1
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Moriscot C, Schoehn G, Housset D. High pressure freezing and cryo-sectioning can be used for protein structure determination by electron diffraction. Ultramicroscopy 2023; 254:113834. [PMID: 37666105 DOI: 10.1016/j.ultramic.2023.113834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 07/17/2023] [Accepted: 08/17/2023] [Indexed: 09/06/2023]
Abstract
Electron diffraction of three-dimensional nanometer sized crystals has emerged since 2013 as an efficient technique to solve the structure of both small organic molecules and model proteins. However, the major bottleneck of the technique when applied to protein samples is to produce nano-crystals that do not exceed 200 to 300 nm in at least one dimension and to deposit them on a grid while keeping the minimum amount of solvent around them. Since the presence of amorphous solvent around the crystal, necessary to preserve its integrity, increases the amount of diffuse scattering, thus degrading the signal-to noise ratio of the diffraction signal, other sample preparation strategies have been developed. One of them is the milling of thin crystal lamella using focused ion beam (FIB), which was successfully applied to several protein crystals. Here, we present a new approach that uses cryo-sectioning after high pressure freezing of dextran embedded protein crystals. 150 to 200 nm thick cryo-sections of hen egg white lysozyme tetragonal crystals where used for electron diffraction experiments. Complete diffraction data up to 2.9 Å resolution have been collected and the lysozyme structure has been solved by molecular replacement and refined against these data. Our data demonstrate that cryo-sectioning can preserve protein structure at high resolution and can be used as a new sample preparation technique for 3D electron diffraction experiments of protein crystals. The different orientations found in the crystal chips and their large number resulting from the cryo-sectioning make the latter an attractive approach as it combines advantages from both blotting approaches (number of crystals) and FIB-milling (controlled thickness and absence of solvent around the crystal).
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Affiliation(s)
| | - Guy Schoehn
- Univ. Grenoble Alpes, CNRS, CEA, IBS, F-38000 Grenoble, France
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2
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Prabhakaran A, Dhanabalan B, Andrusenko I, Pianetti A, Lauciello S, Prato M, Marras S, Solokha P, Gemmi M, Brovelli S, Manna L, Arciniegas MP. Stable Sn-Based Hybrid Perovskite-Related Structures with Tunable Color Coordinates via Organic Cations in Low-Temperature Synthesis. ACS ENERGY LETTERS 2023; 8:2630-2640. [PMID: 37324542 PMCID: PMC10262684 DOI: 10.1021/acsenergylett.3c00791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Accepted: 05/11/2023] [Indexed: 06/17/2023]
Abstract
Organic-inorganic Pb-free layered perovskites are efficient broadband emitters and thus are promising materials for lighting applications. However, their synthetic protocols require a controlled atmosphere, high temperature, and long preparation time. This hinders the potential tunability of their emission through organic cations, as is instead common practice in Pb-based structures. Here, we present a set of Sn-Br layered perovskite-related structures that display different chromaticity coordinates and photoluminescence quantum yield (PLQY) up to 80%, depending on the choice of the organic monocation. We first develop a synthetic protocol that is performed under air and at 4 °C, requiring only a few steps. X-ray and 3D electron diffraction analyses show that the structures exhibit diverse octahedra connectivity (disconnected and face-sharing) and thus optical properties, while preserving the organic-inorganic layer intercalation. These results provide key insight into a previously underexplored strategy to tune the color coordinates of Pb-free layered perovskites through organic cations with complex molecular configurations.
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Affiliation(s)
- Aarya Prabhakaran
- Center
for Convergent Technologies, Istituto Italiano
di Tecnologia, Via Morego 30, 16163 Genova, Italy
- Dipartimento
di Chimica e Chimica Industriale, Università
degli Studi di Genova, Via Dodecaneso, 31, 16146 Genova, Italy
| | - Balaji Dhanabalan
- Center
for Convergent Technologies, Istituto Italiano
di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | - Iryna Andrusenko
- Electron
Crystallography, Center for Materials Interfaces, Istituto Italiano di Tecnologia, Viale Rinaldo Piaggio 34, 56025 Pontedera, Italy
| | - Andrea Pianetti
- Dipartimento
di Scienza dei Materiali, Università
degli Studi di Milano-Bicocca, via R. Cozzi 55, 20125 Milano, Italy
| | - Simone Lauciello
- Center
for Convergent Technologies, Istituto Italiano
di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | - Mirko Prato
- Center
for Convergent Technologies, Istituto Italiano
di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | - Sergio Marras
- Center
for Convergent Technologies, Istituto Italiano
di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | - Pavlo Solokha
- Dipartimento
di Chimica e Chimica Industriale, Università
degli Studi di Genova, Via Dodecaneso, 31, 16146 Genova, Italy
| | - Mauro Gemmi
- Electron
Crystallography, Center for Materials Interfaces, Istituto Italiano di Tecnologia, Viale Rinaldo Piaggio 34, 56025 Pontedera, Italy
| | - Sergio Brovelli
- Dipartimento
di Scienza dei Materiali, Università
degli Studi di Milano-Bicocca, via R. Cozzi 55, 20125 Milano, Italy
| | - Liberato Manna
- Center
for Convergent Technologies, Istituto Italiano
di Tecnologia, Via Morego 30, 16163 Genova, Italy
| | - Milena P. Arciniegas
- Center
for Convergent Technologies, Istituto Italiano
di Tecnologia, Via Morego 30, 16163 Genova, Italy
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3
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Simoncic P, Romeijn E, Hovestreydt E, Steinfeld G, Santiso-Quiñones G, Merkelbach J. Electron crystallography and dedicated electron-diffraction instrumentation. Acta Crystallogr E Crystallogr Commun 2023; 79:410-422. [PMID: 37151820 PMCID: PMC10162091 DOI: 10.1107/s2056989023003109] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 04/04/2023] [Indexed: 05/09/2023]
Abstract
Electron diffraction (known also as ED, 3D ED or microED) is gaining momentum in science and industry. The application of electron diffraction in performing nano-crystallography on crystals smaller than 1 µm is a disruptive technology that is opening up fascinating new perspectives for a wide variety of compounds required in the fields of chemical, pharmaceutical and advanced materials research. Electron diffraction enables the characterization of solid compounds complementary to neutron, powder X-ray and single-crystal X-ray diffraction, as it has the unique capability to measure nanometre-sized crystals. The recent introduction of dedicated instrumentation to perform ED experiments is a key aspect of the continued growth and success of this technology. In addition to the ultra-high-speed hybrid-pixel detectors enabling ED data collection in continuous rotation mode, a high-precision goniometer and horizontal layout have been determined as essential features of an electron diffractometer, both of which are embodied in the Eldico ED-1. Four examples of data collected on an Eldico ED-1 are showcased to demonstrate the potential and advantages of a dedicated electron diffractometer, covering selected applications and challenges of electron diffraction: (i) multiple reciprocal lattices, (ii) absolute structure of a chiral compound, and (iii) R-values achieved by kinematic refinement comparable to X-ray data.
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Affiliation(s)
- Petra Simoncic
- Eldico Scientific AG, PARK INNOVAARE: delivery LAB, Villigen, Aargau5234, Switzerland
- Correspondence e-mail:
| | - Eva Romeijn
- Eldico Scientific AG, PARK INNOVAARE: delivery LAB, Villigen, Aargau5234, Switzerland
| | - Eric Hovestreydt
- Eldico Scientific AG, PARK INNOVAARE: delivery LAB, Villigen, Aargau5234, Switzerland
| | - Gunther Steinfeld
- Eldico Scientific AG, PARK INNOVAARE: delivery LAB, Villigen, Aargau5234, Switzerland
| | | | - Johannes Merkelbach
- Eldico Scientific AG, PARK INNOVAARE: delivery LAB, Villigen, Aargau5234, Switzerland
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4
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Romagnoli L, D’Annibale A, Blundo E, Patra A, Polimeni A, Meggiolaro D, Andrusenko I, Marchetti D, Gemmi M, Latini A. 4,4'-(Anthracene-9,10-diylbis(ethyne-2,1-diyl))bis(1-methyl-1-pyridinium) Lead Iodide C 30H 22N 2Pb 2I 6: A Highly Luminescent, Chemically and Thermally Stable One-Dimensional Hybrid Iodoplumbate. CHEMISTRY OF MATERIALS : A PUBLICATION OF THE AMERICAN CHEMICAL SOCIETY 2023; 35:1818-1826. [PMID: 36873626 PMCID: PMC9979375 DOI: 10.1021/acs.chemmater.2c03798] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 02/02/2023] [Indexed: 06/17/2023]
Abstract
A new one-dimensional hybrid iodoplumbate, namely, 4,4'-(anthracene-9,10-diylbis(ethyne-2,1-diyl))bis(1-methyl-1-pyridinium) lead iodide C30H22N2Pb2I6 (AEPyPbI), is reported here for the first time with its complete characterization. The material exhibits remarkable thermal stability (up to 300 °C), and it is unreactive under ambient conditions toward water and atmospheric oxygen, due to the quaternary nature of the nitrogen atoms present in the organic cation. The cation exhibits strong visible fluorescence under ultraviolet (UV) irradiation, and when its iodide is combined with PbI2, it forms AEPyPb2I6, an efficient light-emitting material, with a photoluminescence emission intensity comparable to that of high-quality InP epilayers. The structure determination was obtained using three-dimensional electron diffraction, and the material was extensively studied by using a wide range of techniques, such as X-ray powder diffraction, diffuse reflectance UV-visible spectroscopy, thermogravimetry-differential thermal analysis, elemental analysis, Raman and infrared spectroscopies, and photoluminescence spectroscopy. The emissive properties of the material were correlated with its electronic structure by using state-of-the-art theoretical calculations. The complex, highly conjugated electronic structure of the cation interacts strongly with that of the Pb-I network, giving rise to the peculiar optoelectronic properties of AEPyPb2I6. The material, considering its relatively easy synthesis and stability, shows promise for light-emitting and photovoltaic devices. The use of highly conjugated quaternary ammonium cations may be useful for the development of new hybrid iodoplumbates and perovskites with optoelectronic properties tailored for specific applications.
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Affiliation(s)
- Lorenza Romagnoli
- Dipartimento
di Chimica, Sapienza Università di
Roma, Piazzale Aldo Moro 5, Roma 00185, Italy
| | - Andrea D’Annibale
- Dipartimento
di Chimica, Sapienza Università di
Roma, Piazzale Aldo Moro 5, Roma 00185, Italy
| | - Elena Blundo
- Dipartimento
di Fisica, Sapienza Università di
Roma, Piazzale Aldo Moro 5, Roma 00185, Italy
| | - Atanu Patra
- Dipartimento
di Fisica, Sapienza Università di
Roma, Piazzale Aldo Moro 5, Roma 00185, Italy
| | - Antonio Polimeni
- Dipartimento
di Fisica, Sapienza Università di
Roma, Piazzale Aldo Moro 5, Roma 00185, Italy
| | - Daniele Meggiolaro
- Computational
Laboratory for Hybrid/Organic Photovoltaics (CLHYO), Istituto CNR di Scienze e Tecnologie Chimiche “Giulio Natta”
(CNR-SCITEC), Via Elce di Sotto 8, Perugia 06123, Italy
| | - Iryna Andrusenko
- Electron
Crystallography, Center for Materials Interfaces, Istituto Italiano di Tecnologia, Viale Rinaldo Piaggio 34, Pontedera 56025, Italy
| | - Danilo Marchetti
- Electron
Crystallography, Center for Materials Interfaces, Istituto Italiano di Tecnologia, Viale Rinaldo Piaggio 34, Pontedera 56025, Italy
- Department
of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 17/A, Parma (PR) 43124, Italy
| | - Mauro Gemmi
- Electron
Crystallography, Center for Materials Interfaces, Istituto Italiano di Tecnologia, Viale Rinaldo Piaggio 34, Pontedera 56025, Italy
| | - Alessandro Latini
- Dipartimento
di Chimica, Sapienza Università di
Roma, Piazzale Aldo Moro 5, Roma 00185, Italy
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5
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Andrusenko I, Hall CL, Mugnaioli E, Potticary J, Hall SR, Schmidt W, Gao S, Zhao K, Marom N, Gemmi M. True molecular conformation and structure determination by three-dimensional electron diffraction of PAH by-products potentially useful for electronic applications. IUCRJ 2023; 10:131-142. [PMID: 36598508 PMCID: PMC9812223 DOI: 10.1107/s205225252201154x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 11/30/2022] [Indexed: 06/17/2023]
Abstract
The true molecular conformation and the crystal structure of benzo[e]dinaphtho[2,3-a;1',2',3',4'-ghi]fluoranthene, 7,14-diphenylnaphtho[1,2,3,4-cde]bisanthene and 7,16-diphenylnaphtho[1,2,3,4-cde]helianthrene were determined ab initio by 3D electron diffraction. All three molecules are remarkable polycyclic aromatic hydrocarbons. The molecular conformation of two of these compounds could not be determined via classical spectroscopic methods due to the large size of the molecule and the occurrence of multiple and reciprocally connected aromatic rings. The molecular structure of the third molecule was previously considered provisional. These compounds were isolated as by-products in the synthesis of similar products and were at the same time nanocrystalline and available only in very limited amounts. 3D electron diffraction data, taken from submicrometric single crystals, allowed for direct ab initio structure solution and the unbiased determination of the internal molecular conformation. Detailed synthetic routes and spectroscopic analyses are also discussed. Based on many-body perturbation theory simulations, benzo[e]dinaphtho[2,3-a;1',2',3',4'-ghi]fluoranthene may be a promising candidate for triplet-triplet annihilation and 7,14-diphenylnaphtho[1,2,3,4-cde]bisanthene may be a promising candidate for intermolecular singlet fission in the solid state.
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Affiliation(s)
- Iryna Andrusenko
- Center for Material Interfaces, Electron Crystallography, Instituto Italiano di Tecnologia, Pontedera 56025, Italy
| | - Charlie L. Hall
- School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
| | - Enrico Mugnaioli
- Center for Material Interfaces, Electron Crystallography, Instituto Italiano di Tecnologia, Pontedera 56025, Italy
- Department of Earth Sciences, University of Pisa, Pisa 56126, Italy
| | - Jason Potticary
- School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
| | - Simon R. Hall
- School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
| | | | - Siyu Gao
- Department of Materials Science and Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | - Kaiji Zhao
- Department of Materials Science and Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | - Noa Marom
- Department of Materials Science and Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | - Mauro Gemmi
- Center for Material Interfaces, Electron Crystallography, Instituto Italiano di Tecnologia, Pontedera 56025, Italy
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6
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Yang T, Xu H, Zou X. Improving data quality for three-dimensional electron diffraction by a post-column energy filter and a new crystal tracking method. J Appl Crystallogr 2022; 55:1583-1591. [PMID: 36570655 PMCID: PMC9721325 DOI: 10.1107/s1600576722009633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 09/30/2022] [Indexed: 11/30/2022] Open
Abstract
Three-dimensional electron diffraction (3D ED) has become an effective technique to determine the structures of submicrometre- (nanometre-)sized crystals. In this work, energy-filtered 3D ED was implemented using a post-column energy filter in both STEM mode and TEM mode [(S)TEM denoting (scanning) transmission electron microscope]. The setups for performing energy-filtered 3D ED on a Gatan imaging filter are described. The technique and protocol improve the accessibility of energy-filtered 3D ED post-column energy filters, which are available in many TEM laboratories. In addition, a crystal tracking method in STEM mode using high-angle annular dark-field imaging is proposed. This method enables the user to monitor the crystal position while collecting 3D ED data at the same time, allowing a larger tilt range without foregoing any diffraction frames or imposing extra electron dose. In order to compare the differences between energy-filtered and unfiltered 3D ED data sets, three well known crystallized inorganic samples have been studied in detail. For these samples, the final R 1 values improved by 10-30% for the energy-filtered data sets compared with the unfiltered data sets, and the structures became more chemically reasonable. Possible reasons for improvement are also discussed.
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Affiliation(s)
- Taimin Yang
- Department of Materials and Environmental Chemistry (MMK), Stockholm University, Svante Arrhenius väg 16 C, Stockholm, SE-10691, Sweden,Correspondence e-mail: ,
| | - Hongyi Xu
- Department of Materials and Environmental Chemistry (MMK), Stockholm University, Svante Arrhenius väg 16 C, Stockholm, SE-10691, Sweden,Correspondence e-mail: ,
| | - Xiaodong Zou
- Department of Materials and Environmental Chemistry (MMK), Stockholm University, Svante Arrhenius väg 16 C, Stockholm, SE-10691, Sweden
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7
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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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8
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Chua EYD, Mendez JH, Rapp M, Ilca SL, Tan YZ, Maruthi K, Kuang H, Zimanyi CM, Cheng A, Eng ET, Noble AJ, Potter CS, Carragher B. Better, Faster, Cheaper: Recent Advances in Cryo-Electron Microscopy. Annu Rev Biochem 2022; 91:1-32. [PMID: 35320683 PMCID: PMC10393189 DOI: 10.1146/annurev-biochem-032620-110705] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Cryo-electron microscopy (cryo-EM) continues its remarkable growth as a method for visualizing biological objects, which has been driven by advances across the entire pipeline. Developments in both single-particle analysis and in situ tomography have enabled more structures to be imaged and determined to better resolutions, at faster speeds, and with more scientists having improved access. This review highlights recent advances at each stageof the cryo-EM pipeline and provides examples of how these techniques have been used to investigate real-world problems, including antibody development against the SARS-CoV-2 spike during the recent COVID-19 pandemic.
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Affiliation(s)
- Eugene Y D Chua
- New York Structural Biology Center, New York, NY, USA; , , , , , , , , , , ,
- Simons Electron Microscopy Center, New York, NY, USA
- National Center for CryoEM Access and Training, New York, NY, USA
| | - Joshua H Mendez
- New York Structural Biology Center, New York, NY, USA; , , , , , , , , , , ,
- Simons Electron Microscopy Center, New York, NY, USA
- National Center for CryoEM Access and Training, New York, NY, USA
| | - Micah Rapp
- New York Structural Biology Center, New York, NY, USA; , , , , , , , , , , ,
- Simons Electron Microscopy Center, New York, NY, USA
| | - Serban L Ilca
- New York Structural Biology Center, New York, NY, USA; , , , , , , , , , , ,
- Simons Electron Microscopy Center, New York, NY, USA
| | - Yong Zi Tan
- Department of Biological Sciences, National University of Singapore, Singapore;
- Disease Intervention Technology Laboratory, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Kashyap Maruthi
- New York Structural Biology Center, New York, NY, USA; , , , , , , , , , , ,
- Simons Electron Microscopy Center, New York, NY, USA
- National Resource for Automated Molecular Microscopy, New York, NY, USA
| | - Huihui Kuang
- New York Structural Biology Center, New York, NY, USA; , , , , , , , , , , ,
- Simons Electron Microscopy Center, New York, NY, USA
- National Resource for Automated Molecular Microscopy, New York, NY, USA
| | - Christina M Zimanyi
- New York Structural Biology Center, New York, NY, USA; , , , , , , , , , , ,
- Simons Electron Microscopy Center, New York, NY, USA
- National Center for CryoEM Access and Training, New York, NY, USA
| | - Anchi Cheng
- New York Structural Biology Center, New York, NY, USA; , , , , , , , , , , ,
- Simons Electron Microscopy Center, New York, NY, USA
- National Resource for Automated Molecular Microscopy, New York, NY, USA
| | - Edward T Eng
- New York Structural Biology Center, New York, NY, USA; , , , , , , , , , , ,
- Simons Electron Microscopy Center, New York, NY, USA
- National Center for CryoEM Access and Training, New York, NY, USA
| | - Alex J Noble
- New York Structural Biology Center, New York, NY, USA; , , , , , , , , , , ,
- Simons Electron Microscopy Center, New York, NY, USA
- National Resource for Automated Molecular Microscopy, New York, NY, USA
- National Center for In-Situ Tomographic Ultramicroscopy, New York, NY, USA
- Simons Machine Learning Center, New York, NY, USA
| | - Clinton S Potter
- New York Structural Biology Center, New York, NY, USA; , , , , , , , , , , ,
- Simons Electron Microscopy Center, New York, NY, USA
- National Center for CryoEM Access and Training, New York, NY, USA
- National Resource for Automated Molecular Microscopy, New York, NY, USA
- National Center for In-Situ Tomographic Ultramicroscopy, New York, NY, USA
- Simons Machine Learning Center, New York, NY, USA
| | - Bridget Carragher
- New York Structural Biology Center, New York, NY, USA; , , , , , , , , , , ,
- Simons Electron Microscopy Center, New York, NY, USA
- National Center for CryoEM Access and Training, New York, NY, USA
- National Resource for Automated Molecular Microscopy, New York, NY, USA
- National Center for In-Situ Tomographic Ultramicroscopy, New York, NY, USA
- Simons Machine Learning Center, New York, NY, USA
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9
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Bengtsson VEG, Pacoste L, de la Rosa-Trevin JM, Hofer G, Zou X, Xu H. Scipion-ED: a graphical user interface for batch processing and analysis of 3D ED/MicroED data. J Appl Crystallogr 2022; 55:638-646. [PMID: 35719296 PMCID: PMC9172039 DOI: 10.1107/s1600576722002758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 03/10/2022] [Indexed: 12/03/2022] Open
Abstract
The design and usage of Scipion-ED, a graphical user interface program for processing and analysis of three-dimensional electron diffraction (3D ED)/microcrystal electron diffraction (MicroED) data, are presented. A study of the influence of data merging strategies on the ability to resolve unmodelled features of tetragonal lysozyme is included as an illustration of the advantages of Scipion-ED. Three-dimensional electron diffraction (3D ED)/microcrystal electron diffraction (MicroED) techniques are gaining in popularity. However, the data processing often does not fit existing graphical user interface software, instead requiring the use of the terminal or scripting. Scipion-ED, described in this article, provides a graphical user interface and extendable framework for processing of 3D ED/MicroED data. An illustrative project is described, in which multiple 3D ED/MicroED data sets collected on tetragonal lysozyme were processed with DIALS through the Scipion-ED interface. The ability to resolve unmodelled features in the electrostatic potential map was compared between three strategies for merging data sets.
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10
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Two New Organic Co-Crystals Based on Acetamidophenol Molecules. Symmetry (Basel) 2022. [DOI: 10.3390/sym14030431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Herein we present two new organic co-crystals obtained through a simple solution growth process based on an acetamidophenol molecule, either paracetamol or metacetamol, and on 7,7,8,8-tetracyanoquinodimethane (TCNQ). These co-crystals are part of a family of potential organic charge transfer complexes, where the acetamidophenol molecule behaves as an electron donor and TCNQ behaves as an electron acceptor. Due to the sub-micron size of the crystalline domains, 3D electron diffraction was employed for the structure characterization of both systems. Paracetamol-TCNQ structure was solved by standard direct methods, while the analysis of metacetamol-TCNQ was complicated by the low resolution of the available diffraction data and by the low symmetry of the system. The structure determination of metacetamol-TCNQ was eventually achieved after merging two data sets and combining direct methods with simulated annealing. Our study reveals that both paracetamol-TCNQ and metacetamol-TCNQ systems crystallize in a 1:1 stoichiometry, assembling in a mixed-stack configuration and adopting a non-centrosymmetric P1 symmetry. It appears that paracetamol and metacetamol do not form a strong structural scaffold based on hydrogen bonding, as previously observed for orthocetamol-TCNQ and orthocetamol-TCNB (1,2,4,5-tetracyanobenzene) co-crystals.
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11
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Microcrystal electron diffraction in macromolecular and pharmaceutical structure determination. DRUG DISCOVERY TODAY. TECHNOLOGIES 2021; 37:93-105. [PMID: 34895659 DOI: 10.1016/j.ddtec.2020.12.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 12/08/2020] [Accepted: 12/11/2020] [Indexed: 02/05/2023]
Abstract
Microcrystal electron diffraction (MicroED) has recently shown to be a promising technique for structure determination in structural biology and pharmaceutical chemistry. Here, we discuss the unique properties of electrons and motivate its use for diffraction experiments. We review the latest developments in MicroED, and illustrate its applications in macromolecular crystallography, fragment screening and structure guided drug discovery. We discuss the perspectives of MicroED in synthetic chemistry and pharmaceutical development. We anticipate that the rapid advances MicroED showcased here will promote further development of electron crystallography and open up new opportunities for drug discovery.
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12
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A Comparison of Structure Determination of Small Organic Molecules by 3D Electron Diffraction at Cryogenic and Room Temperature. Symmetry (Basel) 2021. [DOI: 10.3390/sym13112131] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
3D electron diffraction (3D ED), also known as micro-crystal electron diffraction (MicroED), is a rapid, accurate, and robust method for structure determination of submicron-sized crystals. 3D ED has mainly been applied in material science until 2013, when MicroED was developed for studying macromolecular crystals. MicroED was considered as a cryo-electron microscopy method, as MicroED data collection is usually carried out in cryogenic conditions. As a result, some researchers may consider that 3D ED/MicroED data collection on crystals of small organic molecules can only be performed in cryogenic conditions. In this work, we determined the structure for sucrose and azobenzene tetracarboxylic acid (H4ABTC). The structure of H4ABTC is the first crystal structure ever reported for this molecule. We compared data quality and structure accuracy among datasets collected under cryogenic conditions and room temperature. With the improvement in data quality by data merging, it is possible to reveal hydrogen atom positions in small organic molecule structures under both temperature conditions. The experimental results showed that, if the sample is stable in the vacuum environment of a transmission electron microscope (TEM), the data quality of datasets collected under room temperature is at least as good as data collected under cryogenic conditions according to various indicators (resolution, I/σ(I), CC1/2 (%), R1, Rint, ADRA).
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13
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Martino E, Chiarugi S, Margheriti F, Garau G. Mapping, Structure and Modulation of PPI. Front Chem 2021; 9:718405. [PMID: 34692637 PMCID: PMC8529325 DOI: 10.3389/fchem.2021.718405] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 09/21/2021] [Indexed: 11/13/2022] Open
Abstract
Because of the key relevance of protein–protein interactions (PPI) in diseases, the modulation of protein-protein complexes is of relevant clinical significance. The successful design of binding compounds modulating PPI requires a detailed knowledge of the involved protein-protein system at molecular level, and investigation of the structural motifs that drive the association of the proteins at the recognition interface. These elements represent hot spots of the protein binding free energy, define the complex lifetime and possible modulation strategies. Here, we review the advanced technologies used to map the PPI involved in human diseases, to investigate the structure-function features of protein complexes, and to discover effective ligands that modulate the PPI for therapeutic intervention.
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Affiliation(s)
- Elisa Martino
- Laboratorio NEST, Scuola Normale Superiore, Pisa, Italy
| | - Sara Chiarugi
- Laboratorio NEST, Scuola Normale Superiore, Pisa, Italy.,BioStructures Lab, Istituto Italiano di Tecnologia (IIT@NEST), Pisa, Italy
| | | | - Gianpiero Garau
- BioStructures Lab, Istituto Italiano di Tecnologia (IIT@NEST), Pisa, Italy
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14
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Andrusenko I, Hamilton V, Lanza AE, Hall CL, Mugnaioli E, Potticary J, Buanz A, Gaisford S, Piras AM, Zambito Y, Hall SR, Gemmi M. Structure determination, thermal stability and dissolution rate of δ-indomethacin. Int J Pharm 2021; 608:121067. [PMID: 34481012 DOI: 10.1016/j.ijpharm.2021.121067] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 08/27/2021] [Accepted: 08/28/2021] [Indexed: 11/17/2022]
Abstract
The structure solution of the δ-polymorph of indomethacin was obtained using three-dimensional electron diffraction. This form shows a significantly enhanced dissolution rate compared with the more common and better studied α- and γ-polymorphs, indicating better biopharmaceutical properties for medicinal applications. The structure was solved in non-centrosymmetric space group P21 and comprises two molecules in the asymmetric unit. Packing and molecule conformation closely resemble indomethacin methyl ester and indomethacin methanol solvate. Knowledge of the structure allowed the rational interpretation of spectroscopic IR and Raman data for δ-polymorph and a tentative interpretation for still unsolved indomethacin polymorphs. Finally, we observed a solid-solid transition from δ-polymorph to α-polymorph that can be driven by similarities in molecular conformation.
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Affiliation(s)
- Iryna Andrusenko
- Center for Nanotechnology Innovation@NEST, Istituto Italiano di Tecnologia, Piazza San Silvestro 12, Pisa 56127, Italy
| | - Victoria Hamilton
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
| | - Arianna E Lanza
- Center for Nanotechnology Innovation@NEST, Istituto Italiano di Tecnologia, Piazza San Silvestro 12, Pisa 56127, Italy
| | - Charlie L Hall
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
| | - Enrico Mugnaioli
- Center for Nanotechnology Innovation@NEST, Istituto Italiano di Tecnologia, Piazza San Silvestro 12, Pisa 56127, Italy
| | - Jason Potticary
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
| | - Asma Buanz
- UCL School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Simon Gaisford
- UCL School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Anna M Piras
- Department of Pharmacy, University of Pisa, Via Bonanno 33, Pisa 56126, Italy
| | - Ylenia Zambito
- Department of Pharmacy, University of Pisa, Via Bonanno 33, Pisa 56126, Italy.
| | - Simon R Hall
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK.
| | - Mauro Gemmi
- Center for Nanotechnology Innovation@NEST, Istituto Italiano di Tecnologia, Piazza San Silvestro 12, Pisa 56127, Italy.
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15
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Determination of Spinel Content in Cycled Li1.2Ni0.13Mn0.54Co0.13O2 Using Three-Dimensional Electron Diffraction and Precession Electron Diffraction. Symmetry (Basel) 2021. [DOI: 10.3390/sym13111989] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Among lithium battery cathode materials, Li1.2Ni0.13Mn0.54Co0.13O2 (LR-NMC) has a high theoretical capacity, but suffers from voltage and capacity fade during cycling. This is partially ascribed to transition metal cation migration, which involves the local transformation of the honeycomb layered structure to spinel-like nano-domains. Determination of the honeycomb layered/spinel phase ratio from powder X-ray diffraction data is hindered by the nanoscale of the functional material and the domains, diverse types of twinning, stacking faults, and the possible presence of the rock salt phase. Determining the phase ratio from transmission electron microscopy imaging can only be done for thin regions near the surfaces of the crystals, and the intense beam that is needed for imaging induces the same transformation to spinel as cycling does. In this article, it is demonstrated that the low electron dose sufficient for electron diffraction allows the collection of data without inducing a phase transformation. Using calculated electron diffraction patterns, we demonstrate that it is possible to determine the volume ratio of the different phases in the particles using a pair-wise comparison of the intensities of the reflections. Using this method, the volume ratio of spinel structure to honeycomb layered structure is determined for a submicron sized crystal from experimental three-dimensional electron diffraction (3D ED) and precession electron diffraction (PED) data. Both twinning and the possible presence of the rock salt phase are taken into account. After 150 charge–discharge cycles, 4% of the volume in LR-NMC particles was transformed irreversibly from the honeycomb layered structure to the spinel structure. The proposed method would be applicable to other multi-phase materials as well.
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16
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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.
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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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17
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Hall CL, Andrusenko I, Potticary J, Gao S, Liu X, Schmidt W, Marom N, Mugnaioli E, Gemmi M, Hall SR. 3D Electron Diffraction Structure Determination of Terrylene, a Promising Candidate for Intermolecular Singlet Fission. Chemphyschem 2021; 22:1631-1637. [PMID: 34117821 PMCID: PMC8457070 DOI: 10.1002/cphc.202100320] [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: 04/26/2021] [Revised: 06/05/2021] [Indexed: 12/13/2022]
Abstract
Herein we demonstrate the prowess of the 3D electron diffraction approach by unveiling the structure of terrylene, the third member in the series of peri‐condensed naphthalene analogues, which has eluded structure determination for 65 years. The structure was determined by direct methods using electron diffraction data and corroborated by dispersion‐inclusive density functional theory optimizations. Terrylene crystalizes in the monoclinic space group P21/a, arranging in a sandwich‐herringbone packing motif, similar to analogous compounds. Having solved the crystal structure, we use many‐body perturbation theory to evaluate the excited‐state properties of terrylene in the solid‐state. We find that terrylene is a promising candidate for intermolecular singlet fission, comparable to tetracene and rubrene.
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Affiliation(s)
- Charlie L Hall
- School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK
| | - Iryna Andrusenko
- Istituto Italiano di Tecnologia, Center for Nanotechnology Innovation@NEST, Pisa, 56127, Italy
| | - Jason Potticary
- School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK
| | - Siyu Gao
- Department of Materials Science and Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | - Xingyu Liu
- Department of Materials Science and Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | | | - Noa Marom
- Department of Materials Science and Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | - Enrico Mugnaioli
- Istituto Italiano di Tecnologia, Center for Nanotechnology Innovation@NEST, Pisa, 56127, Italy
| | - Mauro Gemmi
- Istituto Italiano di Tecnologia, Center for Nanotechnology Innovation@NEST, Pisa, 56127, Italy
| | - Simon R Hall
- School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK
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18
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Gruene T, Holstein JJ, Clever GH, Keppler B. Establishing electron diffraction in chemical crystallography. Nat Rev Chem 2021; 5:660-668. [PMID: 37118416 DOI: 10.1038/s41570-021-00302-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/07/2021] [Indexed: 02/06/2023]
Abstract
The emerging field of 3D electron diffraction (3D ED) opens new opportunities for structure determination from sub-micrometre-sized crystals. Although the foundations of this technology emerged earlier, the past decade has seen developments in cryo-electron microscopy and (X-ray) crystallography that particularly enable the widespread use of 3D ED. This Perspective describes to chemists and chemical crystallographers just how similar electron and X-ray diffraction are and discusses their complementary aspects. We wish to establish 3D ED in the broader chemistry community, such that electron crystallography becomes a common part of the analytical chemistry toolkit. With a suitable instrument at their disposal, every skilled crystallographer can quickly learn to perform structure determinations using 3D ED.
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19
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Clabbers MTB, Xu H. Macromolecular crystallography using microcrystal electron diffraction. Acta Crystallogr D Struct Biol 2021; 77:313-324. [PMID: 33645535 PMCID: PMC7919406 DOI: 10.1107/s2059798320016368] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 12/16/2020] [Indexed: 11/10/2022] Open
Abstract
Microcrystal electron diffraction (MicroED) has recently emerged as a promising method for macromolecular structure determination in structural biology. Since the first protein structure was determined in 2013, the method has been evolving rapidly. Several protein structures have been determined and various studies indicate that MicroED is capable of (i) revealing atomic structures with charges, (ii) solving new protein structures by molecular replacement, (iii) visualizing ligand-binding interactions and (iv) determining membrane-protein structures from microcrystals embedded in lipidic mesophases. However, further development and optimization is required to make MicroED experiments more accurate and more accessible to the structural biology community. Here, we provide an overview of the current status of the field, and highlight the ongoing development, to provide an indication of where the field may be going in the coming years. We anticipate that MicroED will become a robust method for macromolecular structure determination, complementing existing methods in structural biology.
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Affiliation(s)
- Max T. B. Clabbers
- Department of Materials and Environmental Chemistry, Stockholm University, 106 91 Stockholm, Sweden
| | - Hongyi Xu
- Department of Materials and Environmental Chemistry, Stockholm University, 106 91 Stockholm, Sweden
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20
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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.
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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
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21
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Andrusenko I, Potticary J, Hall SR, Gemmi M. A new olanzapine cocrystal obtained from volatile deep eutectic solvents and determined by 3D electron diffraction. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2020; 76:1036-1044. [PMID: 33289715 DOI: 10.1107/s2052520620012779] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 09/20/2020] [Indexed: 06/12/2023]
Abstract
A previously unknown cocrystal of olanzapine and phenol was identified from a volatile deep eutectic solvent as the intermediate species in the crystallization of olanzapine. This new nanocrystalline phase was investigated by electron diffraction, powder X-ray diffraction and differential scanning calorimetry. The structure was determined by simulated annealing using 3D electron diffraction data and confirmed using DFT-D optimizations. Olanzapine and phenol cocrystallize in the triclinic space group P1, supporting the hypothesis of a dimeric growth unit, where a centrosymmetric dimer is stabilized by multiple weak C-H...π interactions and forms double N-H...N hydrogen bonding with adjacent dimers.
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Affiliation(s)
- Iryna Andrusenko
- Center for Nanotechnology Innovation@NEST, Istituto Italiano di Tecnologia, Piazza San Silvestro 12, Pisa, Italy
| | - Jason Potticary
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, United Kingdom
| | - Simon R Hall
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, United Kingdom
| | - Mauro Gemmi
- Center for Nanotechnology Innovation@NEST, Istituto Italiano di Tecnologia, Piazza San Silvestro 12, Pisa, Italy
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22
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Mugnaioli E, Lanza AE, Bortolozzi G, Righi L, Merlini M, Cappello V, Marini L, Athanassiou A, Gemmi M. Electron Diffraction on Flash-Frozen Cowlesite Reveals the Structure of the First Two-Dimensional Natural Zeolite. ACS CENTRAL SCIENCE 2020; 6:1578-1586. [PMID: 32999933 PMCID: PMC7517411 DOI: 10.1021/acscentsci.9b01100] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Indexed: 05/24/2023]
Abstract
Cowlesite, ideally Ca6Al12Si18O60·36H2O, is to date the only natural zeolite whose structure could not be determined by X-ray methods. In this paper, we present the ab initio structure determination of this mineral obtained by three-dimensional (3D) electron diffraction data collected from single-crystal domains of a few hundreds of nanometers. The structure of cowlesite consists of an alternation of rigid zeolitic layers and low-density interlayers supported by water and cations. This makes cowlesite the only two-dimensional (2D) zeolite known in nature. When cowlesite gets in contact with a transmission electron microscope vacuum, a phase transition to a conventional 3D zeolite framework occurs in few seconds. The original cowlesite structure could be preserved only by adopting a cryo-plunging sample preparation protocol usually employed for macromolecular samples. Such a protocol allows the investigation by 3D electron diffraction of very hydrated and very beam-sensitive inorganic materials, which were previously considered intractable by transmission electron microscopy crystallographic methods.
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Affiliation(s)
- Enrico Mugnaioli
- Center
for Nanotechnology Innovation@NEST, Istituto
Italiano di Tecnologia, Piazza San Silvestro 12, 56127 Pisa, Italy
| | - Arianna E. Lanza
- Center
for Nanotechnology Innovation@NEST, Istituto
Italiano di Tecnologia, Piazza San Silvestro 12, 56127 Pisa, Italy
| | - Giorgio Bortolozzi
- Associazione
Micromineralogica Italiana (AMI), via Gioconda 3, 26100 Cremona, Italy
| | - Lara Righi
- Department
of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 17/A, Parma, 43124, Italy
- IMEM-CNR, Parco Area
delle Scienze 37/A, 43123 Parma, Italy
| | - Marco Merlini
- Dipartimento
di Scienze della Terra, Università
degli Studi di Milano, Via Botticelli 23, 20133 Milano, Italy
| | - Valentina Cappello
- Center
for Nanotechnology Innovation@NEST, Istituto
Italiano di Tecnologia, Piazza San Silvestro 12, 56127 Pisa, Italy
| | - Lara Marini
- Smart Materials, Istituto Italiano di Tecnologia, via Morego 30, 16163 Genova, Italy
| | | | - Mauro Gemmi
- Center
for Nanotechnology Innovation@NEST, Istituto
Italiano di Tecnologia, Piazza San Silvestro 12, 56127 Pisa, Italy
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23
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Zhao R, Wang M, Chen J, Tong Y, Wei GW. The de Rham-Hodge Analysis and Modeling of Biomolecules. Bull Math Biol 2020; 82:108. [PMID: 32770408 PMCID: PMC8137271 DOI: 10.1007/s11538-020-00783-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Accepted: 07/20/2020] [Indexed: 12/18/2022]
Abstract
Biological macromolecules have intricate structures that underpin their biological functions. Understanding their structure-function relationships remains a challenge due to their structural complexity and functional variability. Although de Rham-Hodge theory, a landmark of twentieth-century mathematics, has had a tremendous impact on mathematics and physics, it has not been devised for macromolecular modeling and analysis. In this work, we introduce de Rham-Hodge theory as a unified paradigm for analyzing the geometry, topology, flexibility, and Hodge mode analysis of biological macromolecules. Geometric characteristics and topological invariants are obtained either from the Helmholtz-Hodge decomposition of the scalar, vector, and/or tensor fields of a macromolecule or from the spectral analysis of various Laplace-de Rham operators defined on the molecular manifolds. We propose Laplace-de Rham spectral-based models for predicting macromolecular flexibility. We further construct a Laplace-de Rham-Helfrich operator for revealing cryo-EM natural frequencies. Extensive experiments are carried out to demonstrate that the proposed de Rham-Hodge paradigm is one of the most versatile tools for the multiscale modeling and analysis of biological macromolecules and subcellular organelles. Accurate, reliable, and topological structure-preserving algorithms for implementing discrete exterior calculus (DEC) have been developed to facilitate the aforementioned modeling and analysis of biological macromolecules. The proposed de Rham-Hodge paradigm has potential applications to subcellular organelles and the structure construction from medium- or low-resolution cryo-EM maps, and functional predictions from massive biomolecular datasets.
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Affiliation(s)
- Rundong Zhao
- Department of Computer Science and Engineering, Michigan State University, East Lansing, MI, 48824, USA
| | - Menglun Wang
- Department of Mathematics, Michigan State University, East Lansing, MI, 48824, USA
| | - Jiahui Chen
- Department of Mathematics, Michigan State University, East Lansing, MI, 48824, USA
| | - Yiying Tong
- Department of Computer Science and Engineering, Michigan State University, East Lansing, MI, 48824, USA.
| | - Guo-Wei Wei
- Department of Mathematics, Michigan State University, East Lansing, MI, 48824, USA.
- Department of Electrical and Computer Engineering, Michigan State University, East Lansing, MI, 48824, USA.
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA.
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24
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Gallagher-Jones M, Bustillo KC, Ophus C, Richards LS, Ciston J, Lee S, Minor AM, Rodriguez JA. Atomic structures determined from digitally defined nanocrystalline regions. IUCRJ 2020; 7:490-499. [PMID: 32431832 PMCID: PMC7201287 DOI: 10.1107/s2052252520004030] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 03/22/2020] [Indexed: 06/11/2023]
Abstract
Nanocrystallography has transformed our ability to interrogate the atomic structures of proteins, peptides, organic molecules and materials. By probing atomic level details in ordered sub-10 nm regions of nanocrystals, scanning nanobeam electron diffraction extends the reach of nanocrystallography and in principle obviates the need for diffraction from large portions of one or more crystals. Scanning nanobeam electron diffraction is now applied to determine atomic structures from digitally defined regions of beam-sensitive peptide nanocrystals. Using a direct electron detector, thousands of sparse diffraction patterns over multiple orientations of a given crystal are recorded. Each pattern is assigned to a specific location on a single nanocrystal with axial, lateral and angular coordinates. This approach yields a collection of patterns that represent a tilt series across an angular wedge of reciprocal space: a scanning nanobeam diffraction tomogram. Using this diffraction tomogram, intensities can be digitally extracted from any desired region of a scan in real or diffraction space, exclusive of all other scanned points. Intensities from multiple regions of a crystal or from multiple crystals can be merged to increase data completeness and mitigate missing wedges. It is demonstrated that merged intensities from digitally defined regions of two crystals of a segment from the OsPYL/RCAR5 protein produce fragment-based ab initio solutions that can be refined to atomic resolution, analogous to structures determined by selected-area electron diffraction. In allowing atomic structures to now be determined from digitally outlined regions of a nanocrystal, scanning nanobeam diffraction tomography breaks new ground in nanocrystallography.
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Affiliation(s)
- Marcus Gallagher-Jones
- Department of Chemistry and Biochemistry, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
- UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
- STROBE, NSF Science and Technology Center, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
| | - Karen C. Bustillo
- National Center for Electron Microscopy, Molecular Foundry, Lawrence Berkeley National Laboratory, California, USA
| | - Colin Ophus
- National Center for Electron Microscopy, Molecular Foundry, Lawrence Berkeley National Laboratory, California, USA
| | - Logan S. Richards
- Department of Chemistry and Biochemistry, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
- UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
- STROBE, NSF Science and Technology Center, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
| | - Jim Ciston
- National Center for Electron Microscopy, Molecular Foundry, Lawrence Berkeley National Laboratory, California, USA
| | - Sangho Lee
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Andrew M. Minor
- National Center for Electron Microscopy, Molecular Foundry, Lawrence Berkeley National Laboratory, California, USA
- Department of Materials Science and Engineering, University of California, Berkeley, California, USA
| | - Jose A. Rodriguez
- Department of Chemistry and Biochemistry, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
- UCLA-DOE Institute for Genomics and Proteomics, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
- STROBE, NSF Science and Technology Center, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
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25
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Plana-Ruiz S, Krysiak Y, Portillo J, Alig E, Estradé S, Peiró F, Kolb U. Fast-ADT: A fast and automated electron diffraction tomography setup for structure determination and refinement. Ultramicroscopy 2020; 211:112951. [DOI: 10.1016/j.ultramic.2020.112951] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 01/20/2020] [Accepted: 01/26/2020] [Indexed: 11/25/2022]
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26
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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: 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.
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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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27
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Woollam GR, Das PP, Mugnaioli E, Andrusenko I, Galanis AS, van de Streek J, Nicolopoulos S, Gemmi M, Wagner T. Structural analysis of metastable pharmaceutical loratadine form II, by 3D electron diffraction and DFT+D energy minimisation. CrystEngComm 2020. [DOI: 10.1039/d0ce01216e] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Coupling 3D electron diffraction and density functional theory provided the metastable pharmaceutical crystal structure within nanometre range, under ambient conditions.
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Affiliation(s)
| | | | - Enrico Mugnaioli
- Center for Nanotechnology Innovation@NEST
- Istituto Italiano di Tecnologia
- 56127 Pisa
- Italy
| | - Iryna Andrusenko
- Center for Nanotechnology Innovation@NEST
- Istituto Italiano di Tecnologia
- 56127 Pisa
- Italy
| | | | | | | | - Mauro Gemmi
- Center for Nanotechnology Innovation@NEST
- Istituto Italiano di Tecnologia
- 56127 Pisa
- Italy
| | - Trixie Wagner
- Novartis Institutes for BioMedical Research
- Basel 4002
- Switzerland
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28
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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.
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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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29
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Allen AJ. Recent trends in crystallography - a current IUCr journals perspective. IUCRJ 2019; 6:984-987. [PMID: 31709052 PMCID: PMC6830219 DOI: 10.1107/s2052252519014507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
This Editorial considers the impact of recent work published in IUCrJ and other IUCr journals, as well as the relationship between IUCrJ and the other journals, in terms of where the most cited recent papers are used.
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Affiliation(s)
- Andrew J. Allen
- Materials Measurement Science Division, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD 20899, USA
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30
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Khakurel KP, Angelov B, Andreasson J. Macromolecular Nanocrystal Structural Analysis with Electron and X-Rays: A Comparative Review. Molecules 2019; 24:E3490. [PMID: 31561479 PMCID: PMC6804143 DOI: 10.3390/molecules24193490] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 09/24/2019] [Accepted: 09/25/2019] [Indexed: 01/10/2023] Open
Abstract
Crystallography has long been the unrivaled method that can provide the atomistic structural models of macromolecules, using either X-rays or electrons as probes. The methodology has gone through several revolutionary periods, driven by the development of new sources, detectors, and other instrumentation. Novel sources of both X-ray and electrons are constantly emerging. The increase in brightness of these sources, complemented by the advanced detection techniques, has relaxed the traditionally strict need for large, high quality, crystals. Recent reports suggest high-quality diffraction datasets from crystals as small as a few hundreds of nanometers can be routinely obtained. This has resulted in the genesis of a new field of macromolecular nanocrystal crystallography. Here we will make a brief comparative review of this growing field focusing on the use of X-rays and electrons sources.
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Affiliation(s)
- Krishna P Khakurel
- Institute of Physics, ELI Beamlines, Academy of Sciences of the Czech Republic, Na Slovance 2, CZ-18221 Prague, Czech Republic.
| | - Borislav Angelov
- Institute of Physics, ELI Beamlines, Academy of Sciences of the Czech Republic, Na Slovance 2, CZ-18221 Prague, Czech Republic.
| | - Jakob Andreasson
- Institute of Physics, ELI Beamlines, Academy of Sciences of the Czech Republic, Na Slovance 2, CZ-18221 Prague, Czech Republic.
- Department of Physics, Chalmers University of Technology, 412 96 Gothenburg, Sweden.
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31
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Wang B, Zou X, Smeets S. Automated serial rotation electron diffraction combined with cluster analysis: an efficient multi-crystal workflow for structure determination. IUCRJ 2019; 6:854-867. [PMID: 31576219 PMCID: PMC6760450 DOI: 10.1107/s2052252519007681] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Accepted: 05/27/2019] [Indexed: 05/06/2023]
Abstract
Serial rotation electron diffraction (SerialRED) has been developed as a fully automated technique for three-dimensional electron diffraction data collection that can run autonomously without human intervention. It builds on the previously established serial electron diffraction technique, in which submicrometre-sized crystals are detected using image processing algorithms. Continuous rotation electron diffraction (cRED) data are collected on each crystal while dynamically tracking the movement of the crystal during rotation using defocused diffraction patterns and applying a set of deflector changes. A typical data collection screens up to 500 crystals per hour, and cRED data are collected from suitable crystals. A data processing pipeline is developed to process the SerialRED data sets. Hierarchical cluster analysis is implemented to group and identify the different phases present in the sample and to find the best matching data sets to be merged for subsequent structure analysis. This method has been successfully applied to a series of zeolites and a beam-sensitive metal-organic framework sample to study its capability for structure determination and refinement. Two multi-phase samples were tested to show that the individual crystal phases can be identified and their structures determined. The results show that refined structures obtained using automatically collected SerialRED data are indistinguishable from those collected manually using the cRED technique. At the same time, SerialRED has lower requirements of expertise in transmission electron microscopy and is less labor intensive, making it a promising high-throughput crystal screening and structure analysis tool.
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Affiliation(s)
- Bin Wang
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm 106 91, Sweden
| | - Xiaodong Zou
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm 106 91, Sweden
| | - Stef Smeets
- Department of Materials and Environmental Chemistry, Stockholm University, Stockholm 106 91, Sweden
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32
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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 CENTRAL SCIENCE 2019; 5:1315-1329. [PMID: 31482114 PMCID: PMC6716134 DOI: 10.1021/acscentsci.9b00394] [Citation(s) in RCA: 203] [Impact Index Per Article: 40.6] [Reference Citation Analysis] [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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33
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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] [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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34
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Kolb U, Krysiak Y, Plana-Ruiz S. Automated electron diffraction tomography - development and applications. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2019; 75:463-474. [PMID: 32830704 PMCID: PMC6690130 DOI: 10.1107/s2052520619006711] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 05/10/2019] [Indexed: 06/10/2023]
Abstract
Electron diffraction tomography (EDT) has gained increasing interest, starting with the development of automated electron diffraction tomography (ADT) which enables the collection of three-dimensional electron diffraction data from nano-sized crystals suitable for ab initio structure analysis. A basic description of the ADT method, nowadays recognized as a reliable and established method, as well as its special features and general applicability to different transmission electron microscopes is provided. In addition, the usability of ADT for crystal structure analysis of single nano-sized crystals with and without special crystallographic features, such as twinning, modulations and disorder is demonstrated.
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Affiliation(s)
- Ute Kolb
- Institut für Anorganische Chemie und Analytische Chemie, Johannes Gutenberg-Universität Mainz, Duesbergweg 10-14, Mainz, 55128, Germany
- Institut für Angewandte Geowissenchaften, Technische Universität Darmstadt, Schnittspahnstrasse 9, Darmstadt, 64287, Germany
| | - Yaşar Krysiak
- Institut für Anorganische Chemie und Analytische Chemie, Johannes Gutenberg-Universität Mainz, Duesbergweg 10-14, Mainz, 55128, Germany
| | - Sergi Plana-Ruiz
- Institut für Angewandte Geowissenchaften, Technische Universität Darmstadt, Schnittspahnstrasse 9, Darmstadt, 64287, Germany
- LENS-MIND, Departament d’Enginyeria Electrònica i Biomèdica, Universitat de Barcelona, Martí i Franquès 1, Barcelona, 08028, Spain
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35
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Xu H, Lebrette H, Clabbers MTB, Zhao J, Griese JJ, Zou X, Högbom M. Solving a new R2lox protein structure by microcrystal electron diffraction. SCIENCE ADVANCES 2019; 5:eaax4621. [PMID: 31457106 PMCID: PMC6685719 DOI: 10.1126/sciadv.aax4621] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 06/27/2019] [Indexed: 05/06/2023]
Abstract
Microcrystal electron diffraction (MicroED) has recently shown potential for structural biology. It enables the study of biomolecules from micrometer-sized 3D crystals that are too small to be studied by conventional x-ray crystallography. However, to date, MicroED has only been applied to redetermine protein structures that had already been solved previously by x-ray diffraction. Here, we present the first new protein structure-an R2lox enzyme-solved using MicroED. The structure was phased by molecular replacement using a search model of 35% sequence identity. The resulting electrostatic scattering potential map at 3.0-Å resolution was of sufficient quality to allow accurate model building and refinement. The dinuclear metal cofactor could be located in the map and was modeled as a heterodinuclear Mn/Fe center based on previous studies. Our results demonstrate that MicroED has the potential to become a widely applicable tool for revealing novel insights into protein structure and function.
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Affiliation(s)
- Hongyi Xu
- Department of Materials and Environmental Chemistry, Stockholm University, 10691 Stockholm, Sweden
- Corresponding author. (H.X.); (M.H.); (X.Z.)
| | - Hugo Lebrette
- Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden
| | - Max T. B. Clabbers
- Department of Materials and Environmental Chemistry, Stockholm University, 10691 Stockholm, Sweden
| | - Jingjing Zhao
- Department of Materials and Environmental Chemistry, Stockholm University, 10691 Stockholm, Sweden
| | - Julia J. Griese
- Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden
- Department of Cell and Molecular Biology, Uppsala University, 75124 Uppsala, Sweden
| | - Xiaodong Zou
- Department of Materials and Environmental Chemistry, Stockholm University, 10691 Stockholm, Sweden
- Corresponding author. (H.X.); (M.H.); (X.Z.)
| | - Martin Högbom
- Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden
- Corresponding author. (H.X.); (M.H.); (X.Z.)
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36
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Mugnaioli E, Gorelik TE. Structure analysis of materials at the order–disorder borderline using three-dimensional electron diffraction. ACTA CRYSTALLOGRAPHICA SECTION B-STRUCTURAL SCIENCE CRYSTAL ENGINEERING AND MATERIALS 2019; 75:550-563. [DOI: 10.1107/s2052520619007339] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 05/20/2019] [Indexed: 11/10/2022]
Abstract
Diffuse scattering, observed as intensity distribution between the Bragg peaks, is associated with deviations from the average crystal structure, generally referred to as disorder. In many cases crystal defects are seen as unwanted perturbations of the periodic structure and therefore they are often ignored. Yet, when it comes to the structure analysis of nano-volumes, what electron crystallography is designed for, the significance of defects increases. Twinning and polytypic sequences are other perturbations from ideal crystal structure that are also commonly observed in nanocrystals. Here we present an overview of defect types and review some of the most prominent studies published on the analysis of defective nanocrystalline structures by means of three-dimensional electron diffraction.
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37
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Gemmi M, Lanza AE. 3D electron diffraction techniques. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2019; 75:495-504. [PMID: 32830707 DOI: 10.1107/s2052520619007510] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 05/23/2019] [Indexed: 06/11/2023]
Abstract
3D electron diffraction is an emerging technique for the structural analysis of nanocrystals. The challenges that 3D electron diffraction has to face for providing reliable data for structure solution and the different ways of overcoming these challenges are described. The route from zone axis patterns towards 3D electron diffraction techniques such as precession-assisted electron diffraction tomography, rotation electron diffraction and continuous rotation is also discussed. Finally, the advantages of the new hybrid detectors with high sensitivity and fast readout are demonstrated with a proof of concept experiment of continuous rotation electron diffraction on a natrolite nanocrystal.
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Affiliation(s)
- Mauro Gemmi
- Center for Nanotechnology Innovation@NEST, Istituto Italiano di Tecnologia, Piazza San Silvestro 12, Pisa, 56127, Italy
| | - Arianna E Lanza
- Center for Nanotechnology Innovation@NEST, Istituto Italiano di Tecnologia, Piazza San Silvestro 12, Pisa, 56127, Italy
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38
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Gemmi M, Serravalle E, Roberti di Sarsina P. A New Method Based on Electron Diffraction for Detecting Nanoparticles in Injectable Medicines. J Pharm Sci 2019; 109:891-899. [PMID: 31348938 DOI: 10.1016/j.xphs.2019.07.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 06/13/2019] [Accepted: 07/17/2019] [Indexed: 10/26/2022]
Abstract
A new method for detecting and characterizing nanoparticles in an injectable pharmaceutical solution is presented. The method is based on the simultaneous use, on those nanoparticles that are crystalline, of three-dimensional electron diffraction tomography and energy dispersive X-ray spectrometry. With three-dimensional electron diffraction tomography, the unit cell and the crystal symmetry of the nanoparticles are determined, while with energy dispersive X-ray spectrometry, the chemical composition is derived. With these data, through an inspection of a crystallographic database, it is possible to determine the crystal phase of the nanoparticles. The knowledge of the crystal phase is a valuable element for understanding the provenance and the formation of the nanoparticles, helping the researcher in solving any quality control issue related to the presence of nanoparticles in an injectable solution.
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Affiliation(s)
- Mauro Gemmi
- Center for Nanotechnology Innovation@NEST, Istituto Italiano di Tecnologia, Piazza San Silvestro 12, Pisa, Italy.
| | - Eugenio Serravalle
- AsSIS, Associazione di Studi e Informazione sulla Salute, Via Firenze 8, Pisa, Italy
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39
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Andrusenko I, Hamilton V, Mugnaioli E, Lanza A, Hall C, Potticary J, Hall SR, Gemmi M. The Crystal Structure of Orthocetamol Solved by 3D Electron Diffraction. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201904564] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Iryna Andrusenko
- Center for Nanotechnology Innovation@NESTIstituto Italiano di Tecnologia Piazza San Silvestro 12 Pisa Italy
| | - Victoria Hamilton
- Complex Functional Materials GroupSchool of ChemistryUniversity of Bristol Bristol BS8 1TS UK
- Bristol Centre for Functional NanomaterialsCentre for Nanoscience and Quantum Information Tyndall Avenue Bristol BS8 1FD UK
| | - Enrico Mugnaioli
- Center for Nanotechnology Innovation@NESTIstituto Italiano di Tecnologia Piazza San Silvestro 12 Pisa Italy
| | - Arianna Lanza
- Center for Nanotechnology Innovation@NESTIstituto Italiano di Tecnologia Piazza San Silvestro 12 Pisa Italy
| | - Charlie Hall
- Complex Functional Materials GroupSchool of ChemistryUniversity of Bristol Bristol BS8 1TS UK
- Centre for Doctoral Training in Condensed Matter PhysicsHH Wills Physics Laboratory Tyndall Avenue Bristol BS8 1TL UK
| | - Jason Potticary
- Complex Functional Materials GroupSchool of ChemistryUniversity of Bristol Bristol BS8 1TS UK
| | - Simon R. Hall
- Complex Functional Materials GroupSchool of ChemistryUniversity of Bristol Bristol BS8 1TS UK
| | - Mauro Gemmi
- Center for Nanotechnology Innovation@NESTIstituto Italiano di Tecnologia Piazza San Silvestro 12 Pisa Italy
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40
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Andrusenko I, Hamilton V, Mugnaioli E, Lanza A, Hall C, Potticary J, Hall SR, Gemmi M. The Crystal Structure of Orthocetamol Solved by 3D Electron Diffraction. Angew Chem Int Ed Engl 2019; 58:10919-10922. [PMID: 31210373 DOI: 10.1002/anie.201904564] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 05/14/2019] [Indexed: 12/11/2022]
Abstract
Orthocetamol is a regioisomer of the well-known pain medication paracetamol and a promising analgesic and an anti-arthritic medicament itself. However, orthocetamol cannot be grown as single crystals suitable for X-ray diffraction, so its crystal structure has remained a mystery for more than a century. Here, we report the ab-initio structure determination of orthocetamol obtained by 3D electron diffraction, combining a low-dose acquisition method and a dedicated single-electron detector for recording the diffracted intensities. The structure is monoclinic, with a pseudo-tetragonal cell that favors multiple twinning on a scale of a few tens of nanometers. The successful application of 3D electron diffraction to orthocetamol introduces a new gold standard of total structure solution in all cases where X-ray diffraction and electron-microscope imaging methods fail.
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Affiliation(s)
- Iryna Andrusenko
- Center for Nanotechnology Innovation@NEST, Istituto Italiano di Tecnologia, Piazza San Silvestro 12, Pisa, Italy
| | - Victoria Hamilton
- Complex Functional Materials Group, School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK.,Bristol Centre for Functional Nanomaterials, Centre for Nanoscience and Quantum Information, Tyndall Avenue, Bristol, BS8 1FD, UK
| | - Enrico Mugnaioli
- Center for Nanotechnology Innovation@NEST, Istituto Italiano di Tecnologia, Piazza San Silvestro 12, Pisa, Italy
| | - Arianna Lanza
- Center for Nanotechnology Innovation@NEST, Istituto Italiano di Tecnologia, Piazza San Silvestro 12, Pisa, Italy
| | - Charlie Hall
- Complex Functional Materials Group, School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK.,Centre for Doctoral Training in Condensed Matter Physics, HH Wills Physics Laboratory, Tyndall Avenue, Bristol, BS8 1TL, UK
| | - Jason Potticary
- Complex Functional Materials Group, School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK
| | - Simon R Hall
- Complex Functional Materials Group, School of Chemistry, University of Bristol, Bristol, BS8 1TS, UK
| | - Mauro Gemmi
- Center for Nanotechnology Innovation@NEST, Istituto Italiano di Tecnologia, Piazza San Silvestro 12, Pisa, Italy
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41
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Heidler J, Pantelic R, Wennmacher JTC, Zaubitzer C, Fecteau-Lefebvre A, Goldie KN, Müller E, Holstein JJ, van Genderen E, De Carlo S, Gruene T. Design guidelines for an electron diffractometer for structural chemistry and structural biology. Acta Crystallogr D Struct Biol 2019; 75:458-466. [PMID: 31063148 PMCID: PMC6503764 DOI: 10.1107/s2059798319003942] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 03/22/2019] [Indexed: 11/11/2022] Open
Abstract
3D electron diffraction has reached a stage where the structures of chemical compounds can be solved productively. Instrumentation is lagging behind this development, and to date dedicated electron diffractometers for data collection based on the rotation method do not exist. Current studies use transmission electron microscopes as a workaround. These are optimized for imaging, which is not optimal for diffraction studies. The beam intensity is very high, it is difficult to create parallel beam illumination and the detectors used for imaging are of only limited use for diffraction studies. In this work, the combination of an EIGER hybrid pixel detector with a transmission electron microscope to construct a productive electron diffractometer is described. The construction not only refers to the combination of hardware but also to the calibration of the system, so that it provides rapid access to the experimental parameters that are necessary for processing diffraction data. Until fully integrated electron diffractometers become available, this describes a setup for productive and efficient operation in chemical crystallography.
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Affiliation(s)
- Jonas Heidler
- Paul Scherrer Institut, 5232 Villigen PSI, Switzerland
| | | | | | - Christian Zaubitzer
- Scientific Center for Optical and Electron Microscopy, ETH Zürich, 8093 Zürich, Switzerland
| | | | - Kenneth N Goldie
- Center for Cellular Imaging and NanoAnalytics, University Basel, 4058 Basel, Switzerland
| | | | - Julian J Holstein
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto Hahn Strasse 6, 44227 Dortmund, Germany
| | | | | | - Tim Gruene
- Paul Scherrer Institut, 5232 Villigen PSI, Switzerland
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Baker EN. Why conferences matter - musings from a crystallographic meeting. IUCRJ 2019; 6:152-153. [PMID: 30867911 PMCID: PMC6400196 DOI: 10.1107/s2052252519002215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Despite extraordinary advances in the options available for instant electronic communication, the argument is made that conferences still provide a unique forum for transmission of new ideas and advances in science, with their ability to inspire attendees.
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Affiliation(s)
- Edward N. Baker
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
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