1
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Rütten M, Lang L, Wagler H, Lach M, Mucke N, Laugks U, Seuring C, Keller TF, Stierle A, Ginn HM, Beck T. Assembly of Differently Sized Supercharged Protein Nanocages into Superlattices for Construction of Binary Nanoparticle-Protein Materials. ACS NANO 2024; 18:25325-25336. [PMID: 39189351 DOI: 10.1021/acsnano.4c09551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/28/2024]
Abstract
This study focuses on the design and characterization of binary nanoparticle superlattices: Two differently sized, supercharged protein nanocages are used to create a matrix for nanoparticle arrangement. We have previously established the assembly of protein nanocages of the same size. Here, we present another approach for multicomponent biohybrid material synthesis by successfully assembling two differently sized supercharged protein nanocages with different symmetries. Typically, the ordered assembly of objects with nonmatching symmetry is challenging, but our electrostatic-based approach overcomes the symmetry mismatch by exploiting electrostatic interactions between oppositely charged cages. Moreover, our study showcases the use of nanoparticles as a contrast enhancer in an elegant way to gain insights into the structural details of crystalline biohybrid materials. The assembled materials were characterized with various methods, including transmission electron microscopy (TEM) and single-crystal small-angle X-ray diffraction (SC-SAXD). We employed cryo-plasma-focused ion beam milling (cryo-PFIB) to prepare lamellae for the investigation of nanoparticle sublattices via electron cryo-tomography. Importantly, we refined superlattice structure data obtained from single-crystal SAXD experiments, providing conclusive evidence of the final assembly type. Our findings highlight the versatility of protein nanocages for creating distinctive types of binary superlattices. Because the nanoparticles do not influence the type of assembly, protein cage matrices can combine various nanoparticles in the solid state. This study not only contributes to the expanding repertoire of nanoparticle assembly methods but also demonstrates the power of advanced characterization techniques in elucidating the structural intricacies of these biohybrid materials.
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Affiliation(s)
- Michael Rütten
- Institute of Physical Chemistry, Department of Chemistry, University of Hamburg, Hamburg 20146, Germany
| | - Laurin Lang
- Institute of Physical Chemistry, Department of Chemistry, University of Hamburg, Hamburg 20146, Germany
- The Hamburg Centre for Ultrafast Imaging, University of Hamburg, Hamburg 20146, Germany
| | - Henrike Wagler
- Institute of Physical Chemistry, Department of Chemistry, University of Hamburg, Hamburg 20146, Germany
| | - Marcel Lach
- Institute of Physical Chemistry, Department of Chemistry, University of Hamburg, Hamburg 20146, Germany
| | - Niklas Mucke
- Institute of Physical Chemistry, Department of Chemistry, University of Hamburg, Hamburg 20146, Germany
| | - Ulrike Laugks
- Centre for Structureal Systems Biology (CSSB), Hamburg 22607, Germany
- Department of Structural Cell Biology of Viruses, Leibniz Institute of Virology, Hamburg 20251, Germany
- Department of Chemistry, University of Hamburg, Hamburg 20146, Germany
| | - Carolin Seuring
- The Hamburg Centre for Ultrafast Imaging, University of Hamburg, Hamburg 20146, Germany
- Centre for Structureal Systems Biology (CSSB), Hamburg 22607, Germany
- Department of Structural Cell Biology of Viruses, Leibniz Institute of Virology, Hamburg 20251, Germany
- Department of Chemistry, University of Hamburg, Hamburg 20146, Germany
| | - Thomas F Keller
- Centre for X-ray and Nano Science (CXNS), Deutsches Elektronen-Synchrotron DESY, Hamburg 22607, Germany
- Department of Physics, University of Hamburg, Hamburg 22607, Germany
| | - Andreas Stierle
- Centre for X-ray and Nano Science (CXNS), Deutsches Elektronen-Synchrotron DESY, Hamburg 22607, Germany
- Department of Physics, University of Hamburg, Hamburg 22607, Germany
| | - Helen M Ginn
- Center for Free-Electron Laser Science (CFEL), Deutsches Elektronen-Synchrotron DESY, Hamburg 22607, Germany
- Institute for Nanostructure and Solid State Physics, Department of Physics, University of Hamburg, Hamburg 22761, Germany
| | - Tobias Beck
- Institute of Physical Chemistry, Department of Chemistry, University of Hamburg, Hamburg 20146, Germany
- The Hamburg Centre for Ultrafast Imaging, University of Hamburg, Hamburg 20146, Germany
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2
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Noble AJ, de Marco A. Cryo-focused ion beam for in situ structural biology: State of the art, challenges, and perspectives. Curr Opin Struct Biol 2024; 87:102864. [PMID: 38901373 DOI: 10.1016/j.sbi.2024.102864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 05/24/2024] [Accepted: 05/26/2024] [Indexed: 06/22/2024]
Abstract
Cryogenic-focused ion beam (cryo-FIB) instruments became essential for high-resolution imaging in cryo-preserved cells and tissues. Cryo-FIBs use accelerated ions to thin samples that would otherwise be too thick for cryo-electron microscopy (cryo-EM). This allows visualizing cellular ultrastructures in near-native frozen hydrated states. This review describes the current state-of-the-art capabilities of cryo-FIB technology and its applications in structural cell and tissue biology. We discuss recent advances in instrumentation, imaging modalities, automation, sample preparation protocols, and targeting techniques. We outline remaining challenges and future directions to make cryo-FIB more precise, enable higher throughput, and be widely accessible. Further improvements in targeting, efficiency, robust sample preparation, emerging ion sources, automation, and downstream electron tomography have the potential to reveal intricate molecular architectures across length scales inside cells and tissues. Cryo-FIB is poised to become an indispensable tool for preparing native biological systems in situ for high-resolution 3D structural analysis.
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Affiliation(s)
- Alex J Noble
- Simons Electron Microscopy Center, New York Structural Biology Center, 89 Convent Avenue New York, NY, 10027, USA. https://twitter.com/alexjamesnoble
| | - Alex de Marco
- Simons Electron Microscopy Center, New York Structural Biology Center, 89 Convent Avenue New York, NY, 10027, USA.
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3
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Acehan D, Spoth KA, Budziszewski GR, Snell ME, Campomizzi CS, Lynch ML, Bowman SE. Reaching the potential of electron diffraction. CELL REPORTS. PHYSICAL SCIENCE 2024; 5:102007. [PMID: 39055735 PMCID: PMC11271257 DOI: 10.1016/j.xcrp.2024.102007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/27/2024]
Abstract
Microcrystal electron diffraction (MicroED) is an emerging structural technique in which submicron crystals are used to generate diffraction data for structural studies. Structures allow for the study of molecular-level architecture and drive hypotheses about modes of action, mechanisms, dynamics, and interactions with other molecules. Combining cryoelectron microscopy (cryo-EM) instrumentation with crystallographic techniques, MicroED has led to three-dimensional structural models of small molecules, peptides, and proteins and has generated tremendous interest due to its ability to use vanishingly small crystals. In this perspective, we describe the current state of the field for MicroED methodologies, including making and detecting crystals of the appropriate size for the technique, as well as ways to best handle and characterize these crystals. Our perspective provides insight into ways to unlock the full range of potential for MicroED to access previously intractable samples and describes areas of future development.
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Affiliation(s)
- Devrim Acehan
- Hauptman-Woodward Medical Research Institute, Buffalo, NY 14203, USA
- University at Buffalo, Jacobs School of Medicine and Biomedical Science, Department of Structural Biology, Buffalo, NY 14203, USA
- University of Rochester, School of Medicine and Dentistry, Department of Biochemistry and Biophysics, Rochester, NY 14642, USA
| | | | | | | | | | - Miranda L. Lynch
- Hauptman-Woodward Medical Research Institute, Buffalo, NY 14203, USA
- University at Buffalo, Jacobs School of Medicine and Biomedical Science, Department of Structural Biology, Buffalo, NY 14203, USA
| | - Sarah E.J. Bowman
- Hauptman-Woodward Medical Research Institute, Buffalo, NY 14203, USA
- University at Buffalo, Jacobs School of Medicine and Biomedical Science, Department of Structural Biology, Buffalo, NY 14203, USA
- University at Buffalo, Jacobs School of Medicine and Biomedical Science, Department of Biochemistry, Buffalo, NY 14203, USA
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4
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Aragon M, Bowman SEJ, Chen CH, de la Cruz MJ, Decato DA, Eng ET, Flatt KM, Gulati S, Li Y, Lomba CJ, Mercado B, Miller J, Palatinus L, Rice WJ, Waterman D, Zimanyi CM. Applying 3D ED/MicroED workflows toward the next frontiers. Acta Crystallogr C Struct Chem 2024; 80:179-189. [PMID: 38712546 PMCID: PMC11150879 DOI: 10.1107/s2053229624004078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 05/02/2024] [Indexed: 05/08/2024] Open
Abstract
We report on the latest advancements in Microcrystal Electron Diffraction (3D ED/MicroED), as discussed during a symposium at the National Center for CryoEM Access and Training housed at the New York Structural Biology Center. This snapshot describes cutting-edge developments in various facets of the field and identifies potential avenues for continued progress. Key sections discuss instrumentation access, research applications for small molecules and biomacromolecules, data collection hardware and software, data reduction software, and finally reporting and validation. 3D ED/MicroED is still early in its wide adoption by the structural science community with ample opportunities for expansion, growth, and innovation.
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Affiliation(s)
- Mahira Aragon
- Simons Electron Microscopy Center, New York Structural Biology Center, 89 Convent Ave, New York, New York 10027, USA
| | - Sarah E. J. Bowman
- Hauptman-Woodward Medical Research Institute, 700 Ellicott St, Buffalo, New York 14203, USA
| | - Chun-Hsing Chen
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27514, USA
| | - M. Jason de la Cruz
- Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, New York 10065, USA
| | - Daniel A. Decato
- Chemistry and Biochemistry, University of Montana, 32 Campus Drive, Missoula, Montana 59812, USA
| | - Edward T. Eng
- Simons Electron Microscopy Center, New York Structural Biology Center, 89 Convent Ave, New York, New York 10027, USA
| | - Kristen M. Flatt
- Materials Research Laboratory, University of Illinois at Urbana Champaign, Urbana, Illinois 61801, USA
| | | | - Yuchen Li
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
| | - Charles J. Lomba
- Department of Physics, Quantitative Biology Institute, Yale University, 260 Whitney Ave., New Haven, Connecticut 06520-8103, USA
| | - Brandon Mercado
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, USA
| | - Jessalyn Miller
- Simons Electron Microscopy Center, New York Structural Biology Center, 89 Convent Ave, New York, New York 10027, USA
| | - Lukáš Palatinus
- Institute of Physics of the CAS/NanED, Na Slovance 1999/2, Prague 192000, Czech Republic
| | - William J. Rice
- Department of Cell Biology, NYU Grossman School of Medicine, 540 First Ave, New York, New York 10016, USA
| | - David Waterman
- Research Complex at Harwell, UKRI–STFC Rutherford Appleton Laboratory, Harwell, Didcot, Oxfordshire, OX11 0FA, England, United Kingdom
| | - Christina M. Zimanyi
- Simons Electron Microscopy Center, New York Structural Biology Center, 89 Convent Ave, New York, New York 10027, USA
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5
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Gillman C, Bu G, Danelius E, Hattne J, Nannenga BL, Gonen T. Eliminating the missing cone challenge through innovative approaches. J Struct Biol X 2024; 9:100102. [PMID: 38962493 PMCID: PMC11220036 DOI: 10.1016/j.yjsbx.2024.100102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 05/28/2024] [Accepted: 05/29/2024] [Indexed: 07/05/2024] Open
Abstract
Microcrystal electron diffraction (MicroED) has emerged as a powerful technique for unraveling molecular structures from microcrystals too small for X-ray diffraction. However, a significant hurdle arises with plate-like crystals that consistently orient themselves flat on the electron microscopy grid. If the normal of the plate correlates with the axes of the crystal lattice, the crystal orientations accessible for measurement are restricted because the crystal cannot be arbitrarily rotated. This limits the information that can be acquired, resulting in a missing cone of information. We recently introduced a novel crystallization strategy called suspended drop crystallization and proposed that crystals in a suspended drop could effectively address the challenge of preferred crystal orientation. Here we demonstrate the success of the suspended drop approach in eliminating the missing cone in two samples that crystallize as thin plates: bovine liver catalase and the SARS‑CoV‑2 main protease (Mpro). This innovative solution proves indispensable for crystals exhibiting systematic preferred orientations, unlocking new possibilities for structure determination by MicroED.
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Affiliation(s)
- Cody Gillman
- Department of Biological Chemistry, University of California, Los Angeles, CA, USA
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Guanhong Bu
- Department of Biological Chemistry, University of California, Los Angeles, CA, USA
| | - Emma Danelius
- Department of Biological Chemistry, University of California, Los Angeles, CA, USA
- Howard Hughes Medical Institute, University of California, Los Angeles CA, USA
| | - Johan Hattne
- Department of Biological Chemistry, University of California, Los Angeles, CA, USA
- Howard Hughes Medical Institute, University of California, Los Angeles CA, USA
| | - Brent L. Nannenga
- Chemical Engineering, School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ, USA
- Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Tamir Gonen
- Department of Biological Chemistry, University of California, Los Angeles, CA, USA
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Howard Hughes Medical Institute, University of California, Los Angeles CA, USA
- Department of Physiology, University of California, Los Angeles, CA, USA
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6
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Bardin AA, Haymaker A, Banihashemi F, Lin JYS, Martynowycz MW, Nannenga BL. Focused ion beam milling and MicroED structure determination of metal-organic framework crystals. Ultramicroscopy 2024; 257:113905. [PMID: 38086288 PMCID: PMC10843726 DOI: 10.1016/j.ultramic.2023.113905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 11/30/2023] [Accepted: 12/04/2023] [Indexed: 01/05/2024]
Abstract
We report new advancements in the determination and high-resolution structural analysis of beam-sensitive metal organic frameworks (MOFs) using microcrystal electron diffraction (MicroED) coupled with focused ion beam milling at cryogenic temperatures (cryo-FIB). A microcrystal of the beam-sensitive MOF, ZIF-8, was ion-beam milled in a thin lamella approximately 150 nm thick. MicroED data were collected from this thin lamella using an energy filter and a direct electron detector operating in counting mode. Using this approach, we achieved a greatly improved resolution of 0.59 Å with a minimal total exposure of only 0.64 e-/A2. These innovations not only improve model statistics but also further demonstrate that ion-beam milling is compatible with beam-sensitive materials, augmenting the capabilities of electron diffraction in MOF research.
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Affiliation(s)
- Andrey A Bardin
- Chemical Engineering, School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ, United States; Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, United States
| | - Alison Haymaker
- Chemical Engineering, School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ, United States; Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, United States
| | - Fateme Banihashemi
- Chemical Engineering, School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ, United States
| | - Jerry Y S Lin
- Chemical Engineering, School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ, United States
| | - Michael W Martynowycz
- Department of Biological Chemistry, University of California, Los Angeles, CA 90095, United States.
| | - Brent L Nannenga
- Chemical Engineering, School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ, United States; Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, United States.
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7
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Gillman C, Bu G, Danelius E, Hattne J, Nannenga B, Gonen T. Eliminating the Missing Cone Challenge through Innovative Approaches. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.11.575283. [PMID: 38293160 PMCID: PMC10827066 DOI: 10.1101/2024.01.11.575283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Microcrystal electron diffraction (MicroED) has emerged as a powerful technique for unraveling molecular structures from microcrystals too small for X-ray diffraction. However, a significant hurdle arises with plate-like crystals that consistently orient themselves flat on the electron microscopy grid. If, as is typically the case, the normal of the plate correlates with the axes of the crystal lattice, the crystal orientations accessible for measurement are restricted because the grid cannot be arbitrarily rotated. This limits the information that can be acquired, resulting in a missing cone of information. We recently introduced a novel crystallization strategy called suspended drop crystallization and proposed that this method could effectively address the challenge of preferred crystal orientation. Here we demonstrate the success of the suspended drop crystallization approach in eliminating the missing cone in two samples that crystallize as thin plates: bovine liver catalase and the COVID-19 main protease (Mpro). This innovative solution proves indispensable for crystals exhibiting preferred orientations, unlocking new possibilities for structure determination by MicroED.
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8
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Haymaker A, Bardin AA, Gonen T, Martynowycz MW, Nannenga BL. Structure determination of a DNA crystal by MicroED. Structure 2023; 31:1499-1503.e2. [PMID: 37541248 PMCID: PMC10805983 DOI: 10.1016/j.str.2023.07.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 06/21/2023] [Accepted: 07/11/2023] [Indexed: 08/06/2023]
Abstract
Microcrystal electron diffraction (MicroED) is a powerful tool for determining high-resolution structures of microcrystals from a diverse array of biomolecular, chemical, and material samples. In this study, we apply MicroED to DNA crystals, which have not been previously analyzed using this technique. We utilized the d(CGCGCG)2 DNA duplex as a model sample and employed cryo-FIB milling to create thin lamella for diffraction data collection. The MicroED data collection and subsequent processing resulted in a 1.10 Å resolution structure of the d(CGCGCG)2 DNA, demonstrating the successful application of cryo-FIB milling and MicroED to the investigation of nucleic acid crystals.
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Affiliation(s)
- Alison Haymaker
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA; School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ, USA
| | - Andrey A Bardin
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA; School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ, USA
| | - Tamir Gonen
- 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; Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Michael W Martynowycz
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA.
| | - Brent L Nannenga
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA; School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ, USA.
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9
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Haymaker A, Bardin AA, Gonen T, Martynowycz MW, Nannenga BL. Structure determination of a DNA crystal by MicroED. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.25.538338. [PMID: 37163108 PMCID: PMC10168392 DOI: 10.1101/2023.04.25.538338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Microcrystal electron diffraction (MicroED) is a powerful tool for determining high-resolution structures of microcrystals from a diverse array of biomolecular, chemical, and material samples. In this study, we apply MicroED to DNA crystals, which have not been previously analyzed using this technique. We utilized the d(CGCGCG) 2 DNA duplex as a model sample and employed cryo-FIB milling to create thin lamella for diffraction data collection. The MicroED data collection and subsequent processing resulted in a 1.10 Å resolution structure of the d(CGCGCG) 2 DNA, demonstrating the successful application of cryo-FIB milling and MicroED to the investigation of nucleic acid crystals.
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10
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Martynowycz MW, Shiriaeva A, Clabbers MTB, Nicolas WJ, Weaver SJ, Hattne J, Gonen T. A robust approach for MicroED sample preparation of lipidic cubic phase embedded membrane protein crystals. Nat Commun 2023; 14:1086. [PMID: 36841804 PMCID: PMC9968316 DOI: 10.1038/s41467-023-36733-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 02/15/2023] [Indexed: 02/26/2023] Open
Abstract
Crystallizing G protein-coupled receptors (GPCRs) in lipidic cubic phase (LCP) often yields crystals suited for the cryogenic electron microscopy (cryoEM) method microcrystal electron diffraction (MicroED). However, sample preparation is challenging. Embedded crystals cannot be targeted topologically. Here, we use an integrated fluorescence light microscope (iFLM) inside of a focused ion beam and scanning electron microscope (FIB-SEM) to identify fluorescently labeled GPCR crystals. Crystals are targeted using the iFLM and LCP is milled using a plasma focused ion beam (pFIB). The optimal ion source for preparing biological lamellae is identified using standard crystals of proteinase K. Lamellae prepared using either argon or xenon produced the highest quality data and structures. MicroED data are collected from the milled lamellae and the structures are determined. This study outlines a robust approach to identify and mill membrane protein crystals for MicroED and demonstrates plasma ion-beam milling is a powerful tool for preparing biological lamellae.
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Affiliation(s)
- Michael W Martynowycz
- Howard Hughes Medical Institute, University of California, Los Angeles, CA, 90095, USA.,Department of Biological Chemistry, University of California, Los Angeles, CA, 90095, USA
| | - Anna Shiriaeva
- Howard Hughes Medical Institute, University of California, Los Angeles, CA, 90095, USA.,Department of Biological Chemistry, University of California, Los Angeles, CA, 90095, USA
| | - Max T B Clabbers
- Howard Hughes Medical Institute, University of California, Los Angeles, CA, 90095, USA.,Department of Biological Chemistry, University of California, Los Angeles, CA, 90095, USA
| | - William J Nicolas
- Howard Hughes Medical Institute, University of California, Los Angeles, CA, 90095, USA.,Department of Biological Chemistry, University of California, Los Angeles, CA, 90095, USA
| | - Sara J Weaver
- Howard Hughes Medical Institute, University of California, Los Angeles, CA, 90095, USA.,Department of Biological Chemistry, University of California, Los Angeles, CA, 90095, USA
| | - Johan Hattne
- Howard Hughes Medical Institute, University of California, Los Angeles, CA, 90095, USA.,Department of Biological Chemistry, University of California, Los Angeles, CA, 90095, USA
| | - Tamir Gonen
- Howard Hughes Medical Institute, University of California, Los Angeles, CA, 90095, USA. .,Department of Biological Chemistry, University of California, Los Angeles, CA, 90095, USA. .,Department of Physiology, University of California, Los Angeles, CA, 90095, USA.
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11
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Abstract
Electron crystallography has a storied history which rivals that of its more established X-ray-enabled counterpart. Recent advances in data collection and analysis have sparked a renaissance in the field, opening a new chapter for this venerable technique. Burgeoning interest in electron crystallography has spawned innovative methods described by various interchangeable labels (3D ED, MicroED, cRED, etc.). This Review covers concepts and findings relevant to the practicing crystallographer, with an emphasis on experiments aimed at using electron diffraction to elucidate the atomic structure of three-dimensional molecular crystals.
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Affiliation(s)
- Ambarneil Saha
- UCLA−DOE
Institute for Genomics and Proteomics, University
of California, Los Angeles, Los Angeles, California 90095, United States
- Department
of Chemistry and Biochemistry, University
of California, Los Angeles, Los
Angeles, California 90095, United States
| | - Shervin S. Nia
- UCLA−DOE
Institute for Genomics and Proteomics, University
of California, Los Angeles, Los Angeles, California 90095, United States
- Department
of Chemistry and Biochemistry, University
of California, Los Angeles, Los
Angeles, California 90095, United States
| | - José A. Rodríguez
- UCLA−DOE
Institute for Genomics and Proteomics, University
of California, Los Angeles, Los Angeles, California 90095, United States
- Department
of Chemistry and Biochemistry, University
of California, Los Angeles, Los
Angeles, California 90095, United States
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12
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Clabbers MTB, Shiriaeva A, Gonen T. MicroED: conception, practice and future opportunities. IUCRJ 2022; 9:169-179. [PMID: 35371502 PMCID: PMC8895021 DOI: 10.1107/s2052252521013063] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 12/08/2021] [Indexed: 06/14/2023]
Abstract
This article documents a keynote seminar presented at the IUCr Congress in Prague, 2021. The cryo-EM method microcrystal electron diffraction is described and put in the context of macromolecular electron crystallography from its origins in 2D crystals of membrane proteins to today's application to 3D crystals a millionth the size of that needed for X-ray crystallography. Milestones in method development and applications are described with an outlook to the future.
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Affiliation(s)
- Max T. B. Clabbers
- Department of Biological Chemistry, University of California, Los Angeles, CA 90095, USA
| | - Anna Shiriaeva
- Department of Biological Chemistry, University of California, Los Angeles, CA 90095, USA
| | - Tamir Gonen
- Department of Biological Chemistry, University of California, Los Angeles, CA 90095, USA
- Howard Hughes Medical Institute, University of California, Los Angeles, CA 90095, USA
- Department of Physiology, University of California, Los Angeles, CA 90095, USA
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13
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Synthetic Biology Advanced Natural Product Discovery. Metabolites 2021; 11:metabo11110785. [PMID: 34822443 PMCID: PMC8617713 DOI: 10.3390/metabo11110785] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 11/10/2021] [Accepted: 11/12/2021] [Indexed: 01/16/2023] Open
Abstract
A wide variety of bacteria, fungi and plants can produce bioactive secondary metabolites, which are often referred to as natural products. With the rapid development of DNA sequencing technology and bioinformatics, a large number of putative biosynthetic gene clusters have been reported. However, only a limited number of natural products have been discovered, as most biosynthetic gene clusters are not expressed or are expressed at extremely low levels under conventional laboratory conditions. With the rapid development of synthetic biology, advanced genome mining and engineering strategies have been reported and they provide new opportunities for discovery of natural products. This review discusses advances in recent years that can accelerate the design, build, test, and learn (DBTL) cycle of natural product discovery, and prospects trends and key challenges for future research directions.
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