1
|
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.
Collapse
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
| |
Collapse
|
2
|
Vlahakis N, Holton J, Sauter NK, Ercius P, Brewster AS, Rodriguez JA. 3D Nanocrystallography and the Imperfect Molecular Lattice. Annu Rev Phys Chem 2024; 75:483-508. [PMID: 38941528 DOI: 10.1146/annurev-physchem-083122-105226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2024]
Abstract
Crystallographic analysis relies on the scattering of quanta from arrays of atoms that populate a repeating lattice. While large crystals built of lattices that appear ideal are sought after by crystallographers, imperfections are the norm for molecular crystals. Additionally, advanced X-ray and electron diffraction techniques, used for crystallography, have opened the possibility of interrogating micro- and nanoscale crystals, with edges only millions or even thousands of molecules long. These crystals exist in a size regime that approximates the lower bounds for traditional models of crystal nonuniformity and imperfection. Accordingly, data generated by diffraction from both X-rays and electrons show increased complexity and are more challenging to conventionally model. New approaches in serial crystallography and spatially resolved electron diffraction mapping are changing this paradigm by better accounting for variability within and between crystals. The intersection of these methods presents an opportunity for a more comprehensive understanding of the structure and properties of nanocrystalline materials.
Collapse
Affiliation(s)
- Niko Vlahakis
- Department of Chemistry and Biochemistry; UCLA-DOE Institute for Genomics and Proteomics; and STROBE, NSF Science and Technology Center, University of California, Los Angeles, California, USA;
| | - James Holton
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA;
- Department of Biochemistry and Biophysics, University of California, San Francisco, California, USA
- Stanford Synchrotron Radiation Lightsource, Stanford Linear Accelerator Center National Accelerator Laboratory, Menlo Park, California, USA
| | - Nicholas K Sauter
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA;
| | - Peter Ercius
- National Center for Electron Microscopy, Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California, USA;
| | - Aaron S Brewster
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA;
| | - Jose A Rodriguez
- Department of Chemistry and Biochemistry; UCLA-DOE Institute for Genomics and Proteomics; and STROBE, NSF Science and Technology Center, University of California, Los Angeles, California, USA;
| |
Collapse
|
3
|
Takaba K, Maki-Yonekura S, Inoue I, Tono K, Fukuda Y, Shiratori Y, Peng Y, Morimoto J, Inoue S, Higashino T, Sando S, Hasegawa T, Yabashi M, Yonekura K. Comprehensive Application of XFEL Microcrystallography for Challenging Targets in Various Organic Compounds. J Am Chem Soc 2024; 146:5872-5882. [PMID: 38415585 DOI: 10.1021/jacs.3c11523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/29/2024]
Abstract
There is a growing demand for structure determination from small crystals, and the three-dimensional electron diffraction (3D ED) technique can be employed for this purpose. However, 3D ED has certain limitations related to the crystal thickness and data quality. We here present the application of serial X-ray crystallography (SX) with X-ray free electron lasers (XFELs) to small (a few μm or less) and thin (a few hundred nm or less) crystals of novel compounds dispersed on a substrate. For XFEL exposures, two-dimensional (2D) scanning of the substrate coupled with rotation enables highly efficient data collection. The recorded patterns can be successfully indexed using lattice parameters obtained through 3D ED. This approach is especially effective for challenging targets, including pharmaceuticals and organic materials that form preferentially oriented flat crystals in low-symmetry space groups. Some of these crystals have been difficult to solve or have yielded incomplete solutions using 3D ED. Our extensive analyses confirmed the superior quality of the SX data regardless of crystal orientations. Additionally, 2D scanning with XFEL pulses gives an overall distribution of the samples on the substrate, which can be useful for evaluating the properties of crystal grains and the quality of layered crystals. Therefore, this study demonstrates that XFEL crystallography has become a powerful tool for conducting structure studies of small crystals of organic compounds.
Collapse
Affiliation(s)
- Kiyofumi Takaba
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | | | - Ichiro Inoue
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
| | - Kensuke Tono
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan
| | - Yasuhiro Fukuda
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Yota Shiratori
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Yiying Peng
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Jumpei Morimoto
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Satoru Inoue
- Department of Applied Physics, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Toshiki Higashino
- Research Institute for Advanced Electronics and Photonics, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8565, Japan
| | - Shinsuke Sando
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Tatsuo Hasegawa
- Department of Applied Physics, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Makina Yabashi
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
- Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5198, Japan
| | - Koji Yonekura
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan
| |
Collapse
|
4
|
de la Cruz MJ, Eng ET. Scaling up cryo-EM for biology and chemistry: The journey from niche technology to mainstream method. Structure 2023; 31:1487-1498. [PMID: 37820731 PMCID: PMC10841453 DOI: 10.1016/j.str.2023.09.009] [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: 07/29/2023] [Revised: 08/31/2023] [Accepted: 09/14/2023] [Indexed: 10/13/2023]
Abstract
Cryoelectron microscopy (cryo-EM) methods have made meaningful contributions in a wide variety of scientific research fields. In structural biology, cryo-EM routinely elucidates molecular structure from isolated biological macromolecular complexes or in a cellular context by harnessing the high-resolution power of the electron in order to image samples in a frozen, hydrated environment. For structural chemistry, the cryo-EM method popularly known as microcrystal electron diffraction (MicroED) has facilitated atomic structure generation of peptides and small molecules from their three-dimensional crystal forms. As cryo-EM has grown from an emerging technology, it has undergone modernization to enable multimodal transmission electron microscopy (TEM) techniques becoming more routine, reproducible, and accessible to accelerate research across multiple disciplines. We review recent advances in modern cryo-EM and assess how they are contributing to the future of the field with an eye to the past.
Collapse
Affiliation(s)
- M Jason de la Cruz
- Structural Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
| | - Edward T Eng
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027, USA.
| |
Collapse
|
5
|
Schmidt EM, Klar PB, Krysiak Y, Svora P, Goodwin AL, Palatinus L. Quantitative three-dimensional local order analysis of nanomaterials through electron diffraction. Nat Commun 2023; 14:6512. [PMID: 37845256 PMCID: PMC10579245 DOI: 10.1038/s41467-023-41934-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 09/22/2023] [Indexed: 10/18/2023] Open
Abstract
Structure-property relationships in ordered materials have long been a core principle in materials design. However, the introduction of disorder into materials provides structural flexibility and thus access to material properties that are not attainable in conventional, ordered materials. To understand disorder-property relationships, the disorder - i.e., the local ordering principles - must be quantified. Local order can be probed experimentally by diffuse scattering. The analysis is notoriously difficult, especially if only powder samples are available. Here, we combine the advantages of three-dimensional electron diffraction - a method that allows single crystal diffraction measurements on sub-micron sized crystals - and three-dimensional difference pair distribution function analysis (3D-ΔPDF) to address this problem. In this work, we compare the 3D-ΔPDF from electron diffraction data with those obtained from neutron and x-ray experiments of yttria-stabilized zirconia (Zr0.82Y0.18O1.91) and demonstrate the reliability of the proposed approach.
Collapse
Affiliation(s)
- Ella Mara Schmidt
- Faculty of Geosciences and MAPEX Center for Materials and Processes, University of Bremen, Bremen, Germany.
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany.
- Inorganic Chemistry Laboratory, University of Oxford, Oxford, United Kingdom.
| | - Paul Benjamin Klar
- Faculty of Geosciences and MAPEX Center for Materials and Processes, University of Bremen, Bremen, Germany
- Institute of Physics of the Czech Academy of Sciences, Prague, Czechia
| | - Yaşar Krysiak
- Institute of Physics of the Czech Academy of Sciences, Prague, Czechia
- Institute of Inorganic Chemistry, Leibniz University Hannover, Hannover, Germany
| | - Petr Svora
- Institute of Physics of the Czech Academy of Sciences, Prague, Czechia
| | - Andrew L Goodwin
- Inorganic Chemistry Laboratory, University of Oxford, Oxford, United Kingdom
| | - Lukas Palatinus
- Institute of Physics of the Czech Academy of Sciences, Prague, Czechia
| |
Collapse
|
6
|
Andrusenko I, Gemmi M. 3D
electron diffraction for structure determination of small‐molecule nanocrystals: A possible breakthrough for the pharmaceutical industry. WIRES NANOMEDICINE AND NANOBIOTECHNOLOGY 2022; 14:e1810. [PMID: 35595285 PMCID: PMC9539612 DOI: 10.1002/wnan.1810] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 04/29/2022] [Accepted: 05/02/2022] [Indexed: 11/10/2022]
Affiliation(s)
- Iryna Andrusenko
- Center for Materials Interfaces, Electron Crystallography Istituto Italiano di Tecnologia Pontedera
| | - Mauro Gemmi
- Center for Materials Interfaces, Electron Crystallography Istituto Italiano di Tecnologia Pontedera
| |
Collapse
|
7
|
Gruene T, Mugnaioli E. 3D Electron Diffraction for Chemical Analysis: Instrumentation Developments and Innovative Applications. Chem Rev 2021; 121:11823-11834. [PMID: 34533919 PMCID: PMC8517952 DOI: 10.1021/acs.chemrev.1c00207] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Indexed: 01/26/2023]
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.
Collapse
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
| |
Collapse
|
8
|
Gruene T, Holstein JJ, Clever GH, Keppler B. Establishing electron diffraction in chemical crystallography. Nat Rev Chem 2021; 5:660-668. [PMID: 37118416 DOI: 10.1038/s41570-021-00302-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/07/2021] [Indexed: 02/06/2023]
Abstract
The emerging field of 3D electron diffraction (3D ED) opens new opportunities for structure determination from sub-micrometre-sized crystals. Although the foundations of this technology emerged earlier, the past decade has seen developments in cryo-electron microscopy and (X-ray) crystallography that particularly enable the widespread use of 3D ED. This Perspective describes to chemists and chemical crystallographers just how similar electron and X-ray diffraction are and discusses their complementary aspects. We wish to establish 3D ED in the broader chemistry community, such that electron crystallography becomes a common part of the analytical chemistry toolkit. With a suitable instrument at their disposal, every skilled crystallographer can quickly learn to perform structure determinations using 3D ED.
Collapse
|
9
|
Ge M, Yang T, Wang Y, Carraro F, Liang W, Doonan C, Falcaro P, Zheng H, Zou X, Huang Z. On the completeness of three-dimensional electron diffraction data for structural analysis of metal-organic frameworks. Faraday Discuss 2021; 231:66-80. [PMID: 34227643 DOI: 10.1039/d1fd00020a] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Three-dimensional electron diffraction (3DED) has been proven as an effective and accurate method for structure determination of nano-sized crystals. In the past decade, the crystal structures of various new complex metal-organic frameworks (MOFs) have been revealed by 3DED, which has been the key to understand their properties. However, due to the design of transmission electron microscopes (TEMs), one drawback of 3DED experiments is the limited tilt range of goniometers, which often leads to incomplete 3DED data, particularly when the crystal symmetry is low. This drawback can be overcome by high throughput data collection using continuous rotation electron diffraction (cRED), where data from a large number of crystals can be collected and merged. Here, we investigate the effects of improving completeness on structural analysis of MOFs. We use ZIF-EC1, a zeolitic imidazolate framework (ZIF), as an example. ZIF-EC1 crystallizes in a monoclinic system with a plate-like morphology. cRED data of ZIF-EC1 with different completeness and resolution were analyzed. The data completeness increased to 92.0% by merging ten datasets. Although the structures could be solved from individual datasets with a completeness as low as 44.5% and refined to a high precision (better than 0.04 Å), we demonstrate that a high data completeness could improve the structural model, especially on the electrostatic potential map. We further discuss the strategy adopted during data merging. We also show that ZIF-EC1 doped with cobalt can act as an efficient electrocatalyst for oxygen reduction reactions.
Collapse
Affiliation(s)
- Meng Ge
- 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.
| | - Yanzhi Wang
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Francesco Carraro
- Institute of Physical and Theoretical Chemistry, Graz University of Technology, Stremayrgasse 9, 8010 Graz, Austria
| | - Weibin Liang
- Department of Chemistry and the Centre for Advanced Nanomaterials, The University of Adelaide, Adelaide, 5005 South Australia, Australia
| | - Christian Doonan
- Department of Chemistry and the Centre for Advanced Nanomaterials, The University of Adelaide, Adelaide, 5005 South Australia, Australia
| | - Paolo Falcaro
- Institute of Physical and Theoretical Chemistry, Graz University of Technology, Stremayrgasse 9, 8010 Graz, Austria
| | - Haoquan Zheng
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Xiaodong Zou
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm SE-106 91, Sweden.
| | - Zhehao Huang
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm SE-106 91, Sweden.
| |
Collapse
|
10
|
Bücker R, Hogan-Lamarre P, Miller RJD. Serial Electron Diffraction Data Processing With diffractem and CrystFEL. Front Mol Biosci 2021; 8:624264. [PMID: 34095217 PMCID: PMC8171297 DOI: 10.3389/fmolb.2021.624264] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 04/28/2021] [Indexed: 12/03/2022] Open
Abstract
Serial electron diffraction (SerialED) is an emerging technique, which applies the snapshot data-collection mode of serial X-ray crystallography to three-dimensional electron diffraction (3D Electron Diffraction), forgoing the conventional rotation method. Similarly to serial X-ray crystallography, this approach leads to almost complete absence of radiation damage effects even for the most sensitive samples, and allows for a high level of automation. However, SerialED also necessitates new techniques of data processing, which combine existing pipelines for rotation electron diffraction and serial X-ray crystallography with some more particular solutions for challenges arising in SerialED specifically. Here, we introduce our analysis pipeline for SerialED data, and its implementation using the CrystFEL and diffractem program packages. Detailed examples are provided in extensive supplementary code.
Collapse
Affiliation(s)
- Robert Bücker
- Max Planck Institute for the Structure and Dynamics of Matter, Center for Free-Electron Laser Science, Hamburg, Germany.,Centre for Structural Systems Biology, Department of Chemistry, University of Hamburg, Hamburg, Germany
| | - Pascal Hogan-Lamarre
- Max Planck Institute for the Structure and Dynamics of Matter, Center for Free-Electron Laser Science, Hamburg, Germany.,Department of Physics, University of Toronto, Toronto, ON, Canada.,Department of Chemistry, University of Toronto, Toronto, ON, Canada
| | - R J Dwayne Miller
- Department of Physics, University of Toronto, Toronto, ON, Canada.,Department of Chemistry, University of Toronto, Toronto, ON, Canada
| |
Collapse
|
11
|
Gleason PR, Nannenga BL, Mills JH. Rapid Structural Analysis of a Synthetic Non-canonical Amino Acid by Microcrystal Electron Diffraction. Front Mol Biosci 2021; 7:609999. [PMID: 33490105 PMCID: PMC7821094 DOI: 10.3389/fmolb.2020.609999] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 12/07/2020] [Indexed: 02/03/2023] Open
Abstract
Structural characterization of small molecules is a crucial component of organic synthesis. In this work, we applied microcrystal electron diffraction (MicroED) to analyze the structure of the product of an enzymatic reaction that was intended to produce the unnatural amino acid 2,4-dihydroxyphenylalanine (24DHF). Characterization of our isolated product with nuclear magnetic resonance spectroscopy (NMR) and mass spectrometry (MS) suggested that an isomer of 24DHF had been formed. Microcrystals present in the isolated product were then used to determine its structure to 0.62 Å resolution, which confirmed its identity as 2-amino-2-(2,4-dihydroxyphenyl)propanoic acid (24DHPA). Moreover, the MicroED structural model indicated that both enantiomeric forms of 24DHPA were present in the asymmetric unit. Notably, the entire structure determination process including setup, data collection, and refinement was completed in ~1 h. The MicroED data not only bolstered previous results obtained using NMR and MS but also immediately provided information about the stereoisomers present in the product, which is difficult to achieve using NMR and MS alone. Our results therefore demonstrate that MicroED methods can provide useful structural information on timescales that are similar to many commonly used analytical methods and can be added to the existing suite of small molecule structure determination tools in future studies.
Collapse
Affiliation(s)
- Patrick R. Gleason
- School of Molecular Sciences, Arizona State University, Tempe, AZ, United States,Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, AZ, United States
| | - Brent L. Nannenga
- Chemical Engineering, School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ, United States,Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, United States,*Correspondence: Brent L. Nannenga
| | - Jeremy H. Mills
- School of Molecular Sciences, Arizona State University, Tempe, AZ, United States,Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, AZ, United States,Jeremy H. Mills
| |
Collapse
|
12
|
Huang Z, Grape ES, Li J, Inge AK, Zou X. 3D electron diffraction as an important technique for structure elucidation of metal-organic frameworks and covalent organic frameworks. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2020.213583] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
|
13
|
Richards LS, Millán C, Miao J, Martynowycz MW, Sawaya MR, Gonen T, Borges RJ, Usón I, Rodriguez JA. Fragment-based determination of a proteinase K structure from MicroED data using ARCIMBOLDO_SHREDDER. Acta Crystallogr D Struct Biol 2020; 76:703-712. [PMID: 32744252 PMCID: PMC7397493 DOI: 10.1107/s2059798320008049] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 06/16/2020] [Indexed: 12/15/2022] Open
Abstract
Structure determination of novel biological macromolecules by X-ray crystallography can be facilitated by the use of small structural fragments, some of only a few residues in length, as effective search models for molecular replacement to overcome the phase problem. Independence from the need for a complete pre-existing model with sequence similarity to the crystallized molecule is the primary appeal of ARCIMBOLDO, a suite of programs which employs this ab initio algorithm for phase determination. Here, the use of ARCIMBOLDO is investigated to overcome the phase problem with the electron cryomicroscopy (cryoEM) method known as microcrystal electron diffraction (MicroED). The results support the use of the ARCIMBOLDO_SHREDDER pipeline to provide phasing solutions for a structure of proteinase K from 1.6 Å resolution data using model fragments derived from the structures of proteins sharing a sequence identity of as low as 20%. ARCIMBOLDO_SHREDDER identified the most accurate polyalanine fragments from a set of distantly related sequence homologues. Alternatively, such templates were extracted in spherical volumes and given internal degrees of freedom to refine towards the target structure. Both modes relied on the rotation function in Phaser to identify or refine fragment models and its translation function to place them. Model completion from the placed fragments proceeded through phase combination of partial solutions and/or density modification and main-chain autotracing using SHELXE. The combined set of fragments was sufficient to arrive at a solution that resembled that determined by conventional molecular replacement using the known target structure as a search model. This approach obviates the need for a single, complete and highly accurate search model when phasing MicroED data, and permits the evaluation of large fragment libraries for this purpose.
Collapse
Affiliation(s)
- Logan S. Richards
- Department of Chemistry and Biochemistry; UCLA–DOE Institute for Genomics and Proteomics; STROBE, NSF Science and Technology Center, University of California Los Angeles (UCLA), Los Angeles, CA 90095, USA
| | - Claudia Millán
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB–CSIC), Barcelona Science Park, Helix Building, Baldiri Reixac 15, 08028 Barcelona, Spain
| | - Jennifer Miao
- Department of Chemistry and Biochemistry; UCLA–DOE Institute for Genomics and Proteomics; STROBE, NSF Science and Technology Center, University of California Los Angeles (UCLA), Los Angeles, CA 90095, USA
| | - Michael W. Martynowycz
- Howard Hughes Medical Institute, University of California Los Angeles (UCLA), Los Angeles, California, USA
- Department of Biological Chemistry, University of California Los Angeles (UCLA), Los Angeles, CA 90095, USA
| | - Michael R. Sawaya
- Howard Hughes Medical Institute, University of California Los Angeles (UCLA), Los Angeles, California, USA
- Department of Biological Chemistry, University of California Los Angeles (UCLA), Los Angeles, CA 90095, USA
| | - Tamir Gonen
- Howard Hughes Medical Institute, University of California Los Angeles (UCLA), Los Angeles, California, USA
- Department of Biological Chemistry, University of California Los Angeles (UCLA), Los Angeles, CA 90095, USA
- Department of Physiology, University of California Los Angeles (UCLA), Los Angeles, California, USA
| | - Rafael J. Borges
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB–CSIC), Barcelona Science Park, Helix Building, Baldiri Reixac 15, 08028 Barcelona, Spain
| | - Isabel Usón
- Crystallographic Methods, Institute of Molecular Biology of Barcelona (IBMB–CSIC), Barcelona Science Park, Helix Building, Baldiri Reixac 15, 08028 Barcelona, Spain
- ICREA, Institució Catalana de Recerca i Estudis Avançats, Passeig Lluís Companys 23, 08003 Barcelona, Spain
| | - Jose A. Rodriguez
- Department of Chemistry and Biochemistry; UCLA–DOE Institute for Genomics and Proteomics; STROBE, NSF Science and Technology Center, University of California Los Angeles (UCLA), Los Angeles, CA 90095, USA
| |
Collapse
|
14
|
Beale EV, Warren AJ, Trincão J, Beilsten-Edmands J, Crawshaw AD, Sutton G, Stuart D, Evans G. Scanning electron microscopy as a method for sample visualization in protein X-ray crystallography. IUCRJ 2020; 7:500-508. [PMID: 32431833 PMCID: PMC7201292 DOI: 10.1107/s2052252520003875] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 03/16/2020] [Indexed: 05/24/2023]
Abstract
Developing methods to determine high-resolution structures from micrometre- or even submicrometre-sized protein crystals has become increasingly important in recent years. This applies to both large protein complexes and membrane proteins, where protein production and the subsequent growth of large homogeneous crystals is often challenging, and to samples which yield only micro- or nanocrystals such as amyloid or viral polyhedrin proteins. The versatile macromolecular crystallography microfocus (VMXm) beamline at Diamond Light Source specializes in X-ray diffraction measurements from micro- and nanocrystals. Because of the possibility of measuring data from crystalline samples that approach the resolution limit of visible-light microscopy, the beamline design includes a scanning electron microscope (SEM) to visualize, locate and accurately centre crystals for X-ray diffraction experiments. To ensure that scanning electron microscopy is an appropriate method for sample visualization, tests were carried out to assess the effect of SEM radiation on diffraction quality. Cytoplasmic polyhedrosis virus polyhedrin protein crystals cryocooled on electron-microscopy grids were exposed to SEM radiation before X-ray diffraction data were collected. After processing the data with DIALS, no statistically significant difference in data quality was found between datasets collected from crystals exposed and not exposed to SEM radiation. This study supports the use of an SEM as a tool for the visualization of protein crystals and as an integrated visualization tool on the VMXm beamline.
Collapse
Affiliation(s)
- Emma V. Beale
- Life Science, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Anna J. Warren
- Life Science, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - José Trincão
- Life Science, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - James Beilsten-Edmands
- Life Science, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Adam D. Crawshaw
- Life Science, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Geoff Sutton
- Division of Structural Biology, University of Oxford, Wellcome Centre for Human Genetics, Oxford, Oxfordshire OX3 7BN, UK
| | - David Stuart
- Life Science, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
- Division of Structural Biology, University of Oxford, Wellcome Centre for Human Genetics, Oxford, Oxfordshire OX3 7BN, UK
| | - Gwyndaf Evans
- Life Science, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| |
Collapse
|
15
|
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: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [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.
Collapse
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.
| |
Collapse
|
16
|
Liebschner D, Afonine PV, Moriarty NW, Adams PD. What are the current limits on determination of protonation state using neutron macromolecular crystallography? Methods Enzymol 2020; 634:225-255. [PMID: 32093835 PMCID: PMC7571246 DOI: 10.1016/bs.mie.2020.01.008] [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] [Indexed: 03/30/2024]
Abstract
The rate of deposition of models determined by neutron diffraction, or a hybrid approach that combines X-ray and neutron diffraction, has increased in recent years. The benefit of neutron diffraction is that hydrogen atom (H) positions are detectable, allowing for the determination of protonation state and water molecule orientation. This study analyses all neutron models deposited in the Protein Data Bank to date, focusing on protonation state and properties of H (or deuterium, D) atoms as well as the details of water molecules. In particular, clashes and hydrogen bonds involving H or D atoms are investigated. As water molecules are typically the least reproducible part of a structural model, their positions in neutron models were compared to those in homologous high-resolution X-ray structures. For models determined by joint refinement against X-ray and neutron data, the water structure comparison was also carried out for models re-refined against the X-ray data alone. The homologues have generally fewer conserved water molecules where X-ray only was used and the positions of equivalent waters vary more than in the case of the hybrid X-ray model. As neutron diffraction data are generally less complete than X-ray data, the influence of neutron data completeness on nuclear density maps was also analyzed. We observe and discuss systematic map quality deterioration as result of data incompleteness.
Collapse
Affiliation(s)
- Dorothee Liebschner
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA, United States.
| | - Pavel V Afonine
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA, United States
| | - Nigel W Moriarty
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA, United States
| | - Paul D Adams
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA, United States; Department of Bioengineering, University of California Berkeley, Berkeley, CA, United States
| |
Collapse
|
17
|
Nannenga BL. MicroED methodology and development. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2020; 7:014304. [PMID: 32071929 PMCID: PMC7018523 DOI: 10.1063/1.5128226] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 01/24/2020] [Indexed: 06/10/2023]
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.
Collapse
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
| |
Collapse
|
18
|
Förster A, Schulze-Briese C. A shared vision for macromolecular crystallography over the next five years. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2019; 6:064302. [PMID: 31832486 PMCID: PMC6892709 DOI: 10.1063/1.5131017] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 11/19/2019] [Indexed: 05/12/2023]
Abstract
Macromolecular crystallography (MX) is the dominant means of determining the three-dimensional structures of biological macromolecules, but the method has reached a critical juncture. New diffraction-limited storage rings and upgrades to the existing sources will provide beamlines with higher flux and brilliance, and even the largest detectors can collect at rates of several hundred hertz. Electron cryomicroscopy is successfully competing for structural biologists' most exciting projects. As a result, formerly scarce beam time is becoming increasingly abundant, and beamlines must innovate to attract users and ensure continued funding. Here, we will show how data collection has changed over the preceding five years and how alternative methods have emerged. We then explore how MX at synchrotrons might develop over the next five years. We predict that, despite the continued dominance of rotation crystallography, applications previously considered niche or experimental, such as serial crystallography, pink-beam crystallography, and crystallography at energies above 25 keV and below 5 keV, will rise in prominence as beamlines specialize to offer users the best value. Most of these emerging methods will require new hardware and software. With these advances, MX will more efficiently provide the high-resolution structures needed for drug development. MX will also be able to address a broader range of questions than before and contribute to a deeper understanding of biological processes in the context of integrative structural biology.
Collapse
|