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Yonekura K, Maki-Yonekura S, Takaba K. Applications and limitations of electron 3D crystallography. Structure 2023; 31:1328-1334. [PMID: 37797620 DOI: 10.1016/j.str.2023.09.007] [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: 08/02/2023] [Revised: 08/27/2023] [Accepted: 09/08/2023] [Indexed: 10/07/2023]
Abstract
Three-dimensional electron diffraction (3D ED) is a measurement and analysis technique in transmission electron microscopy that is used for determining atomic structures from small crystals. Diverse targets such as proteins, polypeptides, and organic compounds, whose crystals exist in aqueous solutions and organic solvents, or as dried powders, can be studied with 3D ED. We have been involved in the development of this technique, which can now rapidly process a large number of data collected through AI control, enabling efficient structure determination. Here, we introduce this method and describe our recent results. These include the structures and pathogenic mechanisms of wild-type and mutant polypeptides associated with the debilitating disease amyotrophic lateral sclerosis (ALS), the double helical structure of nanographene promoting nanofiber formation, and the structural properties of an organic semiconductor containing disordered regions. We also discuss the limitations and prospects of 3D ED compared to microcrystallography with X-ray free electron lasers.
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Affiliation(s)
- Koji Yonekura
- Biostructural Mechanism Laboratory, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan; Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan.
| | - Saori Maki-Yonekura
- Biostructural Mechanism Laboratory, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan; Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan
| | - Kiyofumi Takaba
- Biostructural Mechanism Laboratory, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
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2
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Abe K, Ozako M, Inukai M, Matsuyuki Y, Kitayama S, Kanai C, Nagai C, Gopalasingam CC, Gerle C, Shigematsu H, Umekubo N, Yokoshima S, Yoshimori A. Deep learning driven de novo drug design based on gastric proton pump structures. Commun Biol 2023; 6:956. [PMID: 37726448 PMCID: PMC10509173 DOI: 10.1038/s42003-023-05334-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 09/08/2023] [Indexed: 09/21/2023] Open
Abstract
Existing drugs often suffer in their effectiveness due to detrimental side effects, low binding affinity or pharmacokinetic problems. This may be overcome by the development of distinct compounds. Here, we exploit the rich structural basis of drug-bound gastric proton pump to develop compounds with strong inhibitory potency, employing a combinatorial approach utilizing deep generative models for de novo drug design with organic synthesis and cryo-EM structural analysis. Candidate compounds that satisfy pharmacophores defined in the drug-bound proton pump structures, were designed in silico utilizing our deep generative models, a workflow termed Deep Quartet. Several candidates were synthesized and screened according to their inhibition potencies in vitro, and their binding poses were in turn identified by cryo-EM. Structures reaching up to 2.10 Å resolution allowed us to evaluate and re-design compound structures, heralding the most potent compound in this study, DQ-18 (N-methyl-4-((2-(benzyloxy)-5-chlorobenzyl)oxy)benzylamine), which shows a Ki value of 47.6 nM. Further high-resolution cryo-EM analysis at 2.08 Å resolution unambiguously determined the DQ-18 binding pose. Our integrated approach offers a framework for structure-based de novo drug development based on the desired pharmacophores within the protein structure.
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Affiliation(s)
- Kazuhiro Abe
- Cellular and Structural Physiology Institute, Nagoya University, Nagoya, Aichi, 464-8601, Japan.
- Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Aichi, 464-8601, Japan.
- Center for One Medicine Innovative Translational Research (COMIT), Nagoya University, Nagoya, Aichi, 464-8601, Japan.
| | - Mami Ozako
- Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Aichi, 464-8601, Japan
| | - Miki Inukai
- Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Aichi, 464-8601, Japan
| | - Yoe Matsuyuki
- Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Aichi, 464-8601, Japan
| | - Shinnosuke Kitayama
- Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Aichi, 464-8601, Japan
| | - Chisato Kanai
- INTAGE Healthcare, Inc., 3-5-7, Kawaramachi Chuo-ku, Osaka, 541-0048, Japan
| | - Chiaki Nagai
- Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Aichi, 464-8601, Japan
| | | | - Christoph Gerle
- RIKEN SPring-8 Center, Kouto, Sayo-gun, Hyogo, 679-5148, Japan
| | - Hideki Shigematsu
- Japan Synchrotron Radiation Research Institute (JASRI), SPring-8, 1-1-1 Kouto, Sayo, Hyogo, 679-5148, Japan
| | - Nariyoshi Umekubo
- Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Aichi, 464-8601, Japan
| | - Satoshi Yokoshima
- Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Aichi, 464-8601, Japan.
| | - Atsushi Yoshimori
- Institute for Theoretical Medicine, Inc., 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa, 251-0012, Japan.
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3
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Aizawa H, Sato T, Maki-Yonekura S, Yonekura K, Takaba K, Hamaguchi T, Minato T, Yamamoto HM. Enantioselectivity of discretized helical supramolecule consisting of achiral cobalt phthalocyanines via chiral-induced spin selectivity effect. Nat Commun 2023; 14:4530. [PMID: 37507380 PMCID: PMC10382588 DOI: 10.1038/s41467-023-40133-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 07/10/2023] [Indexed: 07/30/2023] Open
Abstract
Enantioselectivity of helical aggregation is conventionally directed either by its homochiral ingredients or by introduction of chiral catalysis. The fundamental question, then, is whether helical aggregation that consists only of achiral components can obtain enantioselectivity in the absence of chiral catalysis. Here, by exploiting enantiospecific interaction due to chiral-induced spin selectivity (CISS) that has been known to work to enantio-separate a racemic mixture of chiral molecules, we demonstrate the enantioselectivity in the assembly of mesoscale helical supramolecules consisting of achiral cobalt phthalocyanines. The helical nature in our supramolecules is revealed to be mesoscopically incorporated by dislocation-induced discretized twists, unlike the case of chiral molecules whose chirality are determined microscopically by chemical bond. The relevance of CISS effect in the discretized helical supramolecules is further confirmed by the appearance of spin-polarized current through the system. These observations mean that the application of CISS-based enantioselectivity is no longer limited to systems with microscopic chirality but is expanded to the one with mesoscopic chirality.
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Affiliation(s)
- Hiroki Aizawa
- Institute for Molecular Science, Myodaiji, Okazaki, 444-8585, Japan
- the Graduate University for Advanced Studies, Myodaiji, Okazaki, 444-8585, Japan
| | - Takuro Sato
- Institute for Molecular Science, Myodaiji, Okazaki, 444-8585, Japan.
- the Graduate University for Advanced Studies, Myodaiji, Okazaki, 444-8585, Japan.
| | - Saori Maki-Yonekura
- Biostructural Mechanism Laboratory, RIKEN SPring-8 Center, Hyogo, 679-5148, Japan
| | - Koji Yonekura
- Biostructural Mechanism Laboratory, RIKEN SPring-8 Center, Hyogo, 679-5148, Japan
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, 980-8577, Japan
- Advanced Electron Microscope Development Unit, RIKEN-JEOL Collaboration Center, RIKEN Baton Zone Program, 1-1-1 Kouto, Sayo, Hyogo, 679-5148, Japan
| | - Kiyofumi Takaba
- Biostructural Mechanism Laboratory, RIKEN SPring-8 Center, Hyogo, 679-5148, Japan
| | - Tasuku Hamaguchi
- Biostructural Mechanism Laboratory, RIKEN SPring-8 Center, Hyogo, 679-5148, Japan
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, 980-8577, Japan
| | - Taketoshi Minato
- Institute for Molecular Science, Myodaiji, Okazaki, 444-8585, Japan
| | - Hiroshi M Yamamoto
- Institute for Molecular Science, Myodaiji, Okazaki, 444-8585, Japan.
- the Graduate University for Advanced Studies, Myodaiji, Okazaki, 444-8585, Japan.
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4
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Maki-Yonekura S, Kawakami K, Takaba K, Hamaguchi T, Yonekura K. Measurement of charges and chemical bonding in a cryo-EM structure. Commun Chem 2023; 6:98. [PMID: 37258702 DOI: 10.1038/s42004-023-00900-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 05/08/2023] [Indexed: 06/02/2023] Open
Abstract
Hydrogen bonding, bond polarity, and charges in protein molecules play critical roles in the stabilization of protein structures, as well as affecting their functions such as enzymatic catalysis, electron transfer, and ligand binding. These effects can potentially be measured in Coulomb potentials using cryogenic electron microscopy (cryo-EM). We here present charges and bond properties of hydrogen in a sub-1.2 Å resolution structure of a protein complex, apoferritin, by single-particle cryo-EM. A weighted difference map reveals positive densities for most hydrogen atoms in the core region of the complex, while negative densities around acidic amino-acid side chains are likely related to negative charges. The former positive densities identify the amino- and oxo-termini of asparagine and glutamine side chains. The latter observations were verified by spatial-resolution selection and a dose-dependent frame series. The average position of the hydrogen densities depends on the parent bonded-atom type, and this is validated by the estimated level of the standard uncertainties in the bond lengths.
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Affiliation(s)
- Saori Maki-Yonekura
- Biostructural Mechanism Laboratory, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo, 679-5148, Japan
| | - Keisuke Kawakami
- Biostructural Mechanism Laboratory, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo, 679-5148, Japan
| | - Kiyofumi Takaba
- Biostructural Mechanism Laboratory, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo, 679-5148, Japan
| | - Tasuku Hamaguchi
- Biostructural Mechanism Laboratory, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo, 679-5148, Japan
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, 980-8577, Japan
| | - Koji Yonekura
- Biostructural Mechanism Laboratory, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo, 679-5148, Japan.
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, 980-8577, Japan.
- Advanced Electron Microscope Development Unit, RIKEN-JEOL Collaboration Center, RIKEN Baton Zone Program, 1-1-1 Kouto, Sayo, Hyogo, 679-5148, Japan.
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5
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Fréchin L, Holvec S, von Loeffelholz O, Hazemann I, Klaholz BP. High-resolution cryo-EM performance comparison of two latest-generation cryo electron microscopes on the human ribosome. J Struct Biol 2023; 215:107905. [PMID: 36241135 DOI: 10.1016/j.jsb.2022.107905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 09/23/2022] [Accepted: 10/05/2022] [Indexed: 11/29/2022]
Abstract
Recent technological advances in cryo electron microscopy (cryo-EM) have led to new opportunities in the structural biology field. Here we benchmark the performance of two 300 kV latest-generation cryo electron microscopes, Titan Krios G4 from Thermofisher Scientific and CRYO ARM 300 from Jeol, with regards to achieving high resolution single particle reconstructions on a real case sample. We compare potentially limiting factors such as drift rates, astigmatism & coma aberrations and performance during image processing and show that both microscopes, while comprising rather different technical setups & parameter settings and equipped with different types of energy filters & cameras, achieve a resolution of around 2 Å on the human ribosome, a non-symmetric object which constitutes a key drug target. Astigmatism correction, CTF refinement and correction of higher order aberrations through refinement in separate optics groups helped to account for astigmatism/coma caused by beam tilting during multi-spot and multi-hole acquisition in neighbouring holes without stage movement. The obtained maps resolve Mg2+ ions, water molecules, inhibitors and side-chains including chemical modifications. The fact that both instruments can resolve such detailed features will greatly facilitate understanding molecular mechanisms of various targets and helps in cryo-EM structure based drug design. The methods and analysis tools used here will be useful also to characterize existing instruments and optimize data acquisition settings and are applicable broadly to other drug targets in structural biology.
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Affiliation(s)
- Léo Fréchin
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), 1 rue Laurent Fries, Illkirch, France; Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale (Inserm) U964, Illkirch, France; Université de Strasbourg, Strasbourg, France
| | - Samuel Holvec
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), 1 rue Laurent Fries, Illkirch, France; Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale (Inserm) U964, Illkirch, France; Université de Strasbourg, Strasbourg, France
| | - Ottilie von Loeffelholz
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), 1 rue Laurent Fries, Illkirch, France; Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale (Inserm) U964, Illkirch, France; Université de Strasbourg, Strasbourg, France
| | - Isabelle Hazemann
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), 1 rue Laurent Fries, Illkirch, France; Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale (Inserm) U964, Illkirch, France; Université de Strasbourg, Strasbourg, France
| | - Bruno P Klaholz
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), 1 rue Laurent Fries, Illkirch, France; Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale (Inserm) U964, Illkirch, France; Université de Strasbourg, Strasbourg, France.
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6
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Yang T, Xu H, Zou X. Improving data quality for three-dimensional electron diffraction by a post-column energy filter and a new crystal tracking method. J Appl Crystallogr 2022; 55:1583-1591. [PMID: 36570655 PMCID: PMC9721325 DOI: 10.1107/s1600576722009633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 09/30/2022] [Indexed: 11/30/2022] Open
Abstract
Three-dimensional electron diffraction (3D ED) has become an effective technique to determine the structures of submicrometre- (nanometre-)sized crystals. In this work, energy-filtered 3D ED was implemented using a post-column energy filter in both STEM mode and TEM mode [(S)TEM denoting (scanning) transmission electron microscope]. The setups for performing energy-filtered 3D ED on a Gatan imaging filter are described. The technique and protocol improve the accessibility of energy-filtered 3D ED post-column energy filters, which are available in many TEM laboratories. In addition, a crystal tracking method in STEM mode using high-angle annular dark-field imaging is proposed. This method enables the user to monitor the crystal position while collecting 3D ED data at the same time, allowing a larger tilt range without foregoing any diffraction frames or imposing extra electron dose. In order to compare the differences between energy-filtered and unfiltered 3D ED data sets, three well known crystallized inorganic samples have been studied in detail. For these samples, the final R 1 values improved by 10-30% for the energy-filtered data sets compared with the unfiltered data sets, and the structures became more chemically reasonable. Possible reasons for improvement are also discussed.
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Affiliation(s)
- Taimin Yang
- Department of Materials and Environmental Chemistry (MMK), Stockholm University, Svante Arrhenius väg 16 C, Stockholm, SE-10691, Sweden,Correspondence e-mail: ,
| | - Hongyi Xu
- Department of Materials and Environmental Chemistry (MMK), Stockholm University, Svante Arrhenius väg 16 C, Stockholm, SE-10691, Sweden,Correspondence e-mail: ,
| | - Xiaodong Zou
- Department of Materials and Environmental Chemistry (MMK), Stockholm University, Svante Arrhenius väg 16 C, Stockholm, SE-10691, Sweden
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7
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Grey IE. Diffraction methods in the characterization of new mineral species. J SOLID STATE CHEM 2022. [DOI: 10.1016/j.jssc.2022.123239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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8
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Calcraft T, Rosenthal PB. Cryogenic electron microscopy approaches that combine images and tilt series. Microscopy (Oxf) 2022; 71:i15-i22. [PMID: 35275182 PMCID: PMC8855521 DOI: 10.1093/jmicro/dfab053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 11/29/2021] [Accepted: 01/28/2022] [Indexed: 11/12/2022] Open
Abstract
Cryogenic electron microscopy can be widely applied to biological specimens from the molecular to the cellular scale. In single-particle analysis, 3D structures may be obtained in high resolution by averaging 2D images of single particles in random orientations. For pleomorphic specimens, structures may be obtained by recording the tilt series of a single example of the specimen and calculating tomograms. Where many copies of a single structure such as a protein or nucleic acid assembly are present within the tomogram, averaging of the sub-volumes (subtomogram averaging) has been successfully applied. The choice of data collection method for any given specimen may depend on the structural question of interest and is determined by the radiation sensitivity of the specimen. Here, we survey some recent developments on the use of hybrid methods for recording and analysing data from radiation-sensitive biological specimens. These include single-particle reconstruction from 2D images where additional views are recorded at a single tilt angle of the specimen and methods where image tilt series, initially used for tomogram reconstruction, are processed as individual single-particle images. There is a continuum of approaches now available to maximize structural information obtained from the specimen.
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Affiliation(s)
- Thomas Calcraft
- Structural Biology of Cells and Viruses Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
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9
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Kamyshinsky RA, Kralin VA, Chesnokov MY, Samygina VR, Orekhov AS. Electron Diffraction of Microcrystals on the Example of Lysozyme. CRYSTALLOGR REP+ 2021. [DOI: 10.1134/s1063774521050084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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10
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Machine learning-based real-time object locator/evaluator for cryo-EM data collection. Commun Biol 2021; 4:1044. [PMID: 34493805 PMCID: PMC8423793 DOI: 10.1038/s42003-021-02577-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 08/20/2021] [Indexed: 11/30/2022] Open
Abstract
In cryo-electron microscopy (cryo-EM) data collection, locating a target object is error-prone. Here, we present a machine learning-based approach with a real-time object locator named yoneoLocr using YOLO, a well-known object detection system. Implementation shows its effectiveness in rapidly and precisely locating carbon holes in single particle cryo-EM and in locating crystals and evaluating electron diffraction (ED) patterns in automated cryo-electron crystallography (cryo-EX) data collection. The proposed approach will advance high-throughput and accurate data collection of images and diffraction patterns with minimal human operation. Yonekura et al. present yoneoLocr, a machine learning-based real-time object locator for rapidly and precisely locating carbon holes and crystals for facilitating automated SPA or cryo-EX data collection.
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11
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Gruene T, Holstein JJ, Clever GH, Keppler B. Establishing electron diffraction in chemical crystallography. Nat Rev Chem 2021; 5:660-668. [PMID: 37118416 DOI: 10.1038/s41570-021-00302-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/07/2021] [Indexed: 02/06/2023]
Abstract
The emerging field of 3D electron diffraction (3D ED) opens new opportunities for structure determination from sub-micrometre-sized crystals. Although the foundations of this technology emerged earlier, the past decade has seen developments in cryo-electron microscopy and (X-ray) crystallography that particularly enable the widespread use of 3D ED. This Perspective describes to chemists and chemical crystallographers just how similar electron and X-ray diffraction are and discusses their complementary aspects. We wish to establish 3D ED in the broader chemistry community, such that electron crystallography becomes a common part of the analytical chemistry toolkit. With a suitable instrument at their disposal, every skilled crystallographer can quickly learn to perform structure determinations using 3D ED.
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12
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Takaba K, Maki-Yonekura S, Inoue S, Hasegawa T, Yonekura K. Protein and Organic-Molecular Crystallography With 300kV Electrons on a Direct Electron Detector. Front Mol Biosci 2021; 7:612226. [PMID: 33469549 PMCID: PMC7814344 DOI: 10.3389/fmolb.2020.612226] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 11/30/2020] [Indexed: 12/18/2022] Open
Abstract
Electron 3D crystallography can reveal the atomic structure from undersized crystals of various samples owing to the strong scattering power of electrons. Here, a direct electron detector DE64 was tested for small and thin crystals of protein and an organic molecule using a JEOL CRYO ARM 300 electron microscope. The microscope is equipped with a cold-field emission gun operated at an accelerating voltage of 300 kV, quad condenser lenses for parallel illumination, an in-column energy filter, and a stable rotational goniometer stage. Rotational diffraction data were collected in an unsupervised manner from crystals of a heme-binding enzyme catalase and a representative organic semiconductor material Ph-BTBT-C10. The structures were determined by molecular replacement for catalase and by the direct method for Ph-BTBT-C10. The analyses demonstrate that the system works well for electron 3D crystallography of these molecules with less damaging, a smaller point spread, and less noise than using the conventional scintillator-coupled camera.
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Affiliation(s)
- Kiyofumi Takaba
- Biostructural Mechanism Laboratory, RIKEN SPring-8 Center, Sayo, Japan
| | | | - Satoru Inoue
- Department of Applied Physics, The University of Tokyo, Tokyo, Japan
| | - Tatsuo Hasegawa
- Department of Applied Physics, The University of Tokyo, Tokyo, Japan
| | - Koji Yonekura
- Biostructural Mechanism Laboratory, RIKEN SPring-8 Center, Sayo, Japan.,Advanced Electron Microscope Development Unit, RIKEN-JEOL Collaboration Center, RIKEN Baton Zone Program, Sayo, Japan.,Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, Japan
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