1
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Unge J, Lin J, Weaver SJ, Sae Her A, Gonen T. Compositional Analysis of Complex Mixtures using Automatic MicroED Data Collection. Adv Sci (Weinh) 2024:e2400081. [PMID: 38647272 DOI: 10.1002/advs.202400081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 04/09/2024] [Indexed: 04/25/2024]
Abstract
Quantitative analysis of complex mixtures, including compounds having similar chemical properties, is demonstrated using an automatic and high throughput approach to microcrystal electron diffraction (MicroED). Compositional analysis of organic and inorganic compounds can be accurately executed without the need of diffraction standards. Additionally, with sufficient statistics, small amounts of compounds in mixtures can be reliably detected. These compounds can be distinguished by their crystal structure properties prior to structure solution. In addition, if the crystals are of good quality, the crystal structures can be generated on the fly, providing a complete analysis of the sample. MicroED is an effective method for analyzing the structural properties of sub-micron crystals, which are frequently found in small-molecule powders. By developing and using an automatic and high throughput approach to MicroED, and with the use of SerialEM for data collection, data from thousands of crystals allow sufficient statistics to detect even small amounts of compounds reliably.
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Affiliation(s)
- Johan Unge
- Department of Biological Chemistry, University of California, Los Angeles, 615 Charles E. Young Drive South, Los Angeles, California, 90095, USA
| | - Jieye Lin
- Department of Biological Chemistry, University of California, Los Angeles, 615 Charles E. Young Drive South, Los Angeles, California, 90095, USA
| | - Sara J Weaver
- Department of Biological Chemistry, University of California, Los Angeles, 615 Charles E. Young Drive South, Los Angeles, California, 90095, USA
| | - Ampon Sae Her
- Department of Biological Chemistry, University of California, Los Angeles, 615 Charles E. Young Drive South, Los Angeles, California, 90095, USA
| | - Tamir Gonen
- Department of Biological Chemistry, University of California, Los Angeles, 615 Charles E. Young Drive South, Los Angeles, California, 90095, USA
- Department of Physiology, University of California, Los Angeles, 615 Charles E. Young Drive South, Los Angeles, California, 90095, USA
- Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, California, 90095, USA
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2
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Lightowler M, Li S, Ou X, Cho J, Liu B, Li A, Hofer G, Xu J, Yang T, Zou X, Lu M, Xu H. Phase Identification and Discovery of an Elusive Polymorph of Drug-Polymer Inclusion Complex Using Automated 3D Electron Diffraction. Angew Chem Int Ed Engl 2024; 63:e202317695. [PMID: 38380831 DOI: 10.1002/anie.202317695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 02/16/2024] [Accepted: 02/17/2024] [Indexed: 02/22/2024]
Abstract
3D electron diffraction (3D ED) has shown great potential in crystal structure determination in materials, small organic molecules, and macromolecules. In this work, an automated, low-dose and low-bias 3D ED protocol has been implemented to identify six phases from a multiple-phase melt-crystallisation product of an active pharmaceutical ingredient, griseofulvin (GSF). Batch data collection under low-dose conditions using a widely available commercial software was combined with automated data analysis to collect and process over 230 datasets in three days. Accurate unit cell parameters obtained from 3D ED data allowed direct phase identification of GSF Forms III, I and the known GSF inclusion complex (IC) with polyethylene glycol (PEG) (GSF-PEG IC-I), as well as three minor phases, namely GSF Forms II, V and an elusive new phase, GSF-PEG IC-II. Their structures were then directly determined by 3D ED. Furthermore, we reveal how the stabilities of the two GSF-PEG IC polymorphs are closely related to their crystal structures. These results demonstrate the power of automated 3D ED for accurate phase identification and direct structure determination of complex, beam-sensitive crystallisation products, which is significant for drug development where solid form screening is crucial for the overall efficacy of the drug product.
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Affiliation(s)
- Molly Lightowler
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, SE-106 91, Sweden
| | - Shuting Li
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Xiao Ou
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Jungyoun Cho
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, SE-106 91, Sweden
| | - Binbin Liu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Ao Li
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Gerhard Hofer
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, SE-106 91, Sweden
| | - Jiaoyan Xu
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, SE-106 91, Sweden
| | - Taimin Yang
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, SE-106 91, Sweden
| | - Xiaodong Zou
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, SE-106 91, Sweden
| | - Ming Lu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Hongyi Xu
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm, SE-106 91, Sweden
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3
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Delgadillo D, Burch JE, Kim LJ, de Moraes LS, Niwa K, Williams J, Tang MJ, Lavallo VG, Khatri Chhetri B, Jones CG, Rodriguez IH, Signore JA, Marquez L, Bhanushali R, Woo S, Kubanek J, Quave C, Tang Y, Nelson HM. High-Throughput Identification of Crystalline Natural Products from Crude Extracts Enabled by Microarray Technology and microED. ACS Cent Sci 2024; 10:176-183. [PMID: 38292598 PMCID: PMC10823509 DOI: 10.1021/acscentsci.3c01365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 12/04/2023] [Accepted: 12/04/2023] [Indexed: 02/01/2024]
Abstract
The structural determination of natural products (NPs) can be arduous because of sample heterogeneity. This often demands iterative purification processes and characterization of complex molecules that may be available only in miniscule quantities. Microcrystal electron diffraction (microED) has recently shown promise as a method to solve crystal structures of NPs from nanogram quantities of analyte. However, its implementation in NP discovery remains hampered by sample throughput and purity requirements, akin to traditional NP-discovery workflows. In the methods described herein, we leverage the resolving power of transmission electron microscopy (TEM) and the miniaturization capabilities of deoxyribonucleic acid (DNA) microarray technology to address these challenges through the establishment of an NP screening platform, array electron diffraction (ArrayED). In this workflow, an array of high-performance liquid chromatography (HPLC) fractions taken from crude extracts was deposited onto TEM grids in picoliter-sized droplets. This multiplexing of analytes on TEM grids enables 1200 or more unique samples to be simultaneously inserted into a TEM instrument equipped with an autoloader. Selected area electron diffraction analysis of these microarrayed grids allows for the rapid identification of crystalline metabolites. In this study, ArrayED enabled structural characterization of 14 natural products, including four novel crystal structures and two novel polymorphs, from 20 crude extracts. Moreover, we identify several chemical species that would not be detected by standard mass spectrometry (MS) or ultraviolet-visible (UV/vis) spectroscopy and crystal forms that would not be characterized using traditional methods.
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Affiliation(s)
- David
A. Delgadillo
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
| | - Jessica E. Burch
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
| | - Lee Joon Kim
- Department of Chemistry
and Biochemistry, and Department of Chemical and Biomolecular
Engineering, University of California, Los
Angeles, Los Angeles, California 90095, United States
| | - Lygia S. de Moraes
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
| | - Kanji Niwa
- Department of Chemistry
and Biochemistry, and Department of Chemical and Biomolecular
Engineering, University of California, Los
Angeles, Los Angeles, California 90095, United States
| | - Jason Williams
- Department of Chemistry
and Biochemistry, and Department of Chemical and Biomolecular
Engineering, University of California, Los
Angeles, Los Angeles, California 90095, United States
| | - Melody J. Tang
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
| | - Vincent G. Lavallo
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
| | - Bhuwan Khatri Chhetri
- School
of Biological Sciences, School of Chemistry
and Biochemistry, and Neuroscience Program, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Christopher G. Jones
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
| | - Isabel Hernandez Rodriguez
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
| | - Joshua A. Signore
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
| | - Lewis Marquez
- Molecular
and Systems Pharmacology, Laney Graduate School, Emory University, Atlanta, Georgia 30322, United States
| | - Riya Bhanushali
- School
of Biological Sciences, School of Chemistry
and Biochemistry, and Neuroscience Program, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Sunmin Woo
- Center
for the Study of Human Health, Emory University, Atlanta, Georgia 30322, United States
| | - Julia Kubanek
- School
of Biological Sciences, School of Chemistry
and Biochemistry, and Neuroscience Program, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Cassandra Quave
- Molecular
and Systems Pharmacology, Laney Graduate School, Emory University, Atlanta, Georgia 30322, United States
- Center
for the Study of Human Health, Emory University, Atlanta, Georgia 30322, United States
- Department
of Dermatology, Emory University School
of Medicine, Atlanta, Georgia 30322, United
States
| | - Yi Tang
- Department of Chemistry
and Biochemistry, and Department of Chemical and Biomolecular
Engineering, University of California, Los
Angeles, Los Angeles, California 90095, United States
| | - Hosea M. Nelson
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
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4
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Hogan-Lamarre P, Luo Y, Bücker R, Miller RJD, Zou X. STEM SerialED: achieving high-resolution data for ab initio structure determination of beam-sensitive nanocrystalline materials. IUCrJ 2024; 11:62-72. [PMID: 38038991 PMCID: PMC10833385 DOI: 10.1107/s2052252523009661] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 11/06/2023] [Indexed: 12/02/2023]
Abstract
Serial electron diffraction (SerialED), which applies a snapshot data acquisition strategy for each crystal, was introduced to tackle the problem of radiation damage in the structure determination of beam-sensitive materials by three-dimensional electron diffraction (3DED). The snapshot data acquisition in SerialED can be realized using both transmission and scanning transmission electron microscopes (TEM/STEM). However, the current SerialED workflow based on STEM setups requires special external devices and software, which limits broader adoption. Here, we present a simplified experimental implementation of STEM-based SerialED on Thermo Fisher Scientific STEMs using common proprietary software interfaced through Python scripts to automate data collection. Specifically, we utilize TEM Imaging and Analysis (TIA) scripting and TEM scripting to access the STEM functionalities of the microscope, and DigitalMicrograph scripting to control the camera for snapshot data acquisition. Data analysis adapts the existing workflow using the software CrystFEL, which was developed for serial X-ray crystallography. Our workflow for STEM SerialED can be used on any Gatan or Thermo Fisher Scientific camera. We apply this workflow to collect high-resolution STEM SerialED data from two aluminosilicate zeolites, zeolite Y and ZSM-25. We demonstrate, for the first time, ab initio structure determination through direct methods using STEM SerialED data. Zeolite Y is relatively stable under the electron beam, and STEM SerialED data extend to 0.60 Å. We show that the structural model obtained using STEM SerialED data merged from 358 crystals is nearly identical to that using continuous rotation electron diffraction data from one crystal. This demonstrates that accurate structures can be obtained from STEM SerialED. Zeolite ZSM-25 is very beam-sensitive and has a complex structure. We show that STEM SerialED greatly improves the data resolution of ZSM-25, compared with serial rotation electron diffraction (SerialRED), from 1.50 to 0.90 Å. This allows, for the first time, the use of standard phasing methods, such as direct methods, for the ab initio structure determination of ZSM-25.
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Affiliation(s)
- Pascal Hogan-Lamarre
- Department of Physics, University of Toronto, 80 George Street, Toronto, Ontario M5S 3H6, Canada
- Max Planck Institute for the Structure and Dynamics of Matter, Hamburg, Germany
| | - Yi Luo
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm SE-106, Sweden
| | - Robert Bücker
- Max Planck Institute for the Structure and Dynamics of Matter, Hamburg, Germany
| | - R. J. Dwayne Miller
- Department of Physics, University of Toronto, 80 George Street, Toronto, Ontario M5S 3H6, Canada
- Department of Chemistry, University of Toronto, 80 George Street, Toronto, Ontario M5S 3H6, Canada
| | - Xiaodong Zou
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm SE-106, Sweden
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5
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Luo M, Zhou B, Reddem ER, Tang B, Chen B, Zhou R, Liu H, Liu L, Katsamba PS, Au KK, Man HO, To KKW, Yuen KY, Shapiro L, Dang S, Ho DD, Chen Z. Structural insights into broadly neutralizing antibodies elicited by hybrid immunity against SARS-CoV-2. Emerg Microbes Infect 2023; 12:2146538. [PMID: 36354024 PMCID: PMC9817130 DOI: 10.1080/22221751.2022.2146538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
ABSTRACTIncreasing spread by SARS-CoV-2 Omicron variants challenges existing vaccines and broadly reactive neutralizing antibodies (bNAbs) against COVID-19. Here we determine the diversity, potency, breadth and structural insights of bNAbs derived from memory B cells of BNT162b2-vaccinee after homogeneous Omicron BA.1 breakthrough infection. The infection activates diverse memory B cell clonotypes for generating potent class I/II and III bNAbs with new epitopes mapped to the receptor-binding domain (RBD). The top eight bNAbs neutralize wildtype and BA.1 potently but display divergent IgH/IgL sequences and neuralization profiles against other variants of concern (VOCs). Two of them (P2D9 and P3E6) belonging to class III NAbs display comparable potency against BA.4/BA.5, although structural analysis reveals distinct modes of action. P3E6 neutralizes all variants tested through a unique bivalent interaction with two RBDs. Our findings provide new insights into hybrid immunity on BNT162b2-induced diverse memory B cells in response to Omicron breakthrough infection for generating diverse bNAbs with distinct structural basis.
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Affiliation(s)
- Mengxiao Luo
- AIDS Institute, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China,Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
| | - Biao Zhou
- AIDS Institute, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China,Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
| | | | - Bingjie Tang
- Division of Life Science, Center of Systems Biology and Human Health, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong Special Administrative Region, People’s Republic of China
| | - Bohao Chen
- AIDS Institute, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China,Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
| | - Runhong Zhou
- AIDS Institute, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China,Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
| | - Hang Liu
- Division of Life Science, Center of Systems Biology and Human Health, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong Special Administrative Region, People’s Republic of China
| | - Lihong Liu
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | | | - Ka-Kit Au
- AIDS Institute, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China,Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
| | - Hiu-On Man
- AIDS Institute, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China,Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
| | - Kelvin Kai-Wang To
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China,Centre for Virology, Vaccinology and Therapeutics, Health@InnoHK, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China,Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, People’s Republic of China,Department of Microbiology, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
| | - Kwok-Yung Yuen
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China,Centre for Virology, Vaccinology and Therapeutics, Health@InnoHK, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China,Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, People’s Republic of China,Department of Microbiology, Queen Mary Hospital, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
| | - Lawrence Shapiro
- Zuckerman Mind Brain Behaviour Institute, New York, NY, USA,Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA, Zhiwei Chen AIDS Institute, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China; Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China; State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China; Centre for Virology, Vaccinology and Therapeutics, Health@InnoHK, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China; Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong, People's Republic of China; Lawrence Shapiro Zuckerman Mind Brain Behaviour Institute, New York, NY 10027, USA, Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA; Shangyu Dang Division of Life Science, Center of Systems Biology and Human Health, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong Special Administrative Region, People's Republic of China, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, People's Republic of China, HKUST-Shenzhen Research Institute, Nanshan, Shenzhen 518057, People's Republic of China; David D. Ho Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Shangyu Dang
- Division of Life Science, Center of Systems Biology and Human Health, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong Special Administrative Region, People’s Republic of China,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, People’s Republic of China,HKUST-Shenzhen Research Institute, Nanshan, People’s Republic of China, Zhiwei Chen AIDS Institute, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China; Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China; State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China; Centre for Virology, Vaccinology and Therapeutics, Health@InnoHK, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China; Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong, People's Republic of China; Lawrence Shapiro Zuckerman Mind Brain Behaviour Institute, New York, NY 10027, USA, Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA; Shangyu Dang Division of Life Science, Center of Systems Biology and Human Health, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong Special Administrative Region, People's Republic of China, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, People's Republic of China, HKUST-Shenzhen Research Institute, Nanshan, Shenzhen 518057, People's Republic of China; David D. Ho Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - David D. Ho
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Zhiwei Chen
- AIDS Institute, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China,Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China,State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China,Centre for Virology, Vaccinology and Therapeutics, Health@InnoHK, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China,Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, People’s Republic of China, Zhiwei Chen AIDS Institute, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China; Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China; State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China; Centre for Virology, Vaccinology and Therapeutics, Health@InnoHK, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China; Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, Guangdong, People's Republic of China; Lawrence Shapiro Zuckerman Mind Brain Behaviour Institute, New York, NY 10027, USA, Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA; Shangyu Dang Division of Life Science, Center of Systems Biology and Human Health, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong Special Administrative Region, People's Republic of China, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, People's Republic of China, HKUST-Shenzhen Research Institute, Nanshan, Shenzhen 518057, People's Republic of China; David D. Ho Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
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6
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Cleeve P, Dierickx D, Naegele L, Kannachel R, Burne L, Buckley G, Gorelick S, Whisstock JC, de Marco A. OpenFIBSEM: A universal API for FIBSEM control. J Struct Biol 2023; 215:107967. [PMID: 37105276 DOI: 10.1016/j.jsb.2023.107967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 04/19/2023] [Accepted: 04/20/2023] [Indexed: 04/29/2023]
Abstract
This paper introduces OpenFIBSEM, a universal API to control Focused Ion Beam Scanning Electron Microscopes (FIBSEM). OpenFIBSEM aims to improve the programmability and automation of electron microscopy workflows in structural biology research. The API is designed to be cross-platform, composable, and extendable: allowing users to use any portion of OpenFIBSEM to develop or integrate with other software tools. The package provides core functionality such as imaging, movement, milling, and manipulator control, as well as system calibration, alignment, and image analysis modules. Further, a library of reusable user interface components integrated with napari is provided, ensuring easy and efficient application development. OpenFIBSEM currently supports ThermoFisher and TESCAN hardware, with support for other manufacturers planned. To demonstrate the improved automation capabilities enabled by OpenFIBSEM, several example applications that are compatible with multiple hardware manufacturers are discussed. We argue that OpenFIBSEM provides the foundation for a cross-platform operating system and development ecosystem for FIBSEM systems. The API and applications are open-source and available on GitHub (https://github.com/DeMarcoLab/fibsem).
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Affiliation(s)
- Patrick Cleeve
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, 3800 Clayton, Victoria, Australia
| | - David Dierickx
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, 3800 Clayton, Victoria, Australia
| | - Lucile Naegele
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, 3800 Clayton, Victoria, Australia
| | - Rohit Kannachel
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, 3800 Clayton, Victoria, Australia
| | - Lachlan Burne
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, 3800 Clayton, Victoria, Australia
| | - Genevieve Buckley
- Ramaciotti Centre for Cryo-Electron Microscopy, Monash University, 3800 Clayton, Victoria, Australia
| | - Sergey Gorelick
- Monash Centre for Electron Microscopy, Monash University, 3800 Clayton, Victoria, Australia
| | - James C Whisstock
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, 3800 Clayton, Victoria, Australia; EMBL Australia, Monash University, 3800 Clayton, Victoria, Australia.
| | - Alex de Marco
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, 3800 Clayton, Victoria, Australia.
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7
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Parkhurst JM, Crawshaw AD, Siebert CA, Dumoux M, Owen CD, Nunes P, Waterman D, Glen T, Stuart DI, Naismith JH, Evans G. Investigation of the milling characteristics of different focused-ion-beam sources assessed by three-dimensional electron diffraction from crystal lamellae. IUCrJ 2023; 10:270-287. [PMID: 36952226 PMCID: PMC10161776 DOI: 10.1107/s2052252523001902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 03/01/2023] [Indexed: 05/06/2023]
Abstract
Three-dimensional electron diffraction (3DED) from nanocrystals of biological macromolecules requires the use of very small crystals. These are typically less than 300 nm-thick in the direction of the electron beam due to the strong interaction between electrons and matter. In recent years, focused-ion-beam (FIB) milling has been used in the preparation of thin samples for 3DED. These instruments typically use a gallium liquid metal ion source. Inductively coupled plasma (ICP) sources in principle offer faster milling rates. Little work has been done to quantify the damage these sources cause to delicate biological samples at cryogenic temperatures. Here, an analysis of the effect that milling with plasma FIB (pFIB) instrumentation has on lysozyme crystals is presented. This work evaluates both argon and xenon plasmas and compares them with crystals milled with a gallium source. A milling protocol was employed that utilizes an overtilt to produce wedge-shaped lamellae with a shallow thickness gradient which yielded very thin crystalline samples. 3DED data were then acquired and standard data-processing statistics were employed to assess the quality of the diffraction data. An upper bound to the depth of the pFIB-milling damage layer of between 42.5 and 50 nm is reported, corresponding to half the thickness of the thinnest lamellae that resulted in usable diffraction data. A lower bound of between 32.5 and 40 nm is also reported, based on a literature survey of the minimum amount of diffracting material required for 3DED.
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Affiliation(s)
- James M Parkhurst
- Rosalind Franklin Insititute, Harwell Science and Innovation Campus, Didcot, Oxford OX11 0QX, United Kingdom
| | - Adam D Crawshaw
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxford OX11 0QS, United Kingdom
| | - C Alistair Siebert
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxford OX11 0QS, United Kingdom
| | - Maud Dumoux
- Rosalind Franklin Insititute, Harwell Science and Innovation Campus, Didcot, Oxford OX11 0QX, United Kingdom
| | - C David Owen
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxford OX11 0QS, United Kingdom
| | - Pedro Nunes
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxford OX11 0QS, United Kingdom
| | - David Waterman
- Research Complex at Harwell, Harwell Science and Innovation Campus, Harwell, Oxford OX11 0FA, United Kingdom
| | - Thomas Glen
- Rosalind Franklin Insititute, Harwell Science and Innovation Campus, Didcot, Oxford OX11 0QX, United Kingdom
| | - David I Stuart
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxford OX11 0QS, United Kingdom
| | - James H Naismith
- Rosalind Franklin Insititute, Harwell Science and Innovation Campus, Didcot, Oxford OX11 0QX, United Kingdom
| | - Gwyndaf Evans
- Rosalind Franklin Insititute, Harwell Science and Innovation Campus, Didcot, Oxford OX11 0QX, United Kingdom
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8
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Danelius E, Patel K, Gonzalez B, Gonen T. MicroED in drug discovery. Curr Opin Struct Biol 2023; 79:102549. [PMID: 36821888 PMCID: PMC10023408 DOI: 10.1016/j.sbi.2023.102549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 01/16/2023] [Accepted: 01/23/2023] [Indexed: 02/23/2023]
Abstract
The cryo-electron microscopy (cryo-EM) method microcrystal electron diffraction (MicroED) was initially described in 2013 and has recently gained attention as an emerging technique for research in drug discovery. As compared to other methods in structural biology, MicroED provides many advantages deriving from the use of nanocrystalline material for the investigations. Here, we review the recent advancements in the field of MicroED and show important examples of small molecule, peptide and protein structures that has contributed to the current development of this method as an important tool for drug discovery.
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Affiliation(s)
- Emma Danelius
- Department of Biological Chemistry, University of California Los Angeles, 615 Charles E.Young Drive South, Los Angeles, CA 90095, USA; Howard Hughes Medical Institute, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Khushboo Patel
- Department of Biological Chemistry, University of California Los Angeles, 615 Charles E.Young Drive South, Los Angeles, CA 90095, USA; Howard Hughes Medical Institute, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Brenda Gonzalez
- Department of Biological Chemistry, University of California Los Angeles, 615 Charles E.Young Drive South, Los Angeles, CA 90095, USA; Howard Hughes Medical Institute, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Tamir Gonen
- Department of Biological Chemistry, University of California Los Angeles, 615 Charles E.Young Drive South, Los Angeles, CA 90095, USA; Howard Hughes Medical Institute, University of California Los Angeles, Los Angeles, CA 90095, USA; Department of Physiology, University of California Los Angeles, 615 Charles E. Young Drive South, Los Angeles, CA 90095, USA.
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9
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Du DX, Simjanoska M, Fitzpatrick AWP. Four-dimensional microED of conformational dynamics in protein microcrystals on the femto-to-microsecond timescales. J Struct Biol 2023; 215:107941. [PMID: 36773734 DOI: 10.1016/j.jsb.2023.107941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 02/03/2023] [Accepted: 02/07/2023] [Indexed: 02/12/2023]
Abstract
As structural determination of protein complexes approaches atomic resolution, there is an increasing focus on conformational dynamics. Here we conceptualize the combination of two techniques which have become established in recent years: microcrystal electron diffraction and ultrafast electron microscopy. We show that the extremely low dose of pulsed photoemission still enables microED due to the strength of the electron bunching from diffraction of the protein crystals. Indeed, ultrafast electron diffraction experiments on protein crystals have already been demonstrated to be effective in measuring intermolecular forces in protein microcrystals. We discuss difficulties that may arise in the acquisition and processing of data and the overall feasibility of the experiment, paying specific attention to dose and signal-to-noise ratio. In doing so, we outline a detailed workflow that may be effective in minimizing the dose on the specimen. A series of model systems that would be good candidates for initial experiments is provided.
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Affiliation(s)
- Daniel X Du
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA; Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, 630 West 168th Street, New York, NY 10032, USA
| | - Marija Simjanoska
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA; Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, 630 West 168th Street, New York, NY 10032, USA
| | - Anthony W P Fitzpatrick
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA; Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, 630 West 168th Street, New York, NY 10032, USA.
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10
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Volokh OI, Sivkina AL, Moiseenko AV, Popinako AV, Karlova MG, Valieva ME, Kotova EY, Kirpichnikov MP, Formosa T, Studitsky VM, Sokolova OS. Mechanism of curaxin-dependent nucleosome unfolding by FACT. Front Mol Biosci 2022; 9:1048117. [PMID: 36483541 PMCID: PMC9723464 DOI: 10.3389/fmolb.2022.1048117] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 11/07/2022] [Indexed: 08/27/2023] Open
Abstract
Human FACT (FACT) is a multifunctional histone chaperone involved in transcription, replication and DNA repair. Curaxins are anticancer compounds that induce FACT-dependent nucleosome unfolding and trapping of FACT in the chromatin of cancer cells (c-trapping) through an unknown molecular mechanism. Here, we analyzed the effects of curaxin CBL0137 on nucleosome unfolding by FACT using spFRET and electron microscopy. By itself, FACT adopted multiple conformations, including a novel, compact, four-domain state in which the previously unresolved NTD of the SPT16 subunit of FACT was localized, apparently stabilizing a compact configuration. Multiple, primarily open conformations of FACT-nucleosome complexes were observed during curaxin-supported nucleosome unfolding. The obtained models of intermediates suggest "decision points" in the unfolding/folding pathway where FACT can either promote disassembly or assembly of nucleosomes, with the outcome possibly being influenced by additional factors. The data suggest novel mechanisms of nucleosome unfolding by FACT and c-trapping by curaxins.
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Affiliation(s)
- Olesya I. Volokh
- Biology Faculty Lomonosov Moscow State University, Moscow, Russia
| | | | - Andrey V. Moiseenko
- Biology Faculty Lomonosov Moscow State University, Moscow, Russia
- Semenov Federal Research Center of Chemical Physics RAS, Moscow, Russia
| | - Anna V. Popinako
- Bach Institute of Biochemistry Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Maria G. Karlova
- Biology Faculty Lomonosov Moscow State University, Moscow, Russia
| | - Maria E. Valieva
- Biology Faculty Lomonosov Moscow State University, Moscow, Russia
- RG Development & Disease Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute for Medical and Human Genetics Charité-Universitätsmedizin Berlin, Berlin, Germany
| | | | | | - Timothy Formosa
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, United States
| | - Vasily M. Studitsky
- Biology Faculty Lomonosov Moscow State University, Moscow, Russia
- Fox Chase Cancer Center, Philadelphia, PA, United States
| | - Olga S. Sokolova
- Biology Faculty Lomonosov Moscow State University, Moscow, Russia
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11
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Yang T, Willhammar T, Xu H, Zou X, Huang Z. Single-crystal structure determination of nanosized metal-organic frameworks by three-dimensional electron diffraction. Nat Protoc 2022. [PMID: 35896741 DOI: 10.1038/s41596-022-00720-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 04/26/2022] [Indexed: 11/08/2022]
Abstract
Metal-organic frameworks (MOFs) have attracted considerable interest due to their well-defined pore architecture and structural tunability on molecular dimensions. While single-crystal X-ray diffraction (SCXRD) has been widely used to elucidate the structures of MOFs at the atomic scale, the formation of large and well-ordered crystals is still a crucial bottleneck for structure determination. To alleviate this challenge, three-dimensional electron diffraction (3D ED) has been developed for structure determination of nano- (submicron-)sized crystals. Such 3D ED data are collected from each single crystal using transmission electron microscopy. In this protocol, we introduce the entire workflow for structural analysis of MOFs by 3D ED, from sample preparation, data acquisition and data processing to structure determination. We describe methods for crystal screening and handling of crystal agglomerates, which are crucial steps in sample preparation for single-crystal 3D ED data collection. We further present how to set up a transmission electron microscope for 3D ED data acquisition and, more importantly, offer suggestions for the optimization of data acquisition conditions. For data processing, including unit cell and space group determination, and intensity integration, we provide guidelines on how to use electron and X-ray crystallography software to process 3D ED data. Finally, we present structure determination from 3D ED data and discuss the important features associated with 3D ED data that need to be considered. We believe that this protocol provides critical details for implementing and utilizing 3D ED as a structure determination platform for nano- (submicron-)sized MOFs as well as other crystalline materials.
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12
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Querques I, Schmitz M, Oberli S, Chanez C, Jinek M. Target site selection and remodelling by type V CRISPR-transposon systems. Nature 2021; 599:497-502. [PMID: 34759315 PMCID: PMC7613401 DOI: 10.1038/s41586-021-04030-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 09/16/2021] [Indexed: 11/09/2022]
Abstract
Canonical CRISPR-Cas systems provide adaptive immunity against mobile genetic elements1. However, type I-F, I-B and V-K systems have been adopted by Tn7-like transposons to direct RNA-guided transposon insertion2-7. Type V-K CRISPR-associated transposons rely on the pseudonuclease Cas12k, the transposase TnsB, the AAA+ ATPase TnsC and the zinc-finger protein TniQ7, but the molecular mechanism of RNA-directed DNA transposition has remained elusive. Here we report cryo-electron microscopic structures of a Cas12k-guide RNA-target DNA complex and a DNA-bound, polymeric TnsC filament from the CRISPR-associated transposon system of the photosynthetic cyanobacterium Scytonema hofmanni. The Cas12k complex structure reveals an intricate guide RNA architecture and critical interactions mediating RNA-guided target DNA recognition. TnsC helical filament assembly is ATP-dependent and accompanied by structural remodelling of the bound DNA duplex. In vivo transposition assays corroborate key features of the structures, and biochemical experiments show that TniQ restricts TnsC polymerization, while TnsB interacts directly with TnsC filaments to trigger their disassembly upon ATP hydrolysis. Together, these results suggest that RNA-directed target selection by Cas12k primes TnsC polymerization and DNA remodelling, generating a recruitment platform for TnsB to catalyse site-specific transposon insertion. Insights from this work will inform the development of CRISPR-associated transposons as programmable site-specific gene insertion tools.
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Affiliation(s)
- Irma Querques
- Department of Biochemistry, University of Zurich, Zurich, 8057, Switzerland
| | - Michael Schmitz
- Department of Biochemistry, University of Zurich, Zurich, 8057, Switzerland
| | - Seraina Oberli
- Department of Biochemistry, University of Zurich, Zurich, 8057, Switzerland
| | - Christelle Chanez
- Department of Biochemistry, University of Zurich, Zurich, 8057, Switzerland
| | - Martin Jinek
- Department of Biochemistry, University of Zurich, Zurich, Switzerland.
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13
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Clark LJ, Bu G, Nannenga BL, Gonen T. MicroED for the study of protein–ligand interactions and the potential for drug discovery. Nat Rev Chem 2021; 5:853-858. [PMID: 37117388 DOI: 10.1038/s41570-021-00332-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/16/2021] [Indexed: 12/18/2022]
Abstract
Microcrystal electron diffraction (MicroED) is an electron cryo-microscopy (cryo-EM) technique used to determine molecular structures with crystals that are a millionth the size needed for traditional single-crystal X-ray crystallography. An exciting use of MicroED is in drug discovery and development, where it can be applied to the study of proteins and small molecule interactions, and for structure determination of natural products. The structures are then used for rational drug design and optimization. In this Perspective, we discuss the current applications of MicroED for structure determination of protein-ligand complexes and potential future applications in drug discovery.
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14
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Abstract
In the past few years, many exciting papers reported results based on crystal structure determination by electron diffraction. The aim of this review is to provide general and practical information to structural chemists interested in stepping into this emerging field. We discuss technical characteristics of electron microscopes for research units that would like to acquire their own instrumentation, as well as those practical aspects that appear different between X-ray and electron crystallography. We also include a discussion about applications where electron crystallography provides information that is different, and possibly complementary, with respect to what is available from X-ray crystallography.
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Affiliation(s)
- Tim Gruene
- University
of Vienna, Faculty of Chemistry,
Department of Inorganic Chemistry, AT-1090 Vienna, Austria
| | - Enrico Mugnaioli
- Center
for Nanotechnology Innovation@NEST, Istituto
Italiano di Tecnologia, Piazza S. Silvestro 12, IT-56127 Pisa, Italy
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15
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Schröder GC, Meilleur F. Metalloprotein catalysis: structural and mechanistic insights into oxidoreductases from neutron protein crystallography. Acta Crystallogr D Struct Biol 2021; 77:1251-1269. [PMID: 34605429 PMCID: PMC8489226 DOI: 10.1107/s2059798321009025] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 08/31/2021] [Indexed: 11/11/2022] Open
Abstract
Metalloproteins catalyze a range of reactions, with enhanced chemical functionality due to their metal cofactor. The reaction mechanisms of metalloproteins have been experimentally characterized by spectroscopy, macromolecular crystallography and cryo-electron microscopy. An important caveat in structural studies of metalloproteins remains the artefacts that can be introduced by radiation damage. Photoreduction, radiolysis and ionization deriving from the electromagnetic beam used to probe the structure complicate structural and mechanistic interpretation. Neutron protein diffraction remains the only structural probe that leaves protein samples devoid of radiation damage, even when data are collected at room temperature. Additionally, neutron protein crystallography provides information on the positions of light atoms such as hydrogen and deuterium, allowing the characterization of protonation states and hydrogen-bonding networks. Neutron protein crystallography has further been used in conjunction with experimental and computational techniques to gain insight into the structures and reaction mechanisms of several transition-state metal oxidoreductases with iron, copper and manganese cofactors. Here, the contribution of neutron protein crystallography towards elucidating the reaction mechanism of metalloproteins is reviewed.
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Affiliation(s)
- Gabriela C. Schröder
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Flora Meilleur
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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16
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Abstract
We present an in-depth protocol to reproducibly prepare crystalline lamellae from protein crystals for subsequent microcrystal electron diffraction (MicroED) experiments. This protocol covers typical soluble proteins and membrane proteins embedded in dense media. Following these steps will allow the user to prepare crystalline lamellae for protein structure determination by MicroED. For complete details on the use and execution of this protocol, please refer to Martynowycz et al. (2019a, 2020a).
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Affiliation(s)
- Michael W. Martynowycz
- Howard Hughes Medical Institute, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Tamir Gonen
- Howard Hughes Medical Institute, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Physiology, University of California Los Angeles, Los Angeles, CA 90095, USA
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17
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Yonekura K, Maki-Yonekura S, Naitow H, Hamaguchi T, Takaba K. Machine learning-based real-time object locator/evaluator for cryo-EM data collection. Commun Biol 2021; 4:1044. [PMID: 34493805 DOI: 10.1038/s42003-021-02577-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [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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18
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Shan H, Su X, Li T, Qin Y, Zhang N, Yang L, Ma L, Bai Y, Qi L, Liu Y, Shen QT. Structural plasticity of mumps virus nucleocapsids with cryo-EM structures. Commun Biol 2021; 4:833. [PMID: 34215847 DOI: 10.1038/s42003-021-02362-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 06/11/2021] [Indexed: 11/08/2022] Open
Abstract
Mumps virus (MuV) is a highly contagious human pathogen and frequently causes worldwide outbreaks despite available vaccines. Similar to other mononegaviruses such as Ebola and rabies, MuV uses a single-stranded negative-sense RNA as its genome, which is enwrapped by viral nucleoproteins into the helical nucleocapsid. The nucleocapsid acts as a scaffold for genome condensation and as a template for RNA replication and transcription. Conformational changes in the MuV nucleocapsid are required to switch between different activities, but the underlying mechanism remains elusive due to the absence of high-resolution structures. Here, we report two MuV nucleoprotein-RNA rings with 13 and 14 protomers, one stacked-ring filament and two nucleocapsids with distinct helical pitches, in dense and hyperdense states, at near-atomic resolutions using cryo-electron microscopy. Structural analysis of these in vitro assemblies indicates that the C-terminal tail of MuV nucleoprotein likely regulates the assembly of helical nucleocapsids, and the C-terminal arm may be relevant for the transition between the dense and hyperdense states of helical nucleocapsids. Our results provide the molecular mechanism for structural plasticity among different MuV nucleocapsids and create a possible link between structural plasticity and genome condensation. Shan et al. describes the high-resolution structures of Nucleoprotein in two different oligomeric states and four different higher-order helical structures. They further describe the structural rearrangements required to transition between the different helical assemblies obtained, highlighting the basis for structural plasticity among different MuV nucleocapsids.
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19
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Peck A, Yao Q, Brewster AS, Zwart PH, Heumann JM, Sauter NK, Jensen GJ. Challenges in solving structures from radiation-damaged tomograms of protein nanocrystals assessed by simulation. Acta Crystallogr D Struct Biol 2021; 77:572-586. [PMID: 33950014 PMCID: PMC8098477 DOI: 10.1107/s2059798321002369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Accepted: 03/02/2021] [Indexed: 11/11/2022] Open
Abstract
Structure-determination methods are needed to resolve the atomic details that underlie protein function. X-ray crystallography has provided most of our knowledge of protein structure, but is constrained by the need for large, well ordered crystals and the loss of phase information. The rapidly developing methods of serial femtosecond crystallography, micro-electron diffraction and single-particle reconstruction circumvent the first of these limitations by enabling data collection from nanocrystals or purified proteins. However, the first two methods also suffer from the phase problem, while many proteins fall below the molecular-weight threshold required for single-particle reconstruction. Cryo-electron tomography of protein nanocrystals has the potential to overcome these obstacles of mainstream structure-determination methods. Here, a data-processing scheme is presented that combines routines from X-ray crystallography and new algorithms that have been developed to solve structures from tomograms of nanocrystals. This pipeline handles image-processing challenges specific to tomographic sampling of periodic specimens and is validated using simulated crystals. The tolerance of this workflow to the effects of radiation damage is also assessed. The simulations indicate a trade-off between a wider tilt range to facilitate merging data from multiple tomograms and a smaller tilt increment to improve phase accuracy. Since phase errors, but not merging errors, can be overcome with additional data sets, these results recommend distributing the dose over a wide angular range rather than using a finer sampling interval to solve the protein structure.
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Affiliation(s)
- Ariana Peck
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Qing Yao
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Aaron S. Brewster
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Petrus H. Zwart
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Center for Advanced Mathematics in Energy Research Applications, Lawrence Berkeley National Laboratory, Berkeley CA 94720, USA
| | - John M. Heumann
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Nicholas K. Sauter
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Grant J. Jensen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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20
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Zhang N, Shan H, Liu M, Li T, Luo R, Yang L, Qi L, Chu X, Su X, Wang R, Liu Y, Sun W, Shen QT. Structure and assembly of double-headed Sendai virus nucleocapsids. Commun Biol 2021; 4:494. [PMID: 33888861 PMCID: PMC8062630 DOI: 10.1038/s42003-021-02027-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Accepted: 03/23/2021] [Indexed: 01/17/2023] Open
Abstract
Paramyxoviruses, including the mumps virus, measles virus, Nipah virus and Sendai virus (SeV), have non-segmented single-stranded negative-sense RNA genomes which are encapsidated by nucleoproteins into helical nucleocapsids. Here, we reported a double-headed SeV nucleocapsid assembled in a tail-to-tail manner, and resolved its helical stems and clam-shaped joint at the respective resolutions of 2.9 and 3.9 Å, via cryo-electron microscopy. Our structures offer important insights into the mechanism of the helical polymerization, in particular via an unnoticed exchange of a N-terminal hole formed by three loops of nucleoproteins, and unveil the clam-shaped joint in a hyper-closed state for nucleocapsid dimerization. Direct visualization of the loop from the disordered C-terminal tail provides structural evidence that C-terminal tail is correlated to the curvature of nucleocapsid and links nucleocapsid condensation and genome replication and transcription with different assembly forms.
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Affiliation(s)
- Na Zhang
- iHuman Institute, School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hong Shan
- iHuman Institute, School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Mingdong Liu
- iHuman Institute, School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Tianhao Li
- iHuman Institute, School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Rui Luo
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Liuyan Yang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Lei Qi
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xiaofeng Chu
- iHuman Institute, School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xin Su
- iHuman Institute, School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Rui Wang
- iHuman Institute, School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Yunhui Liu
- iHuman Institute, School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Wenzhi Sun
- Chinese Institute for Brain Research, Beijing, China
- School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Qing-Tao Shen
- iHuman Institute, School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
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21
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Abstract
A detailed protocol for preparing small molecule samples for microcrystal electron diffraction (MicroED) experiments is described. MicroED has been developed to solve structures of proteins and small molecules using standard electron cryo-microscopy (cryo-EM) equipment. In this way, small molecules, peptides, soluble proteins, and membrane proteins have recently been determined to high resolutions. Protocols are presented here for preparing grids of small-molecule pharmaceuticals using the drug carbamazepine as an example. Protocols for screening and collecting data are presented. Additional steps in the overall process, such as data integration, structure determination, and refinement are presented elsewhere. The time required to prepare the small-molecule grids is estimated to be less than 30 min.
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Affiliation(s)
- Michael W. Martynowycz
- Howard Hughes Medical Institute, University of California Los Angeles,Department of Biological Chemistry, University of California Los Angeles
| | - Tamir Gonen
- Howard Hughes Medical Institute, University of California Los Angeles; Department of Biological Chemistry, University of California Los Angeles; Department of Physiology, University of California Los Angeles;
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22
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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23
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Blum TB, Housset D, Clabbers MTB, van Genderen E, Bacia-Verloop M, Zander U, McCarthy AA, Schoehn G, Ling WL, Abrahams JP. Statistically correcting dynamical electron scattering improves the refinement of protein nanocrystals, including charge refinement of coordinated metals. Acta Crystallogr D Struct Biol 2021; 77:75-85. [PMID: 33404527 PMCID: PMC7787111 DOI: 10.1107/s2059798320014540] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 11/02/2020] [Indexed: 11/10/2022] Open
Abstract
Electron diffraction allows protein structure determination when only nanosized crystals are available. Nevertheless, multiple elastic (or dynamical) scattering, which is prominent in electron diffraction, is a concern. Current methods for modeling dynamical scattering by multi-slice or Bloch wave approaches are not suitable for protein crystals because they are not designed to cope with large molecules. Here, dynamical scattering of nanocrystals of insulin, thermolysin and thaumatin was limited by collecting data from thin crystals. To accurately measure the weak diffraction signal from the few unit cells in the thin crystals, a low-noise hybrid pixel Timepix electron-counting detector was used. The remaining dynamical component was further reduced in refinement using a likelihood-based correction, which was introduced previously for analyzing electron diffraction data of small-molecule nanocrystals and was adapted here for protein crystals. The procedure is shown to notably improve the structural refinement, in one case allowing the location of solvent molecules. It also allowed refinement of the charge states of bound metal atoms, an important element in protein function, through B-factor analysis of the metal atoms and their ligands. These results clearly increase the value of macromolecular electron crystallography as a complementary structural biology technique.
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Affiliation(s)
- Thorsten B. Blum
- Department of Biology and Chemistry, Paul Scherrer Institute, 5232 Villigen, Switzerland
| | - Dominique Housset
- Université Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Max T. B. Clabbers
- Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Eric van Genderen
- Department of Biology and Chemistry, Paul Scherrer Institute, 5232 Villigen, Switzerland
| | - Maria Bacia-Verloop
- Université Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Ulrich Zander
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Andrew A. McCarthy
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Guy Schoehn
- Université Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Wai Li Ling
- Université Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Jan Pieter Abrahams
- Department of Biology and Chemistry, Paul Scherrer Institute, 5232 Villigen, Switzerland
- Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, Mattenstrasse 26, 4058 Basel, Switzerland
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24
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Abstract
Automated coordination of microscope and camera functions for MicroED data collection simplifies the procedure for robust dataset acquisition and enables unattended sequential collection of many crystal targets. This chapter discusses the prerequisites for an algorithm of data collection automation for continuous-rotation MicroED and presents a practical protocol for achieving this goal using the popular TEM control software program SerialEM.
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25
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Abstract
Microcrystal electron diffraction (MicroED) is a technique for structure determination that relies on the strong interaction of electrons with a minuscule, crystalline sample. While some of the electrons used to probe the crystal interact without altering the crystal, others deposit energy which changes the sample through a series of damage events. It follows that the sample cannot be observed without damaging it, and the frames obtained at the beginning of data collection reflect a crystal that differs from the one that yields the last frames of the dataset. Data acquisition at cryogenic temperatures has been found to reduce the rate of damage progression and is routinely used to increase the dose tolerance of the crystal, allowing more useful data to be obtained before the sample is destroyed. Low-dose data collection can further prolong the lifetime of the crystal, such that less damage is inflicted over the course of data acquisition. Ideally, lower doses increase the measurable volume of a single-crystal lattice by reducing the damage caused by probing electrons. However, the information that can be recovered from a diffraction image is directly related to the number of electrons used to probe the sample. The signal from a weakly exposed crystal runs the risk of being lost in the noise contributed by solvent, crystal disorder, and the electron detection process. This work focuses on obtaining the best possible data from a MicroED measurement, which requires considering several aspects such as sample, dose, and camera type.
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26
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Abstract
Microcrystal Electron Diffraction (MicroED) enables structure determination of very small crystals that are much too small to be of use for other conventional diffraction techniques. MicroED has been used to determine the structures of many proteins and small organic molecules, and the technique can be performed on most standard cryo-TEM instruments equipped with high-speed detectors capable of collecting electron diffraction data. Here, we present protocols for MicroED sample preparation and data collection for protein microcrystals.
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Affiliation(s)
- Guanhong Bu
- Chemical Engineering, School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ, USA
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Brent L Nannenga
- Chemical Engineering, School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ, USA.
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ, USA.
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27
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Abstract
Microcrystal electron diffraction (MicroED) was first coined and developed in 2013 at the Janelia Research Campus as a new modality in electron cryomicroscopy (cryoEM). Since then, MicroED has not only made important contributions in pushing the resolution limits of cryoEM protein structure characterization but also of peptides, small-organic and inorganic molecules, and natural-products that have resisted structure determination by other methods. This review showcases important recent developments in MicroED, highlighting the importance of the technique in fields of studies beyond protein structure determination where MicroED is beginning to have paradigm shifting roles.
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Affiliation(s)
- Chi Nguyen
- Department of Biological Chemistry, University of California Los Angeles, 615 Charles E Young Drive South, Los Angeles, CA90095, United States
| | - Tamir Gonen
- Department of Biological Chemistry, University of California Los Angeles, 615 Charles E Young Drive South, Los Angeles, CA90095, United States; Department of Physiology, University of California Los Angeles, 615 Charles E Young Drive South, Los Angeles, CA90095, United States; Howard Hughes Medical Institute, University of California Los Angeles, Los Angeles, CA90095, United States.
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28
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Roslova M, Smeets S, Wang B, Thersleff T, Xu H, Zou X. InsteaDMatic: towards cross-platform automated continuous rotation electron diffraction. J Appl Crystallogr 2020; 53:1217-1224. [PMID: 33117109 PMCID: PMC7534539 DOI: 10.1107/s1600576720009590] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 07/14/2020] [Indexed: 11/26/2022] Open
Abstract
A DigitalMicrograph script named InsteaDMatic has been developed for automated continuous rotation electron diffraction (cRED) data acquisition. InsteaDMatic coordinates functions of the transmission electron microscope goniometer and camera in order to tune up diffraction-frame recording simultaneously with crystal rotation. Exploiting fast and automated data collection, the influence of the electron dose rate on the quality of cRED data was studied, and structural models obtained for two different parallel-beam illumination modes (aperture selection and nanoprobe) were compared. A DigitalMicrograph script, InsteaDMatic, has been developed to facilitate rapid automated 3D electron diffraction/microcrystal electron diffraction data acquisition by continuous rotation of a crystal with a constant speed, denoted as continuous rotation electron diffraction. The script coordinates microscope functions, such as stage rotation, and camera functions relevant for data collection, and stores the experiment metadata. The script is compatible with any microscope that can be controlled by DigitalMicrograph and has been tested on both JEOL and Thermo Fisher Scientific microscopes. A proof of concept has been performed through employing InsteaDMatic for data collection and structure determination of a ZSM-5 zeolite. The influence of illumination settings and electron dose rate on the quality of diffraction data, unit-cell determination and structure solution has been investigated in order to optimize the data acquisition procedure.
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Affiliation(s)
- Maria Roslova
- Department of Materials and Environmental Chemistry (MMK), Stockholm University, Svante Arrhenius väg 16C, Stockholm SE-10691, Sweden
| | - Stef Smeets
- Department of Materials and Environmental Chemistry (MMK), Stockholm University, Svante Arrhenius väg 16C, Stockholm SE-10691, Sweden
| | - Bin Wang
- Department of Materials and Environmental Chemistry (MMK), Stockholm University, Svante Arrhenius väg 16C, Stockholm SE-10691, Sweden
| | - Thomas Thersleff
- Department of Materials and Environmental Chemistry (MMK), Stockholm University, Svante Arrhenius väg 16C, Stockholm SE-10691, Sweden
| | - Hongyi Xu
- Department of Materials and Environmental Chemistry (MMK), Stockholm University, Svante Arrhenius väg 16C, Stockholm SE-10691, Sweden
| | - Xiaodong Zou
- Department of Materials and Environmental Chemistry (MMK), Stockholm University, Svante Arrhenius väg 16C, Stockholm SE-10691, Sweden
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29
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Takaba K, Maki-Yonekura S, Yonekura K. Collecting large datasets of rotational electron diffraction with ParallEM and SerialEM. J Struct Biol 2020; 211:107549. [DOI: 10.1016/j.jsb.2020.107549] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 06/03/2020] [Accepted: 06/09/2020] [Indexed: 10/24/2022]
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30
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Bücker R, Hogan-Lamarre P, Mehrabi P, Schulz EC, Bultema LA, Gevorkov Y, Brehm W, Yefanov O, Oberthür D, Kassier GH, Dwayne Miller RJ. Serial protein crystallography in an electron microscope. Nat Commun 2020; 11:996. [PMID: 32081905 PMCID: PMC7035385 DOI: 10.1038/s41467-020-14793-0] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 01/27/2020] [Indexed: 12/16/2022] Open
Abstract
Serial X-ray crystallography at free-electron lasers allows to solve biomolecular structures from sub-micron-sized crystals. However, beam time at these facilities is scarce, and involved sample delivery techniques are required. On the other hand, rotation electron diffraction (MicroED) has shown great potential as an alternative means for protein nano-crystallography. Here, we present a method for serial electron diffraction of protein nanocrystals combining the benefits of both approaches. In a scanning transmission electron microscope, crystals randomly dispersed on a sample grid are automatically mapped, and a diffraction pattern at fixed orientation is recorded from each at a high acquisition rate. Dose fractionation ensures minimal radiation damage effects. We demonstrate the method by solving the structure of granulovirus occlusion bodies and lysozyme to resolutions of 1.55 Å and 1.80 Å, respectively. Our method promises to provide rapid structure determination for many classes of materials with minimal sample consumption, using readily available instrumentation.
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Affiliation(s)
- Robert Bücker
- Max Planck Institute for the Structure and Dynamics of Matter, CFEL, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Pascal Hogan-Lamarre
- Max Planck Institute for the Structure and Dynamics of Matter, CFEL, Luruper Chaussee 149, 22761, Hamburg, Germany
- Departments of Chemistry and Physics, University of Toronto, 80 St. George Street, Toronto, ON, M5S 3H6, Canada
| | - Pedram Mehrabi
- Max Planck Institute for the Structure and Dynamics of Matter, CFEL, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Eike C Schulz
- Max Planck Institute for the Structure and Dynamics of Matter, CFEL, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Lindsey A Bultema
- Max Planck Institute for the Structure and Dynamics of Matter, CFEL, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - Yaroslav Gevorkov
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607, Hamburg, Germany
- Institute of Vision Systems, Hamburg University of Technology, Harburger Schlossstrasse 20, 21079, Hamburg, Germany
| | - Wolfgang Brehm
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Oleksandr Yefanov
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Dominik Oberthür
- Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607, Hamburg, Germany
| | - Günther H Kassier
- Max Planck Institute for the Structure and Dynamics of Matter, CFEL, Luruper Chaussee 149, 22761, Hamburg, Germany
| | - R J Dwayne Miller
- Max Planck Institute for the Structure and Dynamics of Matter, CFEL, Luruper Chaussee 149, 22761, Hamburg, Germany.
- Departments of Chemistry and Physics, University of Toronto, 80 St. George Street, Toronto, ON, M5S 3H6, Canada.
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31
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Abstract
Microcrystal electron diffraction, or MicroED, is a method that is capable of determining structure from very small and thin 3D crystals using a transmission electron microscope. MicroED has been successfully used on microcrystalline samples, including proteins, peptides, and small organic molecules, in many cases to very high resolutions. In this work, the MicroED workflow will be briefly described and areas of future method development will be highlighted. These areas include improvements in sample preparation, data collection, and structure determination.
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Affiliation(s)
- Brent L Nannenga
- Chemical Engineering, School for Engineering of Matter, Transport, and Energy, Arizona State University, Tempe, Arizona 85287, USA and Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona 85281, USA
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32
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Hattne J, Martynowycz MW, Penczek PA, Gonen T. MicroED with the Falcon III direct electron detector. IUCrJ 2019; 6:921-926. [PMID: 31576224 PMCID: PMC6760445 DOI: 10.1107/s2052252519010583] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 07/25/2019] [Indexed: 05/06/2023]
Abstract
Microcrystal electron diffraction (MicroED) combines crystallography and electron cryo-microscopy (cryo-EM) into a method that is applicable to high-resolution structure determination. In MicroED, nanosized crystals, which are often intractable using other techniques, are probed by high-energy electrons in a transmission electron microscope. Diffraction data are recorded by a camera in movie mode: the nanocrystal is continuously rotated in the beam, thus creating a sequence of frames that constitute a movie with respect to the rotation angle. Until now, diffraction-optimized cameras have mostly been used for MicroED. Here, the use of a direct electron detector that was designed for imaging is reported. It is demonstrated that data can be collected more rapidly using the Falcon III for MicroED and with markedly lower exposure than has previously been reported. The Falcon III was operated at 40 frames per second and complete data sets reaching atomic resolution were recorded in minutes. The resulting density maps to 2.1 Å resolution of the serine protease proteinase K showed no visible signs of radiation damage. It is thus demonstrated that dedicated diffraction-optimized detectors are not required for MicroED, as shown by the fact that the very same cameras that are used for imaging applications in electron microscopy, such as single-particle cryo-EM, can also be used effectively for diffraction measurements.
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Affiliation(s)
- Johan Hattne
- Howard Hughes Medical Institute, Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Michael W. Martynowycz
- Howard Hughes Medical Institute, Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Pawel A. Penczek
- Department of Biochemistry and Molecular Biology, The University of Texas McGovern Medical School, Houston, TX 77030, USA
| | - Tamir Gonen
- Howard Hughes Medical Institute, Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
- Howard Hughes Medical Institute, Department of Physiology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
- Correspondence e-mail:
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33
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Gemmi M, Mugnaioli E, Gorelik TE, Kolb U, Palatinus L, Boullay P, Hovmöller S, Abrahams JP. 3D Electron Diffraction: The Nanocrystallography Revolution. ACS Cent Sci 2019; 5:1315-1329. [PMID: 31482114 PMCID: PMC6716134 DOI: 10.1021/acscentsci.9b00394] [Citation(s) in RCA: 177] [Impact Index Per Article: 35.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Indexed: 05/20/2023]
Abstract
Crystallography of nanocrystalline materials has witnessed a true revolution in the past 10 years, thanks to the introduction of protocols for 3D acquisition and analysis of electron diffraction data. This method provides single-crystal data of structure solution and refinement quality, allowing the atomic structure determination of those materials that remained hitherto unknown because of their limited crystallinity. Several experimental protocols exist, which share the common idea of sampling a sequence of diffraction patterns while the crystal is tilted around a noncrystallographic axis, namely, the goniometer axis of the transmission electron microscope sample stage. This Outlook reviews most important 3D electron diffraction applications for different kinds of samples and problematics, related with both materials and life sciences. Structure refinement including dynamical scattering is also briefly discussed.
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Affiliation(s)
- Mauro Gemmi
- Center
for Nanotechnology Innovation@NEST, Istituto
Italiano di Tecnologia, Piazza S. Silvestro 12, 56127 Pisa, Italy
| | - Enrico Mugnaioli
- Center
for Nanotechnology Innovation@NEST, Istituto
Italiano di Tecnologia, Piazza S. Silvestro 12, 56127 Pisa, Italy
| | - Tatiana E. Gorelik
- University
of Ulm, Central Facility for Electron Microscopy, Electron Microscopy
Group of Materials Science (EMMS), Albert Einstein Allee 11, 89081 Ulm, Germany
| | - Ute Kolb
- Institut
für Anorganische Chemie und Analytische Chemie, Johannes Gutenberg-Universität, Duesbergweg 10-14, 55128 Mainz, Germany
- Institut
für Angewandte Geowissenschaften, Technische Universität Darmstadt, Schnittspahnstraße 9, 64287 Darmstadt, Germany
| | - Lukas Palatinus
- Department
of Structure Analysis, Institute of Physics
of the CAS, Na Slovance 2, 182 21 Prague 8, Czechia
| | - Philippe Boullay
- CRISMAT,
Normandie Université, ENSICAEN, UNICAEN, CNRS UMR 6508, 6 Bd Maréchal Juin, F-14050 Cedex Caen, France
| | - Sven Hovmöller
- Inorganic
and Structural Chemistry, Department of Materials and Environmental
Chemistry, Stockholm University, 106 91 Stockholm, Sweden
| | - Jan Pieter Abrahams
- Center
for Cellular Imaging and NanoAnalytics (C−CINA), Biozentrum, Basel University, Mattenstrasse 26, CH-4058 Basel, Switzerland
- Department
of Biology and Chemistry, Paul Scherrer
Institut (PSI), CH-5232 Villigen PSI, Switzerland
- Leiden
Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
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34
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Glynn C, Rodriguez JA. Data-driven challenges and opportunities in crystallography. Emerg Top Life Sci 2019; 3:423-432. [PMID: 33523208 PMCID: PMC7289006 DOI: 10.1042/etls20180177] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 06/13/2019] [Accepted: 06/24/2019] [Indexed: 11/17/2022]
Abstract
Abstract
Structural biology is in the midst of a revolution fueled by faster and more powerful instruments capable of delivering orders of magnitude more data than their predecessors. This increased pace in data gathering introduces new experimental and computational challenges, frustrating real-time processing and interpretation of data and requiring long-term solutions for data archival and retrieval. This combination of challenges and opportunities is driving the exploration of new areas of structural biology, including studies of macromolecular dynamics and the investigation of molecular ensembles in search of a better understanding of conformational landscapes. The next generation of instruments promises to yield even greater data rates, requiring a concerted effort by institutions, centers and individuals to extract meaning from every bit and make data accessible to the community at large, facilitating data mining efforts by individuals or groups as analysis tools improve.
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35
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Zhou H, Luo F, Luo Z, Li D, Liu C, Li X. Programming Conventional Electron Microscopes for Solving Ultrahigh-Resolution Structures of Small and Macro-Molecules. Anal Chem 2019; 91:10996-11003. [PMID: 31334636 DOI: 10.1021/acs.analchem.9b01162] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Microcrystal electron diffraction (MicroED) is becoming a powerful tool in determining the crystal structures of biological macromolecules and small organic compounds. However, wide applications of this technique are still limited by the special requirement for radiation-tolerated movie-mode camera and the lack of automated data collection methods. Herein, we develop a stage-camera synchronization scheme to minimize the hardware requirements and enable the use of the conventional electron cryo-microscope with a single-frame CCD camera, which ensures not only the acquisition of ultrahigh-resolution diffraction data but also low cost in practice. This method renders the structure determination of both peptide and small organic compounds at ultrahigh resolution up to ∼0.60 Å with unambiguous assignment of nearly all hydrogen atoms. The present work provides a widely applicable solution for routine structure determination of MicroED and demonstrates the capability of the low-end 120 kV microscope with a CCD camera in solving ultrahigh resolution structures of both organic compounds and biological macromolecules.
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Affiliation(s)
- Heng Zhou
- Key Laboratory of Protein Sciences ( Tsinghua University ), Ministry of Education, Beijing 100084 , China.,School of Life Sciences , Tsinghua University , Beijing 100084 , China
| | - Feng Luo
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry , Chinese Academy of Sciences , Shanghai 201210 , China.,University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Zhipu Luo
- Key Laboratory of Protein Sciences ( Tsinghua University ), Ministry of Education, Beijing 100084 , China.,School of Life Sciences , Tsinghua University , Beijing 100084 , China
| | - Dan Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education , Shanghai Jiao Tong University , Shanghai 200030 , China
| | - Cong Liu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry , Chinese Academy of Sciences , Shanghai 201210 , China.,University of Chinese Academy of Sciences , Beijing 100049 , China
| | - Xueming Li
- Key Laboratory of Protein Sciences ( Tsinghua University ), Ministry of Education, Beijing 100084 , China.,School of Life Sciences , Tsinghua University , Beijing 100084 , China
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36
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Abstract
For automated acquisition of tilt series for electron tomography, software needs to handle complications such as movements of the sample in x/y and z, increased projected thickness at high tilt, specimen drift, etc. In addition, many applications require special functionality such as low dose acquisition, automated sequential (batch) tomography, or montage tomography. After reviewing how these difficulties can be addressed and a closer look at what advanced acquisition strategies are employed in biosciences, this chapter introduces acquisition software both developed in academia as well as by hardware vendors. It covers the hardware requirements and compatibility, the functional principle and workflow implemented, as well as what advanced functions are supported by the individual programs.
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Affiliation(s)
- Guenter P Resch
- Nexperion e.U.-Solutions for Electron Microscopy, Vienna, Austria.
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37
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Nannenga BL, Gonen T. The cryo-EM method microcrystal electron diffraction (MicroED). Nat Methods 2019; 16:369-79. [PMID: 31040436 DOI: 10.1038/s41592-019-0395-x] [Citation(s) in RCA: 126] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Accepted: 03/25/2019] [Indexed: 01/07/2023]
Abstract
In 2013 we established a cryo-electron microscopy (cryo-EM) technique called microcrystal electron diffraction (MicroED). Since that time, data collection and analysis schemes have been fine-tuned, and structures for more than 40 different proteins, oligopeptides and organic molecules have been determined. Here we review the MicroED technique and place it in context with other structure-determination methods. We showcase example structures solved by MicroED and provide practical advice to prospective users.
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