective strengths and successes, and current developments
that promise an even more exciting future for molecular EM in the
structural investigation of proteins and macromolecular complexes,
studied in isolation or in the context of cells and tissues.
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Affiliation(s)
- Henning Stahlberg
- Molecular and Cellular Biology,
College of Biological Sciences, University of California at Davis,
Briggs Hall, 1 Shields Avenue, Davis, California 95616
| | - Thomas Walz
- Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, Massachusetts 02115
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