1
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Ruma YN, Bu G, Hattne J, Gonen T. MicroED structure of the C11 cysteine protease clostripain. J Struct Biol X 2024; 10:100107. [PMID: 39100863 PMCID: PMC11296011 DOI: 10.1016/j.yjsbx.2024.100107] [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: 01/04/2024] [Revised: 07/03/2024] [Accepted: 07/05/2024] [Indexed: 08/06/2024] Open
Abstract
Clostripain secreted from Clostridium histolyticum is the founding member of the C11 family of Clan CD cysteine peptidases, which is an important group of peptidases secreted by numerous bacteria. Clostripain is an arginine-specific endopeptidase. Because of its efficacy as a cysteine peptidase, it is widely used in laboratory settings. Despite its importance the structure of clostripain remains unsolved. Here we describe the first structure of an active form of C. histolyticum clostripain determined at 2.5 Å resolution using microcrystal electron diffraction (MicroED). The structure was determined from a single nanocrystal after focused ion beam milling. The structure of clostripain shows a typical Clan CD α/β/α sandwich architecture and the Cys231/His176 catalytic dyad in the active site. It has a large electronegative substrate binding pocket showing its ability to accommodate large and diverse substrates. A loop in the heavy chain formed between residues 452 and 457 is potentially important for substrate binding. In conclusion, this result demonstrates the importance of MicroED to determine the unknown structure of macromolecules such as clostripain, which can be further used as a platform to study substrate binding and design of potential inhibitors against this class of peptidases.
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Affiliation(s)
- Yasmeen N. Ruma
- Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA 90095, United States
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA 90095, United States
| | - Guanhong Bu
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA 90095, United States
| | - Johan Hattne
- Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA 90095, United States
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA 90095, United States
| | - Tamir Gonen
- Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA 90095, United States
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA 90095, United States
- Department of Physiology, University of California, Los Angeles, Los Angeles, CA 90095, United States
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2
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Kumar A, Jha KK, Olech B, Goral T, Malinska M, Woźniak K, Dominiak PM. TAAM refinement on high-resolution experimental and simulated 3D ED/MicroED data for organic molecules. Acta Crystallogr C Struct Chem 2024; 80:264-277. [PMID: 38934273 PMCID: PMC11225613 DOI: 10.1107/s2053229624005357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 06/05/2024] [Indexed: 06/28/2024] Open
Abstract
3D electron diffraction (3D ED), or microcrystal electron diffraction (MicroED), has become an alternative technique for determining the high-resolution crystal structures of compounds from sub-micron-sized crystals. Here, we considered L-alanine, α-glycine and urea, which are known to form good-quality crystals, and collected high-resolution 3D ED data on our in-house TEM instrument. In this study, we present a comparison of independent atom model (IAM) and transferable aspherical atom model (TAAM) kinematical refinement against experimental and simulated data. TAAM refinement on both experimental and simulated data clearly improves the model fitting statistics (R factors and residual electrostatic potential) compared to IAM refinement. This shows that TAAM better represents the experimental electrostatic potential of organic crystals than IAM. Furthermore, we compared the geometrical parameters and atomic displacement parameters (ADPs) resulting from the experimental refinements with the simulated refinements, with the periodic density functional theory (DFT) calculations and with published X-ray and neutron crystal structures. The TAAM refinements on the 3D ED data did not improve the accuracy of the bond lengths between the non-H atoms. The experimental 3D ED data provided more accurate H-atom positions than the IAM refinements on the X-ray diffraction data. The IAM refinements against 3D ED data had a tendency to lead to slightly longer X-H bond lengths than TAAM, but the difference was statistically insignificant. Atomic displacement parameters were too large by tens of percent for L-alanine and α-glycine. Most probably, other unmodelled effects were causing this behaviour, such as radiation damage or dynamical scattering.
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Affiliation(s)
- Anil Kumar
- Biological and Chemical Research Centre Faculty of Chemistry University of Warsaw, ul Żwirki i Wigury 101 02-089 Warszawa Poland
| | - Kunal Kumar Jha
- Biological and Chemical Research Centre Faculty of Chemistry University of Warsaw, ul Żwirki i Wigury 101 02-089 Warszawa Poland
- Centre of New Technologies University of Warsaw, ul S Banacha 2c 02-097 Warszawa Poland
| | - Barbara Olech
- Biological and Chemical Research Centre Faculty of Chemistry University of Warsaw, ul Żwirki i Wigury 101 02-089 Warszawa Poland
- Centre of New Technologies University of Warsaw, ul S Banacha 2c 02-097 Warszawa Poland
| | - Tomasz Goral
- Biological and Chemical Research Centre Faculty of Chemistry University of Warsaw, ul Żwirki i Wigury 101 02-089 Warszawa Poland
- Centre of New Technologies University of Warsaw, ul S Banacha 2c 02-097 Warszawa Poland
| | - Maura Malinska
- Faculty of Chemistry University of Warsaw, Pasteura 1 02-093 Warszawa Poland
| | - Krzysztof Woźniak
- Centre of New Technologies University of Warsaw, ul S Banacha 2c 02-097 Warszawa Poland
- Faculty of Chemistry University of Warsaw, Pasteura 1 02-093 Warszawa Poland
| | - Paulina Maria Dominiak
- Biological and Chemical Research Centre Faculty of Chemistry University of Warsaw, ul Żwirki i Wigury 101 02-089 Warszawa Poland
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3
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Acehan D, Spoth KA, Budziszewski GR, Snell ME, Campomizzi CS, Lynch ML, Bowman SE. Reaching the potential of electron diffraction. CELL REPORTS. PHYSICAL SCIENCE 2024; 5:102007. [PMID: 39055735 PMCID: PMC11271257 DOI: 10.1016/j.xcrp.2024.102007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/27/2024]
Abstract
Microcrystal electron diffraction (MicroED) is an emerging structural technique in which submicron crystals are used to generate diffraction data for structural studies. Structures allow for the study of molecular-level architecture and drive hypotheses about modes of action, mechanisms, dynamics, and interactions with other molecules. Combining cryoelectron microscopy (cryo-EM) instrumentation with crystallographic techniques, MicroED has led to three-dimensional structural models of small molecules, peptides, and proteins and has generated tremendous interest due to its ability to use vanishingly small crystals. In this perspective, we describe the current state of the field for MicroED methodologies, including making and detecting crystals of the appropriate size for the technique, as well as ways to best handle and characterize these crystals. Our perspective provides insight into ways to unlock the full range of potential for MicroED to access previously intractable samples and describes areas of future development.
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Affiliation(s)
- Devrim Acehan
- Hauptman-Woodward Medical Research Institute, Buffalo, NY 14203, USA
- University at Buffalo, Jacobs School of Medicine and Biomedical Science, Department of Structural Biology, Buffalo, NY 14203, USA
- University of Rochester, School of Medicine and Dentistry, Department of Biochemistry and Biophysics, Rochester, NY 14642, USA
| | | | | | | | | | - Miranda L. Lynch
- Hauptman-Woodward Medical Research Institute, Buffalo, NY 14203, USA
- University at Buffalo, Jacobs School of Medicine and Biomedical Science, Department of Structural Biology, Buffalo, NY 14203, USA
| | - Sarah E.J. Bowman
- Hauptman-Woodward Medical Research Institute, Buffalo, NY 14203, USA
- University at Buffalo, Jacobs School of Medicine and Biomedical Science, Department of Structural Biology, Buffalo, NY 14203, USA
- University at Buffalo, Jacobs School of Medicine and Biomedical Science, Department of Biochemistry, Buffalo, NY 14203, USA
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4
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Khakurel KP, Nemergut M, Džupponová V, Kropielnicki K, Savko M, Žoldák G, Andreasson J. Design and fabrication of 3D-printed in situ crystallization plates for probing microcrystals in an external electric field. J Appl Crystallogr 2024; 57:842-847. [PMID: 38846773 PMCID: PMC11151662 DOI: 10.1107/s1600576724002140] [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: 12/30/2023] [Accepted: 03/05/2024] [Indexed: 06/09/2024] Open
Abstract
X-ray crystallography is an established tool to probe the structure of macromolecules with atomic resolution. Compared with alternative techniques such as single-particle cryo-electron microscopy and micro-electron diffraction, X-ray crystallography is uniquely suited to room-temperature studies and for obtaining a detailed picture of macromolecules subjected to an external electric field (EEF). The impact of an EEF on proteins has been extensively explored through single-crystal X-ray crystallography, which works well with larger high-quality protein crystals. This article introduces a novel design for a 3D-printed in situ crystallization plate that serves a dual purpose: fostering crystal growth and allowing the concurrent examination of the effects of an EEF on crystals of varying sizes. The plate's compatibility with established X-ray crystallography techniques is evaluated.
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Affiliation(s)
- Krishna Prasad Khakurel
- ELI Beamlines Facility, The Extreme Light Infrastructure ERIC, Za Radnicí 835, 25241 Dolní Břežany, Czech Republic
| | - Michal Nemergut
- Center for Interdisciplinary Biosciences, Technology and Innovation Park, P. J. Šafárik University, Košice, Slovakia
| | - Veronika Džupponová
- Center for Interdisciplinary Biosciences, Technology and Innovation Park, P. J. Šafárik University, Košice, Slovakia
| | - Kamil Kropielnicki
- ELI Beamlines Facility, The Extreme Light Infrastructure ERIC, Za Radnicí 835, 25241 Dolní Břežany, Czech Republic
| | | | - Gabriel Žoldák
- Center for Interdisciplinary Biosciences, Technology and Innovation Park, P. J. Šafárik University, Košice, Slovakia
| | - Jakob Andreasson
- ELI Beamlines Facility, The Extreme Light Infrastructure ERIC, Za Radnicí 835, 25241 Dolní Břežany, Czech Republic
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5
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Koga N, Saito Y, Miyake K, Amuti S, Fukuyoshi S, Yoshida S, Sato S, Yamada Y, Ikeda A, Adachi N, Kawasaki M, Takasu A, Aramaki S, Senda T, Rahim A, Najib A, Alam G, Tanaka N, Nakagawa-Goto K. Cyclic Sesquiterpene-Flavanone [4+2] Hybrids, Syzygioblanes A-C, Found in an Indonesian Traditional Medicine, "Jampu Salo" ( Syzygium oblanceolatum). Org Lett 2024; 26:4302-4307. [PMID: 38728049 DOI: 10.1021/acs.orglett.4c01248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
A plant used in an Indonesian traditional herbal medicine as a diabetes treatment and known locally as "Jampu Salo" was collected on Sulawesi Island, Indonesia. It was identified as Syzygium oblanceolatum (C. B. Rob.) Merr. (Myrtaceae) and found for the first time in Sulawesi; it was previously reported only in the eastern Philippines and Borneo. A phytochemical study of S. oblanceolatum led to the isolation of three unprecedented meroterpenoids, syzygioblanes A-C (1-3, respectively). These compounds might be biosynthesized through [4+2] cycloaddition of various germacrane-based cyclic sesquiterpenoids with the flavone desmethoxymatteucinol to form a spiro skeleton. The unique and complex structures were elucidated by microcrystal electron diffraction analysis in addition to general analytical techniques such as high-resolution mass spectrometry, various nuclear magnetic resonance methods, and infrared spectroscopy. Synchrotron X-ray diffraction and calculations of electronic circular dichroism spectra helped to determine the absolute configurations. The newly isolated compounds exhibited collateral sensitivity to more strongly inhibit the growth of a multidrug resistant tumor cell line compared to a chemosensitive tumor cell line.
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Affiliation(s)
- Nona Koga
- School of Pharmaceutical Sciences, College of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa 920-1192, Japan
| | - Yohei Saito
- School of Pharmaceutical Sciences, College of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa 920-1192, Japan
| | - Katsunori Miyake
- School of Pharmacy, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392, Japan
| | - Saidanxia Amuti
- School of Pharmaceutical Sciences, College of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa 920-1192, Japan
| | - Shuichi Fukuyoshi
- School of Pharmaceutical Sciences, College of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa 920-1192, Japan
| | - Satoshi Yoshida
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, Kashiwa, Chiba 277-0882, Japan
| | - Sota Sato
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, Kashiwa, Chiba 277-0882, Japan
- Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan
| | - Yusuke Yamada
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki 305-0801, Japan
| | - Akihito Ikeda
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki 305-0801, Japan
| | - Naruhiko Adachi
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki 305-0801, Japan
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Masato Kawasaki
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki 305-0801, Japan
| | - Akira Takasu
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki 305-0801, Japan
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Shinji Aramaki
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
- Tietz Video and Image Processing Systems Japan G.K., Level 14, Hibiya Central Building, 1-2-9 Nishi Shimbashi, Minato-ku, Tokyo 105-1003, Japan
| | - Toshiya Senda
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki 305-0801, Japan
| | - Abdul Rahim
- School of Pharmaceutical Sciences, College of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa 920-1192, Japan
- Department of Pharmaceutical Sciences and Technology, Faculty of Pharmacy, Hasanuddin University, Makassar 90245, Indonesia
| | - Ahmad Najib
- School of Pharmaceutical Sciences, College of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa 920-1192, Japan
| | - Gemini Alam
- Department of Pharmaceutical Sciences and Technology, Faculty of Pharmacy, Hasanuddin University, Makassar 90245, Indonesia
| | - Nobuyuki Tanaka
- Department of Botany, National Museum of Nature and Science, Amakubo 4-1-1, Tsukuba, Ibaraki 305-0005, Japan
| | - Kyoko Nakagawa-Goto
- School of Pharmaceutical Sciences, College of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa 920-1192, Japan
- Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, The University of North Carolina, Chapel Hill, North Carolina 27599-7568, United States
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6
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Yan Z, Wei D, Li X, Chung LW. Accelerating reliable multiscale quantum refinement of protein-drug systems enabled by machine learning. Nat Commun 2024; 15:4181. [PMID: 38755151 PMCID: PMC11099068 DOI: 10.1038/s41467-024-48453-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 04/24/2024] [Indexed: 05/18/2024] Open
Abstract
Biomacromolecule structures are essential for drug development and biocatalysis. Quantum refinement (QR) methods, which employ reliable quantum mechanics (QM) methods in crystallographic refinement, showed promise in improving the structural quality or even correcting the structure of biomacromolecules. However, vast computational costs and complex quantum mechanics/molecular mechanics (QM/MM) setups limit QR applications. Here we incorporate robust machine learning potentials (MLPs) in multiscale ONIOM(QM:MM) schemes to describe the core parts (e.g., drugs/inhibitors), replacing the expensive QM method. Additionally, two levels of MLPs are combined for the first time to overcome MLP limitations. Our unique MLPs+ONIOM-based QR methods achieve QM-level accuracy with significantly higher efficiency. Furthermore, our refinements provide computational evidence for the existence of bonded and nonbonded forms of the Food and Drug Administration (FDA)-approved drug nirmatrelvir in one SARS-CoV-2 main protease structure. This study highlights that powerful MLPs accelerate QRs for reliable protein-drug complexes, promote broader QR applications and provide more atomistic insights into drug development.
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Affiliation(s)
- Zeyin Yan
- Shenzhen Grubbs Institute, Department of Chemistry and Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Dacong Wei
- Shenzhen Grubbs Institute, Department of Chemistry and Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Xin Li
- Shenzhen Grubbs Institute, Department of Chemistry and Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Lung Wa Chung
- Shenzhen Grubbs Institute, Department of Chemistry and Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, Shenzhen, 518055, China.
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7
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Bu G, Danelius E, Wieske LH, Gonen T. Polymorphic Structure Determination of the Macrocyclic Drug Paritaprevir by MicroED. Adv Biol (Weinh) 2024; 8:e2300570. [PMID: 38381052 PMCID: PMC11090733 DOI: 10.1002/adbi.202300570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 12/20/2023] [Indexed: 02/22/2024]
Abstract
Paritaprevir is an orally bioavailable, macrocyclic drug used for treating chronic Hepatitis C virus (HCV) infection. Its structures have been elusive to the public until recently when one of the crystal forms is solved by microcrystal electron diffraction (MicroED). In this work, the MicroED structures of two distinct polymorphic crystal forms of paritaprevir are reported from the same experiment. The different polymorphs show conformational changes in the macrocyclic core, as well as the cyclopropyl sulfonamide and methyl pyrazinamide substituents. Molecular docking shows that one of the conformations fits well into the active site pocket of the HCV non-structural 3/4A (NS3/4A) serine protease target, and can interact with the pocket and catalytic triad via hydrophobic interactions and hydrogen bonds. These results can provide further insight for optimization of the binding of acyl sulfonamide inhibitors to the HCV NS3/4A serine protease. In addition, this also demonstrates the opportunity to derive different polymorphs and distinct macrocycle conformations from the same experiments using MicroED.
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Affiliation(s)
- Guanhong Bu
- Department of Biological Chemistry, University of California Los Angeles, 615 Charles E. Young Drive South, Los Angeles, CA 90095, USA
| | - Emma Danelius
- Department of Biological Chemistry, University of California Los Angeles, 615 Charles E. Young Drive South, Los Angeles, CA 90095, USA
- Howard Hughes Medical Institute, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Lianne H.E. Wieske
- Department of Chemistry – BMC, Uppsala University, Husargatan 3, 75237 Uppsala, Sweden
| | - Tamir Gonen
- Department of Biological Chemistry, University of California Los Angeles, 615 Charles E. Young Drive South, Los Angeles, CA 90095, USA
- Howard Hughes Medical Institute, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Physiology, University of California Los Angeles, 615 Charles E. Young Drive South, Los Angeles, CA 90095, USA
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8
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Nishiori D, Menzel JP, Armada N, Reyes Cruz EA, Nannenga BL, Batista VS, Moore GF. Breaking a Molecular Scaling Relationship Using an Iron-Iron Fused Porphyrin Electrocatalyst for Oxygen Reduction. J Am Chem Soc 2024; 146:11622-11633. [PMID: 38639470 DOI: 10.1021/jacs.3c08586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2024]
Abstract
The design of efficient electrocatalysts is limited by scaling relationships governing trade-offs between thermodynamic and kinetic performance metrics. This ″iron law″ of electrocatalysis arises from synthetic design strategies, where structural alterations to a catalyst must balance nucleophilic versus electrophilic character. Efforts to circumvent this fundamental impasse have focused on bioinspired applications of extended coordination spheres and charged sites proximal to a catalytic center. Herein, we report evidence for breaking a molecular scaling relationship involving electrocatalysis of the oxygen reduction reaction (ORR) by leveraging ligand design. We achieve this using a binuclear catalyst (a diiron porphyrin), featuring a macrocyclic ligand with extended electronic conjugation. This ligand motif delocalizes electrons across the molecular scaffold, improving the catalyst's nucleophilic and electrophilic character. As a result, our binuclear catalyst exhibits low overpotential and high catalytic turnover frequency, breaking the traditional trade-off between these two metrics.
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Affiliation(s)
- Daiki Nishiori
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287-1604, United States
- Center for Applied Structural Discovery (CASD), The Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States
| | - Jan Paul Menzel
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Nicholas Armada
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287-1604, United States
- Center for Applied Structural Discovery (CASD), The Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States
| | - Edgar A Reyes Cruz
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287-1604, United States
- Center for Applied Structural Discovery (CASD), The Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States
| | - Brent L Nannenga
- Center for Applied Structural Discovery (CASD), The Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States
- Chemical Engineering, School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, Arizona 85287, United States
| | - Victor S Batista
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
- Energy Sciences Institute, Yale University, West Haven, Connecticut 06516, United States
| | - Gary F Moore
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287-1604, United States
- Center for Applied Structural Discovery (CASD), The Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States
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9
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Krysiak Y, Plana-Ruiz S, Fink L, Alig E, Bahnmüller U, Kolb U, Schmidt MU. High Temperature Electron Diffraction on Organic Crystals: In Situ Crystal Structure Determination of Pigment Orange 34. J Am Chem Soc 2024; 146:9880-9887. [PMID: 38536667 PMCID: PMC11009952 DOI: 10.1021/jacs.3c14800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 02/23/2024] [Accepted: 03/14/2024] [Indexed: 04/11/2024]
Abstract
Small molecule structures and their applications rely on good knowledge of their atomic arrangements. However, the crystal structures of these compounds and materials, which are often composed of fine crystalline domains, cannot be determined with single-crystal X-ray diffraction. Three-dimensional electron diffraction (3D ED) is already becoming a reliable method for the structure analysis of submicrometer-sized organic materials. The reduction of electron beam damage is essential for successful structure determination and often prevents the analysis of organic materials at room temperature, not to mention high temperature studies. In this work, we apply advanced 3D ED methods at different temperatures enabling the accurate structure determination of two phases of Pigment Orange 34 (C34H28N8O2Cl2), a biphenyl pyrazolone pigment that has been industrially produced for more than 80 years and used for plastics application. The crystal structure of the high-temperature phase, which can be formed during plastic coloration, was determined at 220 °C. For the first time, we were able to observe a reversible phase transition in an industrial organic pigment in the solid state, even with atomic resolution, despite crystallites being submicrometer in size. By localizing hydrogen atoms, we were even able to detect the tautomeric state of the molecules at different temperatures. This demonstrates that precise, fast, and low-dose 3D ED measurements enable high-temperature studies the door for general in situ studies of nanocrystalline materials at the atomic level.
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Affiliation(s)
- Yaşar Krysiak
- Institute
of Inorganic Chemistry, Leibniz University
Hannover, Callinstraße 9, 30167 Hannover, Germany
| | - Sergi Plana-Ruiz
- Department
of Materials and Geoscience, Technische
Universität Darmstadt, Petersenstrasse 23, 64287 Darmstadt, Germany
- LENS,
MIND/IN2UB, Departament d’Enginyeria Electrònica i Biomèdica, Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Catalonia, Spain
| | - Lothar Fink
- Institute
of Inorganic and Analytical Chemistry, Goethe
University Frankfurt am Main, Max-von-Laue-Str. 7, 60438 Frankfurt am Main, Germany
| | - Edith Alig
- Institute
of Inorganic and Analytical Chemistry, Goethe
University Frankfurt am Main, Max-von-Laue-Str. 7, 60438 Frankfurt am Main, Germany
| | - Ulrich Bahnmüller
- Institute
of Inorganic Chemistry, Leibniz University
Hannover, Callinstraße 9, 30167 Hannover, Germany
| | - Ute Kolb
- Department
of Materials and Geoscience, Technische
Universität Darmstadt, Petersenstrasse 23, 64287 Darmstadt, Germany
- Institute
of Inorganic Chemistry and Analytical Chemistry, Johannes Gutenberg University, Duesbergweg 10-14, 55128 Mainz, Germany
| | - Martin U. Schmidt
- Institute
of Inorganic and Analytical Chemistry, Goethe
University Frankfurt am Main, Max-von-Laue-Str. 7, 60438 Frankfurt am Main, Germany
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10
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Cebi E, Lee J, Subramani VK, Bak N, Oh C, Kim KK. Cryo-electron microscopy-based drug design. Front Mol Biosci 2024; 11:1342179. [PMID: 38501110 PMCID: PMC10945328 DOI: 10.3389/fmolb.2024.1342179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 01/31/2024] [Indexed: 03/20/2024] Open
Abstract
Structure-based drug design (SBDD) has gained popularity owing to its ability to develop more potent drugs compared to conventional drug-discovery methods. The success of SBDD relies heavily on obtaining the three-dimensional structures of drug targets. X-ray crystallography is the primary method used for solving structures and aiding the SBDD workflow; however, it is not suitable for all targets. With the resolution revolution, enabling routine high-resolution reconstruction of structures, cryogenic electron microscopy (cryo-EM) has emerged as a promising alternative and has attracted increasing attention in SBDD. Cryo-EM offers various advantages over X-ray crystallography and can potentially replace X-ray crystallography in SBDD. To fully utilize cryo-EM in drug discovery, understanding the strengths and weaknesses of this technique and noting the key advancements in the field are crucial. This review provides an overview of the general workflow of cryo-EM in SBDD and highlights technical innovations that enable its application in drug design. Furthermore, the most recent achievements in the cryo-EM methodology for drug discovery are discussed, demonstrating the potential of this technique for advancing drug development. By understanding the capabilities and advancements of cryo-EM, researchers can leverage the benefits of designing more effective drugs. This review concludes with a discussion of the future perspectives of cryo-EM-based SBDD, emphasizing the role of this technique in driving innovations in drug discovery and development. The integration of cryo-EM into the drug design process holds great promise for accelerating the discovery of new and improved therapeutic agents to combat various diseases.
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Affiliation(s)
| | | | | | | | - Changsuk Oh
- Department of Precision Medicine, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
| | - Kyeong Kyu Kim
- Department of Precision Medicine, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
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11
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Bardin AA, Haymaker A, Banihashemi F, Lin JYS, Martynowycz MW, Nannenga BL. Focused ion beam milling and MicroED structure determination of metal-organic framework crystals. Ultramicroscopy 2024; 257:113905. [PMID: 38086288 PMCID: PMC10843726 DOI: 10.1016/j.ultramic.2023.113905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 11/30/2023] [Accepted: 12/04/2023] [Indexed: 01/05/2024]
Abstract
We report new advancements in the determination and high-resolution structural analysis of beam-sensitive metal organic frameworks (MOFs) using microcrystal electron diffraction (MicroED) coupled with focused ion beam milling at cryogenic temperatures (cryo-FIB). A microcrystal of the beam-sensitive MOF, ZIF-8, was ion-beam milled in a thin lamella approximately 150 nm thick. MicroED data were collected from this thin lamella using an energy filter and a direct electron detector operating in counting mode. Using this approach, we achieved a greatly improved resolution of 0.59 Å with a minimal total exposure of only 0.64 e-/A2. These innovations not only improve model statistics but also further demonstrate that ion-beam milling is compatible with beam-sensitive materials, augmenting the capabilities of electron diffraction in MOF research.
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Affiliation(s)
- Andrey A Bardin
- Chemical Engineering, School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ, United States; Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, United States
| | - Alison Haymaker
- Chemical Engineering, School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ, United States; Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, United States
| | - Fateme Banihashemi
- Chemical Engineering, School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ, United States
| | - Jerry Y S Lin
- Chemical Engineering, School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ, United States
| | - Michael W Martynowycz
- Department of Biological Chemistry, University of California, Los Angeles, CA 90095, United States.
| | - Brent L Nannenga
- Chemical Engineering, School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ, United States; Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, United States.
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12
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Haymaker A, Nannenga BL. Advances and applications of microcrystal electron diffraction (MicroED). Curr Opin Struct Biol 2024; 84:102741. [PMID: 38086321 PMCID: PMC10882645 DOI: 10.1016/j.sbi.2023.102741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Revised: 11/17/2023] [Accepted: 11/19/2023] [Indexed: 02/08/2024]
Abstract
Microcrystal electron diffraction, commonly referred to as MicroED, has become a powerful tool for high-resolution structure determination. The method makes use of cryogenic transmission electron microscopes to collect electron diffraction data from crystals that are several orders of magnitude smaller than those used by other conventional diffraction techniques. MicroED has been used on a variety of samples including soluble proteins, membrane proteins, small organic molecules, and materials. Here we will review the MicroED method and highlight recent advancements to the methodology, as well as describe applications of MicroED within the fields of structural biology and chemical crystallography.
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Affiliation(s)
- Alison Haymaker
- Chemical Engineering, School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ 85287, USA; Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Brent L Nannenga
- Chemical Engineering, School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ 85287, USA; Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, USA.
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13
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Amaya-Rodriguez CA, Carvajal-Zamorano K, Bustos D, Alegría-Arcos M, Castillo K. A journey from molecule to physiology and in silico tools for drug discovery targeting the transient receptor potential vanilloid type 1 (TRPV1) channel. Front Pharmacol 2024; 14:1251061. [PMID: 38328578 PMCID: PMC10847257 DOI: 10.3389/fphar.2023.1251061] [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: 06/30/2023] [Accepted: 12/14/2023] [Indexed: 02/09/2024] Open
Abstract
The heat and capsaicin receptor TRPV1 channel is widely expressed in nerve terminals of dorsal root ganglia (DRGs) and trigeminal ganglia innervating the body and face, respectively, as well as in other tissues and organs including central nervous system. The TRPV1 channel is a versatile receptor that detects harmful heat, pain, and various internal and external ligands. Hence, it operates as a polymodal sensory channel. Many pathological conditions including neuroinflammation, cancer, psychiatric disorders, and pathological pain, are linked to the abnormal functioning of the TRPV1 in peripheral tissues. Intense biomedical research is underway to discover compounds that can modulate the channel and provide pain relief. The molecular mechanisms underlying temperature sensing remain largely unknown, although they are closely linked to pain transduction. Prolonged exposure to capsaicin generates analgesia, hence numerous capsaicin analogs have been developed to discover efficient analgesics for pain relief. The emergence of in silico tools offered significant techniques for molecular modeling and machine learning algorithms to indentify druggable sites in the channel and for repositioning of current drugs aimed at TRPV1. Here we recapitulate the physiological and pathophysiological functions of the TRPV1 channel, including structural models obtained through cryo-EM, pharmacological compounds tested on TRPV1, and the in silico tools for drug discovery and repositioning.
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Affiliation(s)
- Cesar A. Amaya-Rodriguez
- Centro Interdisciplinario de Neurociencia de Valparaíso, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso, Chile
- Departamento de Fisiología y Comportamiento Animal, Facultad de Ciencias Naturales, Exactas y Tecnología, Universidad de Panamá, Ciudad de Panamá, Panamá
| | - Karina Carvajal-Zamorano
- Centro Interdisciplinario de Neurociencia de Valparaíso, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso, Chile
| | - Daniel Bustos
- Centro de Investigación de Estudios Avanzados del Maule (CIEAM), Vicerrectoría de Investigación y Postgrado Universidad Católica del Maule, Talca, Chile
- Laboratorio de Bioinformática y Química Computacional, Departamento de Medicina Traslacional, Facultad de Medicina, Universidad Católica del Maule, Talca, Chile
| | - Melissa Alegría-Arcos
- Núcleo de Investigación en Data Science, Facultad de Ingeniería y Negocios, Universidad de las Américas, Santiago, Chile
| | - Karen Castillo
- Centro Interdisciplinario de Neurociencia de Valparaíso, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso, Chile
- Centro de Investigación de Estudios Avanzados del Maule (CIEAM), Vicerrectoría de Investigación y Postgrado Universidad Católica del Maule, Talca, Chile
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14
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Ruma YN, Bu G, Gonen T. MicroED structure of the C11 cysteine protease Clostripain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.04.574240. [PMID: 38260293 PMCID: PMC10802345 DOI: 10.1101/2024.01.04.574240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Clostripain secreted from Clostridium histolyticum is the founding member of the C11 family of Clan CD cysteine peptidases, which is an important group of peptidases secreted by numerous bacteria. Clostripain is an arginine specific endopeptidase. Because of its efficacy as a cysteine peptidase, it is widely used in laboratory settings. Despite its importance the structure of clostripain remains unsolved. Here we describe the first structure of an active form of C. histolyticum Clostripain determined at 3.6 Å resolution using microcrystal electron diffraction (MicroED). The structure was determined from a single nanocrystal after focused ion beam milling. The structure of Clostripain shows a typical Clan CD α/β/α sandwich architecture and the Cys231/His176 catalytic dyad in the active site. It has a large electronegative substrate binding pocket showing its ability to accommodate large and diverse substrates. A loop in the heavy chain formed between residues 452 to 457 is potentially important for substrate binding. In conclusion, this result demonstrates the importance of MicroED to determine the unknown structure of macromolecules such as Clostripain, which can be further used as a platform to study substrate binding and design of potential inhibitors against this class of peptidases.
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15
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Fernández FJ, Querol-García J, Navas-Yuste S, Martino F, Vega MC. X-Ray Crystallography for Macromolecular Complexes. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 3234:125-140. [PMID: 38507204 DOI: 10.1007/978-3-031-52193-5_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
X-ray crystallography has for most of the last century been the standard technique to determine the high-resolution structure of biological macromolecules, including multi-subunit protein-protein and protein-nucleic acids as large as the ribosome and viruses. As such, the successful application of X-ray crystallography to many biological problems revolutionized biology and biomedicine by solving the structures of small molecules and vitamins, peptides and proteins, DNA and RNA molecules, and many complexes-affording a detailed knowledge of the structures that clarified biological and chemical mechanisms, conformational changes, interactions, catalysis and the biological processes underlying DNA replication, translation, and protein synthesis. Now reaching well into the first quarter of the twenty-first century, X-ray crystallography shares the structural biology stage with cryo-electron microscopy and other innovative structure determination methods, as relevant and central to our understanding of biological function and structure as ever. In this chapter, we provide an overview of modern X-ray crystallography and how it interfaces with other mainstream structural biology techniques, with an emphasis on macromolecular complexes.
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Affiliation(s)
| | | | - Sergio Navas-Yuste
- Centro de Investigaciones Biológicas Margarita Salas (CIB-CSIC), Madrid, Spain
| | - Fabrizio Martino
- Structural Biology Research Centre, Human Technopole, Milan, Italy
| | - M Cristina Vega
- Centro de Investigaciones Biológicas Margarita Salas (CIB-CSIC), Madrid, Spain.
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16
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Daoud H, Pulleri Vadhyar S, Nikbin E, Lu C, Miller RJD. Synthesis technique and electron beam damage study of nanometer-thin single-crystalline thymine. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2024; 11:014302. [PMID: 38304443 PMCID: PMC10834065 DOI: 10.1063/4.0000221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 01/11/2024] [Indexed: 02/03/2024]
Abstract
Samples suitable for electron diffraction studies must satisfy certain characteristics such as having a thickness in the range of 10-100 nm. We report, to our knowledge, the first successful synthesis technique of nanometer-thin sheets of single-crystalline thymine suitable for electron diffraction and spectroscopy studies. This development provides a well-defined system to explore issues related to UV photochemistry of DNA and high intrinsic stability essential to maintaining integrity of genetic information. The crystals are grown using the evaporation technique, and the nanometer-thin sheets are obtained via microtoming. The sample is characterized via x-ray diffraction and is subsequently studied using electron diffraction via a transmission electron microscope. Thymine is found to be more radiation resistant than similar molecular moieties (e.g., carbamazepine) by a factor of 5. This raises interesting questions about the role of the fast relaxation processes of electron scattering-induced excited states, extending the concept of radiation hardening beyond photoexcited states. The high stability of thymine in particular opens the door for further studies of these ultrafast relaxation processes giving rise to the high stability of DNA to UV radiation.
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Affiliation(s)
- Hazem Daoud
- Department of Physics, University of Toronto, Toronto, Ontario M5S 1A7, Canada
| | | | - Ehsan Nikbin
- Department of Materials Science and Engineering, University of Toronto, Toronto, Ontario M5S 1A7, Canada
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17
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Nannenga BL. A new approach for serial electron diffraction data collection. IUCRJ 2024; 11:7-8. [PMID: 38131390 PMCID: PMC10833380 DOI: 10.1107/s2052252523010953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
This commentary describes a novel method for serial electron diffraction data collection in electron crystallography, utilizing a scanning transmission electron microscope to rapidly obtain patterns with low radiation dose. This approach, demonstrated with zeolite samples, has the potential to provide highly automated and rapid structures from nanocrystalline materials.
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Affiliation(s)
- Brent L. Nannenga
- Chemical Engineering, School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ 85287, USA
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ USA
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18
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Bai XC, Gonen T, Gronenborn AM, Perrakis A, Thorn A, Yang J. Challenges and opportunities in macromolecular structure determination. Nat Rev Mol Cell Biol 2024; 25:7-12. [PMID: 37848590 DOI: 10.1038/s41580-023-00659-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/22/2023] [Indexed: 10/19/2023]
Affiliation(s)
- Xiao-Chen Bai
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| | - Tamir Gonen
- Department of Biological Chemistry, University of California Los Angeles, Los Angeles, CA, USA.
- Howard Hughes Medical Institute, University of California Los Angeles, Los Angeles, CA, USA.
- Department of Physiology, University of California Los Angeles, Los Angeles, CA, USA.
| | | | - Anastassis Perrakis
- Oncode Institute, Division of Biochemistry, Netherlands Cancer Institute, Amsterdam, Netherlands.
| | - Andrea Thorn
- Institute for Nanostructure and Solid State Physics, University of Hamburg, Hamburg, Germany.
| | - Jianyi Yang
- MOE Frontiers Science Center for Nonlinear Expectations, Research Center for Mathematics and Interdisciplinary Sciences, Shandong University, Qingdao, China.
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19
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Plana-Ruiz S, Gómez-Pérez A, Budayova-Spano M, Foley DL, Portillo-Serra J, Rauch E, Grivas E, Housset D, Das PP, Taheri ML, Nicolopoulos S, Ling WL. High-Resolution Electron Diffraction of Hydrated Protein Crystals at Room Temperature. ACS NANO 2023; 17:24802-24813. [PMID: 37890869 PMCID: PMC10753879 DOI: 10.1021/acsnano.3c05378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 10/13/2023] [Accepted: 10/16/2023] [Indexed: 10/29/2023]
Abstract
Structural characterization is crucial to understanding protein function. Compared with X-ray diffraction methods, electron crystallography can be performed on nanometer-sized crystals and can provide additional information from the resulting Coulomb potential map. Whereas electron crystallography has successfully resolved three-dimensional structures of vitrified protein crystals, its widespread use as a structural biology tool has been limited. One main reason is the fragility of such crystals. Protein crystals can be easily damaged by mechanical stress, change in temperature, or buffer conditions as well as by electron irradiation. This work demonstrates a methodology to preserve these nanocrystals in their natural environment at room temperature for electron diffraction experiments as an alternative to existing cryogenic techniques. Lysozyme crystals in their crystallization solution are hermetically sealed via graphene-coated grids, and their radiation damage is minimized by employing a low-dose data collection strategy in combination with a hybrid-pixel direct electron detector. Diffraction patterns with reflections of up to 3 Å are obtained and successfully indexed using a template-matching algorithm. These results demonstrate the feasibility of in situ protein electron diffraction. The method described will also be applicable to structural studies of hydrated nanocrystals important in many research and technological developments.
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Affiliation(s)
- Sergi Plana-Ruiz
- NanoMegas
SRPL, Rue Emile Claus
49, Brussels 1050, Belgium
- Servei
de Recursos Científics i Tècnics, Universitat Rovira i Virgili, Tarragona 43007, Catalonia, Spain
| | | | | | - Daniel L. Foley
- Department
of Materials Science and Engineering, Johns
Hopkins University, Baltimore, Maryland 21218, United States
| | | | - Edgar Rauch
- SIMAP,
Grenoble INP, Université Grenoble Alpes, CNRS, F-38000 Grenoble, France
| | | | | | | | - Mitra L. Taheri
- Department
of Materials Science and Engineering, Johns
Hopkins University, Baltimore, Maryland 21218, United States
| | | | - Wai Li Ling
- Université
Grenoble Alpes, CEA, CNRS, IBS, F-38000 Grenoble, France
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20
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Danelius E, Bu G, Wieske LHE, Gonen T. MicroED as a Powerful Tool for Structure Determination of Macrocyclic Drug Compounds Directly from Their Powder Formulations. ACS Chem Biol 2023; 18:2582-2589. [PMID: 37944119 PMCID: PMC10728894 DOI: 10.1021/acschembio.3c00611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 10/16/2023] [Accepted: 10/26/2023] [Indexed: 11/12/2023]
Abstract
Macrocycles are important drug leads with many advantages including the ability to target flat and featureless binding sites as well as to act as molecular chameleons and thereby reach intracellular targets. However, due to their complex structures and inherent flexibility, macrocycles are difficult to study structurally, and there are limited structural data available. Herein, we use the cryo-EM method MicroED to determine the novel atomic structures of several macrocycles that have previously resisted structural determination. We show that structures of similar complexity can now be obtained rapidly from nanograms of material and that different conformations of flexible compounds can be derived from the same experiment. These results will have an impact on contemporary drug discovery as well as natural product exploration.
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Affiliation(s)
- Emma Danelius
- Howard
Hughes Medical Institute, University of
California Los Angeles, Los Angeles, California 90095, United States
- Department
of Biological Chemistry, University of California
Los Angeles, 615 Charles E.Young Drive South, Los Angeles, California 90095, United States
| | - Guanhong Bu
- Department
of Biological Chemistry, University of California
Los Angeles, 615 Charles E.Young Drive South, Los Angeles, California 90095, United States
| | - Lianne H. E. Wieske
- Department
of Chemistry − BMC, Uppsala University, Husargatan 3, 75237 Uppsala, Sweden
| | - Tamir Gonen
- Howard
Hughes Medical Institute, University of
California Los Angeles, Los Angeles, California 90095, United States
- Department
of Biological Chemistry, University of California
Los Angeles, 615 Charles E.Young Drive South, Los Angeles, California 90095, United States
- Department
of Physiology, University of California
Los Angeles, 615 Charles E. Young Drive South, Los Angeles, California 90095, United States
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21
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Waterman DG, Frisina N, Owen CD, Winter G, Nunes P. A standard data format for 3DED/MicroED. Structure 2023; 31:1510-1517.e1. [PMID: 37536337 DOI: 10.1016/j.str.2023.07.004] [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: 04/26/2023] [Revised: 06/01/2023] [Accepted: 07/10/2023] [Indexed: 08/05/2023]
Abstract
Electron diffraction from three dimensional crystals, as a technique for solving molecular structures, is rapidly increasing in popularity. The development of methodology and software has borrowed, to great effect, from macromolecular X-ray crystallography. However, standardization lags behind the development of the technique, and practitioners are forced to work with inadequate data formats that are unable to capture a full description of their experiments. This creates obstacles that are increasingly difficult to overcome as experiments become ever faster and the need for data autoprocessing becomes more pressing. We present a data format standard based on best practice from macromolecular crystallography and demonstrate how the adoption of this standard enabled autoprocessing of datasets collected with a high-throughput detector system.
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Affiliation(s)
- David Geoffrey Waterman
- STFC, Rutherford Appleton Laboratory, Didcot OX11 0FA, UK; Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot OX11 0FA, UK.
| | - Noemi Frisina
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - C David Owen
- Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot OX11 0FA, UK; Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - Graeme Winter
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - Pedro Nunes
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
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22
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Haymaker A, Bardin AA, Gonen T, Martynowycz MW, Nannenga BL. Structure determination of a DNA crystal by MicroED. Structure 2023; 31:1499-1503.e2. [PMID: 37541248 PMCID: PMC10805983 DOI: 10.1016/j.str.2023.07.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 06/21/2023] [Accepted: 07/11/2023] [Indexed: 08/06/2023]
Abstract
Microcrystal electron diffraction (MicroED) is a powerful tool for determining high-resolution structures of microcrystals from a diverse array of biomolecular, chemical, and material samples. In this study, we apply MicroED to DNA crystals, which have not been previously analyzed using this technique. We utilized the d(CGCGCG)2 DNA duplex as a model sample and employed cryo-FIB milling to create thin lamella for diffraction data collection. The MicroED data collection and subsequent processing resulted in a 1.10 Å resolution structure of the d(CGCGCG)2 DNA, demonstrating the successful application of cryo-FIB milling and MicroED to the investigation of nucleic acid crystals.
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Affiliation(s)
- Alison Haymaker
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA; School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ, USA
| | - Andrey A Bardin
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA; School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ, USA
| | - Tamir Gonen
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA; Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Michael W Martynowycz
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA.
| | - Brent L Nannenga
- Biodesign Center for Applied Structural Discovery, Biodesign Institute, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA; School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ, USA.
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23
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Pelz PM, Griffin SM, Stonemeyer S, Popple D, DeVyldere H, Ercius P, Zettl A, Scott MC, Ophus C. Solving complex nanostructures with ptychographic atomic electron tomography. Nat Commun 2023; 14:7906. [PMID: 38036516 PMCID: PMC10689721 DOI: 10.1038/s41467-023-43634-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Accepted: 11/15/2023] [Indexed: 12/02/2023] Open
Abstract
Transmission electron microscopy (TEM) is essential for determining atomic scale structures in structural biology and materials science. In structural biology, three-dimensional structures of proteins are routinely determined from thousands of identical particles using phase-contrast TEM. In materials science, three-dimensional atomic structures of complex nanomaterials have been determined using atomic electron tomography (AET). However, neither of these methods can determine the three-dimensional atomic structure of heterogeneous nanomaterials containing light elements. Here, we perform ptychographic electron tomography from 34.5 million diffraction patterns to reconstruct an atomic resolution tilt series of a double wall-carbon nanotube (DW-CNT) encapsulating a complex ZrTe sandwich structure. Class averaging the resulting tilt series images and subpixel localization of the atomic peaks reveals a Zr11Te50 structure containing a previously unobserved ZrTe2 phase in the core. The experimental realization of atomic resolution ptychographic electron tomography will allow for the structural determination of a wide range of beam-sensitive nanomaterials containing light elements.
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Affiliation(s)
- Philipp M Pelz
- Institute of Micro- and Nanostructure Research (IMN) & Center for Nanoanalysis and Electron Microscopy (CENEM), Friedrich Alexander-Universität Erlangen-Nürnberg, IZNF, 91058, Erlangen, Germany.
- Department of Materials Science and Engineering, University of California Berkeley, Berkeley, CA, 94720, USA.
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
| | - Sinéad M Griffin
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Scott Stonemeyer
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Kavli Energy NanoSciences Institute at the University of California at Berkeley, Berkeley, CA, 94720, USA
- Department of Chemistry, University of California at Berkeley, Berkeley, CA, 94720, USA
- Department of Physics, University of California at Berkeley, Berkeley, CA, 94720, USA
| | - Derek Popple
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Kavli Energy NanoSciences Institute at the University of California at Berkeley, Berkeley, CA, 94720, USA
- Department of Chemistry, University of California at Berkeley, Berkeley, CA, 94720, USA
- Department of Physics, University of California at Berkeley, Berkeley, CA, 94720, USA
| | - Hannah DeVyldere
- Department of Materials Science and Engineering, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Peter Ercius
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Alex Zettl
- Department of Materials Science and Engineering, University of California Berkeley, Berkeley, CA, 94720, USA
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Kavli Energy NanoSciences Institute at the University of California at Berkeley, Berkeley, CA, 94720, USA
- Department of Physics, University of California at Berkeley, Berkeley, CA, 94720, USA
| | - Mary C Scott
- Department of Materials Science and Engineering, University of California Berkeley, Berkeley, CA, 94720, USA
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Colin Ophus
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
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24
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Bu G, Danelius E, Wieske L, Gonen T. Polymorphic Structure Determination of the Macrocyclic Drug Paritaprevir by MicroED. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.09.556999. [PMID: 37781611 PMCID: PMC10541134 DOI: 10.1101/2023.09.09.556999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
Paritaprevir is an orally bioavailable, macrocyclic drug used for treating chronic Hepatitis C virus infection. Its structures had been elusive to the public until recently when one of the crystal forms was solved by MicroED. In this work, we report the MicroED structures of two distinct polymorphic crystal forms of paritaprevir from the same experiment. The different polymorphs show conformational changes in the macrocyclic core, as well as the cyclopropylsulfonamide and methylpyrazinamide substituents. Molecular docking shows that one of the conformations fits well into the active site pocket of the NS3/4A serine protease target, and can interact with the pocket and catalytic triad via hydrophobic interactions and hydrogen bonds. These results can provide further insight for optimization of the binding of acylsulfonamide inhibitors to the NS3/4A serine protease. In addition, this also demonstrate the opportunity of deriving different polymorphs and distinct macrocycle conformations from the same experiments using MicroED.
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Affiliation(s)
- G Bu
- Department of Biological Chemistry, University of California Los Angeles, 615 Charles E.Young Drive South, Los Angeles, CA 90095, USA
| | - E Danelius
- Department of Biological Chemistry, University of California Los Angeles, 615 Charles E.Young Drive South, Los Angeles, CA 90095, USA
- Howard Hughes Medical Institute, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - L.H Wieske
- Department of Chemistry – BMC, Uppsala University, Husargatan 3, 75237 Uppsala, Sweden
| | - T Gonen
- Department of Biological Chemistry, University of California Los Angeles, 615 Charles E.Young Drive South, Los Angeles, CA 90095, USA
- Howard Hughes Medical Institute, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Physiology, University of California Los Angeles, 615 Charles E. Young Drive South, Los Angeles, CA 90095, USA
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25
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Cordova M, Moutzouri P, Nilsson Lill SO, Cousen A, Kearns M, Norberg ST, Svensk Ankarberg A, McCabe J, Pinon AC, Schantz S, Emsley L. Atomic-level structure determination of amorphous molecular solids by NMR. Nat Commun 2023; 14:5138. [PMID: 37612269 PMCID: PMC10447443 DOI: 10.1038/s41467-023-40853-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 08/10/2023] [Indexed: 08/25/2023] Open
Abstract
Structure determination of amorphous materials remains challenging, owing to the disorder inherent to these materials. Nuclear magnetic resonance (NMR) powder crystallography is a powerful method to determine the structure of molecular solids, but disorder leads to a high degree of overlap between measured signals, and prevents the unambiguous identification of a single modeled periodic structure as representative of the whole material. Here, we determine the atomic-level ensemble structure of the amorphous form of the drug AZD4625 by combining solid-state NMR experiments with molecular dynamics (MD) simulations and machine-learned chemical shifts. By considering the combined shifts of all 1H and 13C atomic sites in the molecule, we determine the structure of the amorphous form by identifying an ensemble of local molecular environments that are in agreement with experiment. We then extract and analyze preferred conformations and intermolecular interactions in the amorphous sample in terms of the stabilization of the amorphous form of the drug.
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Affiliation(s)
- Manuel Cordova
- Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
- National Centre for Computational Design and Discovery of Novel Materials MARVEL, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Pinelopi Moutzouri
- Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Sten O Nilsson Lill
- Data Science & Modelling, Pharmaceutical Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Alexander Cousen
- Early Chemical Development, Pharmaceutical Sciences, R&D, AstraZeneca, Macclesfield, UK
| | - Martin Kearns
- Early Product Development and Manufacturing, Pharmaceutical Sciences, R&D, AstraZeneca, Macclesfield, UK
| | - Stefan T Norberg
- Oral Product Development, Pharmaceutical Technology & Development, Operations, AstraZeneca, Gothenburg, Sweden
| | - Anna Svensk Ankarberg
- Oral Product Development, Pharmaceutical Technology & Development, Operations, AstraZeneca, Gothenburg, Sweden
| | - James McCabe
- Early Product Development and Manufacturing, Pharmaceutical Sciences, R&D, AstraZeneca, Macclesfield, UK
| | - Arthur C Pinon
- Swedish NMR Center, Department of Chemistry and Molecular Biology, University of Gothenburg, 41390, Gothenburg, Sweden
| | - Staffan Schantz
- Oral Product Development, Pharmaceutical Technology & Development, Operations, AstraZeneca, Gothenburg, Sweden.
| | - Lyndon Emsley
- Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland.
- National Centre for Computational Design and Discovery of Novel Materials MARVEL, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
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26
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Abstract
A survey of protein databases indicates that the majority of enzymes exist in oligomeric forms, with about half of those found in the UniProt database being homodimeric. Understanding why many enzymes are in their dimeric form is imperative. Recent developments in experimental and computational techniques have allowed for a deeper comprehension of the cooperative interactions between the subunits of dimeric enzymes. This review aims to succinctly summarize these recent advancements by providing an overview of experimental and theoretical methods, as well as an understanding of cooperativity in substrate binding and the molecular mechanisms of cooperative catalysis within homodimeric enzymes. Focus is set upon the beneficial effects of dimerization and cooperative catalysis. These advancements not only provide essential case studies and theoretical support for comprehending dimeric enzyme catalysis but also serve as a foundation for designing highly efficient catalysts, such as dimeric organic catalysts. Moreover, these developments have significant implications for drug design, as exemplified by Paxlovid, which was designed for the homodimeric main protease of SARS-CoV-2.
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Affiliation(s)
- Ke-Wei Chen
- Lab of Computional Chemistry and Drug Design, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Tian-Yu Sun
- Shenzhen Bay Laboratory, Shenzhen 518132, China
| | - Yun-Dong Wu
- Lab of Computional Chemistry and Drug Design, State Key Laboratory of Chemical Oncogenomics, Peking University Shenzhen Graduate School, Shenzhen 518055, China
- Shenzhen Bay Laboratory, Shenzhen 518132, China
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27
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Danelius E, Bu G, Wieske H, Gonen T. MicroED as a powerful tool for structure determination of macrocyclic drug compounds directly from their powder formulations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.31.551405. [PMID: 37577574 PMCID: PMC10418104 DOI: 10.1101/2023.07.31.551405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Macrocycles are important drug leads with many advantages including the ability to target flat and featureless binding sites as well as act as molecular chameleons and thereby reach intracellular targets. However, due to their complex structures and inherent flexibility, macrocycles are difficult to study structurally and there are limited structural data available. Herein, we use the cryo-EM method MicroED to determine the novel atomic structures of several macrocycles which have previously resisted structural determination. We show that structures of similar complexity can now be obtained rapidly from nanograms of material, and that different conformations of flexible compounds can be derived from the same experiment. These results will have impact on contemporary drug discovery as well as natural product exploration.
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Affiliation(s)
- E Danelius
- Howard Hughes Medical Institute, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Biological Chemistry, University of California Los Angeles, 615 Charles E.Young Drive South, Los Angeles, CA 90095, USA
| | - G Bu
- Department of Biological Chemistry, University of California Los Angeles, 615 Charles E.Young Drive South, Los Angeles, CA 90095, USA
| | - H Wieske
- Department of Chemistry – BMC, Uppsala University, Husargatan 3, 75237 Uppsala, Sweden
| | - T Gonen
- Howard Hughes Medical Institute, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Biological Chemistry, University of California Los Angeles, 615 Charles E.Young Drive South, Los Angeles, CA 90095, USA
- Department of Physiology, University of California Los Angeles, 615 Charles E. Young Drive South, Los Angeles, CA 90095, USA
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28
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Shiriaeva A, Martynowycz MW, Nicolas WJ, Cherezov V, Gonen T. MicroED structure of the human vasopressin 1B receptor. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.05.547888. [PMID: 37461729 PMCID: PMC10350018 DOI: 10.1101/2023.07.05.547888] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/24/2023]
Abstract
The small size and flexibility of G protein-coupled receptors (GPCRs) have long posed a significant challenge to determining their structures for research and therapeutic applications. Single particle cryogenic electron microscopy (cryoEM) is often out of reach due to the small size of the receptor without a signaling partner. Crystallization of GPCRs in lipidic cubic phase (LCP) often results in crystals that may be too small and difficult to analyze using X-ray microcrystallography at synchrotron sources or even serial femtosecond crystallography at X-ray free electron lasers. Here, we determine the previously unknown structure of the human vasopressin 1B receptor (V1BR) using microcrystal electron diffraction (MicroED). To achieve this, we grew V1BR microcrystals in LCP and transferred the material directly onto electron microscopy grids. The protein was labeled with a fluorescent dye prior to crystallization to locate the microcrystals using cryogenic fluorescence microscopy, and then the surrounding material was removed using a plasma-focused ion beam to thin the sample to a thickness amenable to MicroED. MicroED data from 14 crystalline lamellae were used to determine the 3.2 Å structure of the receptor in the crystallographic space group P 1. These results demonstrate the use of MicroED to determine previously unknown GPCR structures that, despite significant effort, were not tractable by other methods.
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Affiliation(s)
- Anna Shiriaeva
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, CA 90095
| | - Michael W. Martynowycz
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, CA 90095
- Howard Hughes Medical Institute, University of California, Los Angeles, CA 90095
| | - William J. Nicolas
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, CA 90095
- Howard Hughes Medical Institute, University of California, Los Angeles, CA 90095
| | - Vadim Cherezov
- Bridge Institute, University of Southern California Michelson Center for Convergent Biosciences, University of Southern California, Los Angeles, CA 90007
- Department of Chemistry, University of Southern California, Los Angeles, CA 90007
| | - Tamir Gonen
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, CA 90095
- Howard Hughes Medical Institute, University of California, Los Angeles, CA 90095
- Department of Physiology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095
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29
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Haymaker A, Bardin AA, Gonen T, Martynowycz MW, Nannenga BL. Structure determination of a DNA crystal by MicroED. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.25.538338. [PMID: 37163108 PMCID: PMC10168392 DOI: 10.1101/2023.04.25.538338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Microcrystal electron diffraction (MicroED) is a powerful tool for determining high-resolution structures of microcrystals from a diverse array of biomolecular, chemical, and material samples. In this study, we apply MicroED to DNA crystals, which have not been previously analyzed using this technique. We utilized the d(CGCGCG) 2 DNA duplex as a model sample and employed cryo-FIB milling to create thin lamella for diffraction data collection. The MicroED data collection and subsequent processing resulted in a 1.10 Å resolution structure of the d(CGCGCG) 2 DNA, demonstrating the successful application of cryo-FIB milling and MicroED to the investigation of nucleic acid crystals.
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30
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Sadybekov AV, Katritch V. Computational approaches streamlining drug discovery. Nature 2023; 616:673-685. [PMID: 37100941 DOI: 10.1038/s41586-023-05905-z] [Citation(s) in RCA: 151] [Impact Index Per Article: 151.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 03/01/2023] [Indexed: 04/28/2023]
Abstract
Computer-aided drug discovery has been around for decades, although the past few years have seen a tectonic shift towards embracing computational technologies in both academia and pharma. This shift is largely defined by the flood of data on ligand properties and binding to therapeutic targets and their 3D structures, abundant computing capacities and the advent of on-demand virtual libraries of drug-like small molecules in their billions. Taking full advantage of these resources requires fast computational methods for effective ligand screening. This includes structure-based virtual screening of gigascale chemical spaces, further facilitated by fast iterative screening approaches. Highly synergistic are developments in deep learning predictions of ligand properties and target activities in lieu of receptor structure. Here we review recent advances in ligand discovery technologies, their potential for reshaping the whole process of drug discovery and development, as well as the challenges they encounter. We also discuss how the rapid identification of highly diverse, potent, target-selective and drug-like ligands to protein targets can democratize the drug discovery process, presenting new opportunities for the cost-effective development of safer and more effective small-molecule treatments.
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Affiliation(s)
- Anastasiia V Sadybekov
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
- Center for New Technologies in Drug Discovery and Development, Bridge Institute, Michelson Center for Convergent Biosciences, University of Southern California, Los Angeles, CA, USA
| | - Vsevolod Katritch
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA.
- Center for New Technologies in Drug Discovery and Development, Bridge Institute, Michelson Center for Convergent Biosciences, University of Southern California, Los Angeles, CA, USA.
- Department of Chemistry, University of Southern California, Los Angeles, CA, USA.
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31
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Gillman C, Nicolas WJ, Martynowycz MW, Gonen T. Design and implementation of suspended drop crystallization. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.28.534639. [PMID: 37034794 PMCID: PMC10081258 DOI: 10.1101/2023.03.28.534639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
We have developed a novel crystal growth method known as suspended drop crystallization. Unlike traditional methods, this technique involves mixing protein and precipitant directly on an electron microscopy grid without any additional support layers. The grid is then suspended within a crystallization chamber which we designed, allowing for vapor diffusion to occur from both sides of the drop. A UV transparent window above and below the grid enables the monitoring of crystal growth via light, UV, or fluorescence microscopy. Once crystals have formed, the grid can be removed and utilized for x-ray crystallography or microcrystal electron diffraction (MicroED) directly without having to manipulate the crystals. To demonstrate the efficacy of this method, we grew crystals of the enzyme proteinase K and determined its structure by MicroED following FIB/SEM milling to render the sample thin enough for cryoEM. Suspended drop crystallization overcomes many of the challenges associated with sample preparation, providing an alternative workflow for crystals embedded in viscous media, sensitive to mechanical stress, and/or suffering from preferred orientation on EM grids.
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Affiliation(s)
- Cody Gillman
- Departments of Biological Chemistry and Physiology, University of California, Los Angeles CA, USA
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - William J. Nicolas
- Departments of Biological Chemistry and Physiology, University of California, Los Angeles CA, USA
- Howard Hughes Medical Institute, University of California, Los Angeles CA, USA
| | - Michael W. Martynowycz
- Departments of Biological Chemistry and Physiology, University of California, Los Angeles CA, USA
| | - Tamir Gonen
- Departments of Biological Chemistry and Physiology, University of California, Los Angeles CA, USA
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Howard Hughes Medical Institute, University of California, Los Angeles CA, USA
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32
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Danelius E, Porter NJ, Unge J, Arnold FH, Gonen T. MicroED Structure of a Protoglobin Reactive Carbene Intermediate. J Am Chem Soc 2023; 145:7159-7165. [PMID: 36948184 PMCID: PMC10080679 DOI: 10.1021/jacs.2c12004] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2023]
Abstract
Microcrystal electron diffraction (MicroED) is an emerging technique that has shown great potential for describing new chemical and biological molecular structures. Several important structures of small molecules, natural products, and peptides have been determined using ab initio methods. However, only a couple of novel protein structures have thus far been derived by MicroED. Taking advantage of recent technological advances, including higher acceleration voltage and using a low-noise detector in counting mode, we have determined the first structure of an Aeropyrum pernix protoglobin (ApePgb) variant by MicroED using an AlphaFold2 model for phasing. The structure revealed that mutations introduced during directed evolution enhance carbene transfer activity by reorienting an α helix of ApePgb into a dynamic loop, making the catalytic active site more readily accessible. After exposing the tiny crystals to the substrate, we also trapped the reactive iron-carbenoid intermediate involved in this engineered ApePgb's new-to-nature activity, a challenging carbene transfer from a diazirine via a putative metallo-carbene. The bound structure discloses how an enlarged active site pocket stabilizes the carbene bound to the heme iron and, presumably, the transition state for the formation of this key intermediate. This work demonstrates that improved MicroED technology and the advancement in protein structure prediction now enable investigation of structures that was previously beyond reach.
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Affiliation(s)
- Emma Danelius
- Department of Biological Chemistry, University of California, Los Angeles, 615 Charles E. Young Drive South, Los Angeles, California 90095, United States
- Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Nicholas J Porter
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, MC 210-41, Pasadena, California 91125, United States
| | - Johan Unge
- Department of Biological Chemistry, University of California, Los Angeles, 615 Charles E. Young Drive South, Los Angeles, California 90095, United States
| | - Frances H Arnold
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, MC 210-41, Pasadena, California 91125, United States
| | - Tamir Gonen
- Department of Biological Chemistry, University of California, Los Angeles, 615 Charles E. Young Drive South, Los Angeles, California 90095, United States
- Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
- Department of Physiology, University of California, Los Angeles, 615 Charles E. Young Drive South, Los Angeles, California 90095, United States
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33
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Martynowycz MW, Shiriaeva A, Clabbers MTB, Nicolas WJ, Weaver SJ, Hattne J, Gonen T. A robust approach for MicroED sample preparation of lipidic cubic phase embedded membrane protein crystals. Nat Commun 2023; 14:1086. [PMID: 36841804 PMCID: PMC9968316 DOI: 10.1038/s41467-023-36733-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 02/15/2023] [Indexed: 02/26/2023] Open
Abstract
Crystallizing G protein-coupled receptors (GPCRs) in lipidic cubic phase (LCP) often yields crystals suited for the cryogenic electron microscopy (cryoEM) method microcrystal electron diffraction (MicroED). However, sample preparation is challenging. Embedded crystals cannot be targeted topologically. Here, we use an integrated fluorescence light microscope (iFLM) inside of a focused ion beam and scanning electron microscope (FIB-SEM) to identify fluorescently labeled GPCR crystals. Crystals are targeted using the iFLM and LCP is milled using a plasma focused ion beam (pFIB). The optimal ion source for preparing biological lamellae is identified using standard crystals of proteinase K. Lamellae prepared using either argon or xenon produced the highest quality data and structures. MicroED data are collected from the milled lamellae and the structures are determined. This study outlines a robust approach to identify and mill membrane protein crystals for MicroED and demonstrates plasma ion-beam milling is a powerful tool for preparing biological lamellae.
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Affiliation(s)
- Michael W Martynowycz
- Howard Hughes Medical Institute, University of California, Los Angeles, CA, 90095, USA.,Department of Biological Chemistry, University of California, Los Angeles, CA, 90095, USA
| | - Anna Shiriaeva
- Howard Hughes Medical Institute, University of California, Los Angeles, CA, 90095, USA.,Department of Biological Chemistry, University of California, Los Angeles, CA, 90095, USA
| | - Max T B Clabbers
- Howard Hughes Medical Institute, University of California, Los Angeles, CA, 90095, USA.,Department of Biological Chemistry, University of California, Los Angeles, CA, 90095, USA
| | - William J Nicolas
- Howard Hughes Medical Institute, University of California, Los Angeles, CA, 90095, USA.,Department of Biological Chemistry, University of California, Los Angeles, CA, 90095, USA
| | - Sara J Weaver
- Howard Hughes Medical Institute, University of California, Los Angeles, CA, 90095, USA.,Department of Biological Chemistry, University of California, Los Angeles, CA, 90095, USA
| | - Johan Hattne
- Howard Hughes Medical Institute, University of California, Los Angeles, CA, 90095, USA.,Department of Biological Chemistry, University of California, Los Angeles, CA, 90095, USA
| | - Tamir Gonen
- Howard Hughes Medical Institute, University of California, Los Angeles, CA, 90095, USA. .,Department of Biological Chemistry, University of California, Los Angeles, CA, 90095, USA. .,Department of Physiology, University of California, Los Angeles, CA, 90095, USA.
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34
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Drevon TR, Waterman DG, Krissinel E. Dynamical diffraction of high-energy electrons by light-atom structures: a multiple forward scattering interpretation. Acta Crystallogr A Found Adv 2023; 79:180-191. [PMID: 36862043 PMCID: PMC9979941 DOI: 10.1107/s2053273322011779] [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: 03/21/2022] [Accepted: 12/08/2022] [Indexed: 02/11/2023] Open
Abstract
Because of the strong electron-atom interaction, the kinematic theory of diffraction cannot be used to describe the scattering of electrons by an assembly of atoms due to the strong dynamical diffraction that needs to be taken into account. In this paper, the scattering of high-energy electrons by a regular array of light atoms is solved exactly by applying the T-matrix formalism to the corresponding Schrödinger's equation in spherical coordinates. The independent atom model is used, where each atom is represented by a sphere with an effective constant potential. The validity of the forward scattering approximation and the phase grating approximation, assumed by the popular multislice method, is discussed, and an alternative interpretation of multiple scattering is proposed and compared with existing interpretations.
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Affiliation(s)
- Tarik R. Drevon
- STFC, Rutherford Appleton Laboratory, Didcot, OX11 0FA, United Kingdom,CCP4, Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, United Kingdom
| | - David G. Waterman
- STFC, Rutherford Appleton Laboratory, Didcot, OX11 0FA, United Kingdom,CCP4, Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, United Kingdom
| | - Eugene Krissinel
- STFC, Rutherford Appleton Laboratory, Didcot, OX11 0FA, United Kingdom,CCP4, Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, United Kingdom,Correspondence e-mail:
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35
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Biswas S, Banerjee S, Shlain MA, Bardin AA, Ulijn RV, Nannenga BL, Rappe AM, Braunschweig AB. Photomechanochemical control over stereoselectivity in the [2 + 2] photodimerization of acenaphthylene. Faraday Discuss 2023; 241:266-277. [PMID: 36134559 PMCID: PMC10088556 DOI: 10.1039/d2fd00122e] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Tuning solubility and mechanical activation alters the stereoselectivity of the [2 + 2] photochemical cycloaddition of acenaphthylene. Photomechanochemical conditions produce the syn cyclobutane, whereas the solid-state reaction in the absence of mechanical activation provides the anti. When the photochemical dimerization occurs in a solubilizing organic solvent, there is no selectivity. Dimerization in H2O, in which acenaphthylene is insoluble, provides the anti product. DFT calculations reveal that insoluble and solid-state reactions proceed via a covalently bonded excimer, which drives anti selectivity. Alternatively, the noncovalently bound syn conformer is more mechanosusceptible than the anti, meaning it experiences greater destabilization, thereby producing the syn product under photomechanochemical conditions. Cyclobutanes are important components of biologically active natural products and organic materials, and we demonstrate stereoselective methods for obtaining syn or anti cyclobutanes under mild conditions and without organic solvents. With this work, we validate photomechanochemistry as a viable new direction for the preparation of complex organic scaffolds.
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Affiliation(s)
- Sankarsan Biswas
- Advanced Science Research Center, Graduate Center, City University of New York, 85 St. Nicholas Terrace, New York, NY, 10031, USA.
- Department of Chemistry, Hunter College, 695 Park Avenue, New York, NY 10065, USA
- PhD Program in Chemistry, Graduate Center, City University of New York, 365 5th Avenue, New York, NY 10016, USA
| | - Sayan Banerjee
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, USA.
| | - Milan A Shlain
- Advanced Science Research Center, Graduate Center, City University of New York, 85 St. Nicholas Terrace, New York, NY, 10031, USA.
- Department of Chemistry, Hunter College, 695 Park Avenue, New York, NY 10065, USA
- PhD Program in Chemistry, Graduate Center, City University of New York, 365 5th Avenue, New York, NY 10016, USA
| | - Andrey A Bardin
- Chemical Engineering, School for Engineering of Matter, Transport, and Energy, Arizona State University, Tempe, AZ 85287, USA
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Rein V Ulijn
- Advanced Science Research Center, Graduate Center, City University of New York, 85 St. Nicholas Terrace, New York, NY, 10031, USA.
- Department of Chemistry, Hunter College, 695 Park Avenue, New York, NY 10065, USA
- PhD Program in Chemistry, Graduate Center, City University of New York, 365 5th Avenue, New York, NY 10016, USA
- PhD Program in Biochemistry, Graduate Center, City University of New York, 365 5th Avenue, New York, NY 10016, USA
| | - Brent L Nannenga
- Chemical Engineering, School for Engineering of Matter, Transport, and Energy, Arizona State University, Tempe, AZ 85287, USA
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA
| | - Andrew M Rappe
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323, USA.
| | - Adam B Braunschweig
- Advanced Science Research Center, Graduate Center, City University of New York, 85 St. Nicholas Terrace, New York, NY, 10031, USA.
- Department of Chemistry, Hunter College, 695 Park Avenue, New York, NY 10065, USA
- PhD Program in Chemistry, Graduate Center, City University of New York, 365 5th Avenue, New York, NY 10016, USA
- PhD Program in Biochemistry, Graduate Center, City University of New York, 365 5th Avenue, New York, NY 10016, USA
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36
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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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37
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Shi D, Huang R. Analysis and comparison of electron radiation damage assessments in Cryo-EM by single particle analysis and micro-crystal electron diffraction. Front Mol Biosci 2022; 9:988928. [PMID: 36275612 PMCID: PMC9585622 DOI: 10.3389/fmolb.2022.988928] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 08/05/2022] [Indexed: 11/25/2022] Open
Abstract
Electron radiation damage to macromolecules is an inevitable resolution limit factor in all major structural determination applications using cryo-electron microscopy (cryo-EM). Single particle analysis (SPA) and micro-crystal electron diffraction (MicroED) have been employed to assess radiation damage with a variety of protein complexes. Although radiation induced sidechain density loss and resolution decay were observed by both methods, the minimum dose of electron irradiation reducing high-resolution limit reported by SPA is more than ten folds higher than measured by MicroED using the conventional dose concept, and there is a gap between the attained resolutions assessed by these two methods. We compared and analyzed these two approaches side-by-side in detail from several aspects to identify some crucial determinants and to explain this discrepancy. Probability of a high energy electron being inelastically scattered by a macromolecule is proportional to number of layers of the molecules in its transmission path. As a result, the same electron dose could induce much more site-specific damage to macromolecules in 3D protein crystal than single particle samples. Major differences in data collection and processing scheme are the key factors to different levels of sensitivity to radiation damage at high resolution between the two methods. High resolution electron diffraction in MicroED dataset is very sensitive to global damage to 3D protein crystals with low dose accumulation, and its intensity attenuation rates at atomic resolution shell could be applied for estimating ratio of damaged and total selected single particles for SPA. More in-depth systematically radiation damage assessments using SPA and MicroED will benefit all applications of cryo-EM, especially cellular structure analysis by tomography.
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Affiliation(s)
- Dan Shi
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, United States
- *Correspondence: Dan Shi,
| | - Rick Huang
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, United States
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38
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Burley SK, Berman HM, Duarte JM, Feng Z, Flatt JW, Hudson BP, Lowe R, Peisach E, Piehl DW, Rose Y, Sali A, Sekharan M, Shao C, Vallat B, Voigt M, Westbrook JD, Young JY, Zardecki C. Protein Data Bank: A Comprehensive Review of 3D Structure Holdings and Worldwide Utilization by Researchers, Educators, and Students. Biomolecules 2022; 12:1425. [PMID: 36291635 PMCID: PMC9599165 DOI: 10.3390/biom12101425] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/23/2022] [Accepted: 09/26/2022] [Indexed: 11/18/2022] Open
Abstract
The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), funded by the United States National Science Foundation, National Institutes of Health, and Department of Energy, supports structural biologists and Protein Data Bank (PDB) data users around the world. The RCSB PDB, a founding member of the Worldwide Protein Data Bank (wwPDB) partnership, serves as the US data center for the global PDB archive housing experimentally-determined three-dimensional (3D) structure data for biological macromolecules. As the wwPDB-designated Archive Keeper, RCSB PDB is also responsible for the security of PDB data and weekly update of the archive. RCSB PDB serves tens of thousands of data depositors (using macromolecular crystallography, nuclear magnetic resonance spectroscopy, electron microscopy, and micro-electron diffraction) annually working on all permanently inhabited continents. RCSB PDB makes PDB data available from its research-focused web portal at no charge and without usage restrictions to many millions of PDB data consumers around the globe. It also provides educators, students, and the general public with an introduction to the PDB and related training materials through its outreach and education-focused web portal. This review article describes growth of the PDB, examines evolution of experimental methods for structure determination viewed through the lens of the PDB archive, and provides a detailed accounting of PDB archival holdings and their utilization by researchers, educators, and students worldwide.
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Affiliation(s)
- Stephen K. Burley
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California San Diego, La Jolla, CA 92093, USA
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Helen M. Berman
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Jose M. Duarte
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California San Diego, La Jolla, CA 92093, USA
| | - Zukang Feng
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Justin W. Flatt
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Brian P. Hudson
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Robert Lowe
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Ezra Peisach
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Dennis W. Piehl
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Yana Rose
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California San Diego, La Jolla, CA 92093, USA
| | - Andrej Sali
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA 94158, USA
| | - Monica Sekharan
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Chenghua Shao
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Brinda Vallat
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA
| | - Maria Voigt
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - John D. Westbrook
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA
| | - Jasmine Y. Young
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Christine Zardecki
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
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39
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Li X, Craven TW, Levine PM. Cyclic Peptide Screening Methods for Preclinical Drug Discovery. J Med Chem 2022; 65:11913-11926. [PMID: 36074956 DOI: 10.1021/acs.jmedchem.2c01077] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cyclic peptides are among the most diverse architectures for current drug discovery efforts. Their size, stability, and ease of synthesis provide attractive scaffolds to engage and modulate some of the most challenging targets, including protein-protein interactions and those considered to be "undruggable". With a variety of sophisticated screening technologies to produce libraries of cyclic peptides, including phage display, mRNA display, split intein circular ligation of peptides, and in silico screening, a new era of cyclic peptide drug discovery is at the forefront of modern medicine. In this perspective, we begin by discussing cyclic peptides approved for clinical use in the past two decades. Particular focus is placed around synthetic chemistries to generate de novo libraries of cyclic peptides and novel methods to screen them. The perspective culminates with future prospects for generating cyclic peptides as viable therapeutic options and discusses the advantages and disadvantages currently being faced with bringing them to market.
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Affiliation(s)
- Xinting Li
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, Washington 98195, United States
| | - Timothy W Craven
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, Washington 98195, United States
| | - Paul M Levine
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, Washington 98195, United States
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40
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De Bolòs E, Martínez-Abadía M, Hernández-Culebras F, Haymaker A, Swain K, Strutyński K, Weare BL, Castells-Gil J, Padial NM, Martí-Gastaldo C, Khlobystov AN, Saeki A, Melle-Franco M, Nannenga BL, Mateo-Alonso A. A Crystalline 1D Dynamic Covalent Polymer. J Am Chem Soc 2022; 144:15443-15450. [PMID: 35993775 PMCID: PMC9446889 DOI: 10.1021/jacs.2c06446] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The synthesis of crystalline one-dimensional polymers provides a fundamental understanding about the structure-property relationship in polymeric materials and allows the preparation of materials with enhanced thermal, mechanical, and conducting properties. However, the synthesis of crystalline one-dimensional polymers remains a challenge because polymers tend to adopt amorphous or semicrystalline phases. Herein, we report the synthesis of a crystalline one-dimensional polymer in solution by dynamic covalent chemistry. The structure of the polymer has been unambiguously confirmed by microcrystal electron diffraction that together with charge transport studies and theoretical calculations show how the π-stacked chains of the polymer generate optimal channels for charge transport.
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Affiliation(s)
- Elisabet De Bolòs
- POLYMAT, University of the Basque Country UPV/EHU, Avenida de Tolosa 72, Donostia-San Sebastián 20018, Spain
| | - Marta Martínez-Abadía
- POLYMAT, University of the Basque Country UPV/EHU, Avenida de Tolosa 72, Donostia-San Sebastián 20018, Spain
| | - Félix Hernández-Culebras
- POLYMAT, University of the Basque Country UPV/EHU, Avenida de Tolosa 72, Donostia-San Sebastián 20018, Spain
| | - Alison Haymaker
- Chemical Engineering, School for Engineering of Matter, Transport, and Energy, Arizona State University, Tempe, Arizona 85287, United States.,Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States
| | - Kyle Swain
- Chemical Engineering, School for Engineering of Matter, Transport, and Energy, Arizona State University, Tempe, Arizona 85287, United States.,Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States
| | - Karol Strutyński
- CICECO - Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, Aveiro 3810-193, Portugal
| | - Benjamin L Weare
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Javier Castells-Gil
- Instituto de Ciencia Molecular, Universidad de Valencia, Paterna 46980, Spain
| | - Natalia M Padial
- Instituto de Ciencia Molecular, Universidad de Valencia, Paterna 46980, Spain
| | | | - Andrei N Khlobystov
- School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom.,The Nanoscale and Microscale Research Centre, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Akinori Saeki
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
| | - Manuel Melle-Franco
- CICECO - Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, Aveiro 3810-193, Portugal
| | - Brent L Nannenga
- Chemical Engineering, School for Engineering of Matter, Transport, and Energy, Arizona State University, Tempe, Arizona 85287, United States.,Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona 85281, United States
| | - Aurelio Mateo-Alonso
- POLYMAT, University of the Basque Country UPV/EHU, Avenida de Tolosa 72, Donostia-San Sebastián 20018, Spain.,Ikerbasque, Basque Foundation for Science, Bilbao 48009, Spain
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41
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Newman JA, Iuzzolino L, Tan M, Orth P, Bruhn J, Lee AY. From Powders to Single Crystals: A Crystallographer's Toolbox for Small-Molecule Structure Determination. Mol Pharm 2022; 19:2133-2141. [PMID: 35576503 PMCID: PMC10152450 DOI: 10.1021/acs.molpharmaceut.2c00020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Although the crystal structures of small-molecule compounds are often determined from single-crystal X-ray diffraction (scXRD), recent advances in three-dimensional electron diffraction (3DED) and crystal structure prediction (CSP) methods promise to expand the structure elucidation toolbox available to the crystallographer. Herein, a comparative assessment of scXRD, 3DED, and CSP in combination with powder X-ray diffraction is carried out on two former drug candidate compounds and a multicomponent crystal of a key building block in the synthesis of gefapixant citrate.
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Affiliation(s)
- Justin A. Newman
- Department
of Analytical Research and Development, Merck & Co., Inc., 126 East Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Luca Iuzzolino
- Department
of Computational and Structural Chemistry, Merck & Co., Inc., Rahway, 126 East Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Melissa Tan
- Department
of Analytical Research and Development, Merck & Co., Inc., 126 East Lincoln Avenue, Rahway, New Jersey 07065, United States
| | - Peter Orth
- Department
of Computational and Structural Chemistry, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Jessica Bruhn
- Nanoimaging
Services, San Diego, California 92121, United States
| | - Alfred Y. Lee
- Department
of Analytical Research and Development, Merck & Co., Inc., 126 East Lincoln Avenue, Rahway, New Jersey 07065, United States
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42
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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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43
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Martynowycz M, Gonen T. Unlocking the potential of MICROCRYSTAL ELECTRON DIFFRACTION. PHYSICS TODAY 2022; 75:38-42. [PMID: 36969383 PMCID: PMC10035054 DOI: 10.1063/pt.3.5019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Atoms stick together in different ways to make the molecules that compose everything we touch and see. Our bodies are made of cells. Cells, in turn, are made of lipids, proteins, nucleic acids, metabolites, and water. Every one of those molecules is made from the same handful of atoms. But although the components are the same, the molecules differ in how many atoms they have and how those atoms are arranged in space.
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44
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Laurents DV. AlphaFold 2 and NMR Spectroscopy: Partners to Understand Protein Structure, Dynamics and Function. Front Mol Biosci 2022; 9:906437. [PMID: 35655760 PMCID: PMC9152297 DOI: 10.3389/fmolb.2022.906437] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 04/25/2022] [Indexed: 11/29/2022] Open
Abstract
The artificial intelligence program AlphaFold 2 is revolutionizing the field of protein structure determination as it accurately predicts the 3D structure of two thirds of the human proteome. Its predictions can be used directly as structural models or indirectly as aids for experimental structure determination using X-ray crystallography, CryoEM or NMR spectroscopy. Nevertheless, AlphaFold 2 can neither afford insight into how proteins fold, nor can it determine protein stability or dynamics. Rare folds or minor alternative conformations are also not predicted by AlphaFold 2 and the program does not forecast the impact of post translational modifications, mutations or ligand binding. The remaining third of human proteome which is poorly predicted largely corresponds to intrinsically disordered regions of proteins. Key to regulation and signaling networks, these disordered regions often form biomolecular condensates or amyloids. Fortunately, the limitations of AlphaFold 2 are largely complemented by NMR spectroscopy. This experimental approach provides information on protein folding and dynamics as well as biomolecular condensates and amyloids and their modulation by experimental conditions, small molecules, post translational modifications, mutations, flanking sequence, interactions with other proteins, RNA and virus. Together, NMR spectroscopy and AlphaFold 2 can collaborate to advance our comprehension of proteins.
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45
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Wang B, Bruhn JF, Weldeab A, Wilson TS, McGilvray PT, Mashore M, Song Q, Scapin G, Lin Y. Absolute configuration determination of pharmaceutical crystalline powders by MicroED via chiral salt formation. Chem Commun (Camb) 2022; 58:4711-4714. [PMID: 35293405 PMCID: PMC9004345 DOI: 10.1039/d2cc00221c] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 03/03/2022] [Indexed: 11/21/2022]
Abstract
Microcrystal electron diffraction (MicroED) has established its complementary role alongside X-ray diffraction in crystal structure elucidation. Unfortunately, kinematical refinement of MicroED data lacks the differentiation power to assign the absolute structure solely based on the measured intensities. Here we report a method for absolute configuration determination via MicroED by employing salt formation with chiral counterions.
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Affiliation(s)
- Bo Wang
- Small Molecule Drug Product Development, Biogen, 115 Broadway, Cambridge, MA 02142, USA.
| | - Jessica F Bruhn
- NanoImaging Services, 4940 Carroll Canyon Road, San Diego, CA 92121, USA
| | - Asmerom Weldeab
- Small Molecule Drug Product Development, Biogen, 115 Broadway, Cambridge, MA 02142, USA.
| | - Timothy S Wilson
- NanoImaging Services, 4940 Carroll Canyon Road, San Diego, CA 92121, USA
| | - Philip T McGilvray
- NanoImaging Services, 4940 Carroll Canyon Road, San Diego, CA 92121, USA
| | - Michael Mashore
- NanoImaging Services, 4940 Carroll Canyon Road, San Diego, CA 92121, USA
| | - Qiong Song
- NanoImaging Services, 4940 Carroll Canyon Road, San Diego, CA 92121, USA
| | - Giovanna Scapin
- NanoImaging Services, 4940 Carroll Canyon Road, San Diego, CA 92121, USA
| | - Yiqing Lin
- Small Molecule Drug Product Development, Biogen, 115 Broadway, Cambridge, MA 02142, USA.
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Zhang J, Kong W. Electron diffraction as a structure tool for charged and neutral nanoclusters formed in superfluid helium droplets. Phys Chem Chem Phys 2022; 24:6349-6362. [PMID: 35257134 PMCID: PMC10508180 DOI: 10.1039/d2cp00048b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This perspective presents the current status and future directions in using electron diffraction to determine the structures of clusters formed in superfluid helium droplets. The details of the experimental setup and data treatment procedures are explained, and several examples are illustrated. The ease of forming atomic and molecular clusters has been recognized since the invention of superfluid helium droplet beams. To resolve atomic structures from clusters formed in droplets, substantial efforts have been devoted to minimizing the contribution of helium to diffraction signals. With active background subtraction, we have obtained structures from clusters containing a few to more than 10 monomers, with and without heavy atoms to assist with the diffraction intensity, for both neutral and ionic species. From fittings of the diffraction profiles using model structures, we have observed that some small clusters adopt the structures of the corresponding solid sample, even for dimers such as iodine and pyrene, while others require trimers or tetramers to reach the structural motif of bulk solids, and smaller clusters such as CS2 dimers adopt gas phase structures. Cationic clusters of argon clusters contain an Ar3+ core, while pyrene dimers demonstrate a change in the intermolecular distance, from 3.5 Å for neutral dimers to 3.0 Å for cations. Future improvements in reducing the background of helium, and in expanding the information content of electron diffraction such as detection of charge distributions, are also discussed.
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Affiliation(s)
- Jie Zhang
- Department of Chemistry, Oregon State University, Corvallis, OR 97331, USA.
| | - Wei Kong
- Department of Chemistry, Oregon State University, Corvallis, OR 97331, USA.
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47
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Studying membrane proteins with MicroED. Biochem Soc Trans 2022; 50:231-239. [PMID: 35191473 PMCID: PMC9022970 DOI: 10.1042/bst20210911] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 01/26/2022] [Accepted: 01/28/2022] [Indexed: 12/27/2022]
Abstract
The structural investigation of biological macromolecules is indispensable in understanding the molecular mechanisms underlying diseases. Several structural biology techniques have been introduced to unravel the structural facets of biomolecules. Among these, the electron cryomicroscopy (cryo-EM) method microcrystal electron diffraction (MicroED) has produced atomic resolution structures of important biological and small molecules. Since its inception in 2013, MicroED established a demonstrated ability for solving structures of difficult samples using vanishingly small crystals. However, membrane proteins remain the next big frontier for MicroED. The intrinsic properties of membrane proteins necessitate improved sample handling and imaging techniques to be developed and optimized for MicroED. Here, we summarize the milestones of electron crystallography of two-dimensional crystals leading to MicroED of three-dimensional crystals. Then, we focus on four different membrane protein families and discuss representatives from each family solved by MicroED.
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48
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Ma H, Jia X, Zhang K, Su Z. Cryo-EM advances in RNA structure determination. Signal Transduct Target Ther 2022; 7:58. [PMID: 35197441 PMCID: PMC8864457 DOI: 10.1038/s41392-022-00916-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 01/27/2022] [Accepted: 01/30/2022] [Indexed: 02/08/2023] Open
Abstract
Cryo-electron microscopy (cryo-EM) has emerged as an unprecedented tool to resolve protein structures at atomic resolution. Structural insights of biological samples not accessible by conventional X-ray crystallography and NMR can be explored with cryo-EM because measurements are carried out under near-native crystal-free conditions, and large protein complexes with conformational and compositional heterogeneity are readily resolved. RNA has remained underexplored in cryo-EM, despite its essential role in various biological processes. This review highlights current challenges and recent progress in using cryo-EM single-particle analysis to determine protein-free RNA structures, enabled by improvement in sample preparation and integration of multiple structural and biochemical methods.
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Affiliation(s)
- Haiyun Ma
- The State Key Laboratory of Biotherapy, Department of Geriatrics and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, 610044, China
| | - Xinyu Jia
- The State Key Laboratory of Biotherapy, Department of Geriatrics and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, 610044, China
| | - Kaiming Zhang
- MOE Key Laboratory for Cellular Dynamics and Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Zhaoming Su
- The State Key Laboratory of Biotherapy, Department of Geriatrics and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, 610044, China.
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49
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Chen P, Liu Y, Zhang C, Huang F, Liu L, Sun J. Crystalline Sponge Method by Three-Dimensional Electron Diffraction. Front Mol Biosci 2022; 8:821927. [PMID: 35198600 PMCID: PMC8859408 DOI: 10.3389/fmolb.2021.821927] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 12/22/2021] [Indexed: 11/23/2022] Open
Abstract
The crystalline sponge method has shown to be a novel strategy for the structure determination of noncrystalline, oily, or trace amount of a compound. A target compound was absorbed and oriented orderly in the pregrown porous crystal for x-ray diffraction analysis. However, the diffusion in the micron-sized crystals is rather difficult. Lots of trial-and-error experiments are needed to optimize the guest-soaking process and to improve data quality. Nanocrystals are better in diffusion, yet it could not conduct a single crystal x-ray diffraction (SCXRD) analysis. Three-dimensional electron diffraction (3D-ED) is a powerful diffraction tool for the structure determination of small crystals. In this work, we successfully carried out the crystalline sponge method by 3D-ED technique using {(ZnI2)3-[2,4,6-tris(4-pyridyl)-1,3,5-triazine]2·x(guest)}n (1-Guest) porous complex nanocrystals. On account of the better diffuse ability of nanocrystals, the time needed for solvent exchange and guest soaking protocols are shortened 50-fold faster versus the original protocol. The crystal structure of the crystalline sponge incorporated with three different guests was fully resolved using a merged dataset. The structure model was identical to previously reported ones using x-ray, showing that the accuracy of the 3D-ED was comparable with SCXRD. The refinement results can also give the precise occupancy of the guest molecule soaked in the porous crystal. This work not only provides a new data collection strategy for crystalline sponge method but also demonstrates the potential of 3D-ED techniques to study host-guest interaction by solving the fine structure of porous material.
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Affiliation(s)
- Pohua Chen
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, China
| | - Yang Liu
- ReadCrystal Technology Co., Jiangsu, China
| | | | - Fei Huang
- ReadCrystal Technology Co., Jiangsu, China
| | | | - Junliang Sun
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, China
- *Correspondence: Junliang Sun,
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50
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Lei L, Zhang J, Trejo M, Bradford SD, Kong W. Resolving the interlayer distance of cationic pyrene clusters embedded in superfluid helium droplets using electron diffraction. J Chem Phys 2022; 156:051101. [DOI: 10.1063/5.0080365] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Lei Lei
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97331, USA
| | - Jie Zhang
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97331, USA
| | - Marisol Trejo
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97331, USA
| | - Stephen D. Bradford
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97331, USA
| | - Wei Kong
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97331, USA
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