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Kudryashev M. The big chill: Growth of in situ structural biology with cryo-electron tomography. QRB DISCOVERY 2024; 5:e10. [PMID: 39687233 PMCID: PMC11649376 DOI: 10.1017/qrd.2024.10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2024] [Revised: 08/23/2024] [Accepted: 08/29/2024] [Indexed: 12/18/2024] Open
Abstract
In situ structural biology with cryo-electron tomography (cryo-ET) and subtomogram averaging (StA) is evolving as a major method to understand the structure, function, and interactions of biological molecules in cells in a single experiment. Since its inception, the method has matured with some stellar highlights and with further opportunities to broaden its applications. In this short review, I want to provide a personal perspective on the developments in cryo-ET as I have seen it for the last ~20 years and outline the major steps that led to its success. This perspective highlights cryo-ET with my eyes as a junior researcher and my view on the present and past developments in hardware and software for in situ structural biology with cryo-ET.
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Affiliation(s)
- Mikhail Kudryashev
- In situ Structural Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Institute of Medical Physics and Biophysics, Charite–Universitatsmedizin Berlin, corporate member of Freie Universitat Berlin and Humboldt Universitat zu Berlin, Institute for Medical Physics and Biophysics, Berlin, Germany
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2
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Zheng T, Cai S. Recent technical advances in cellular cryo-electron tomography. Int J Biochem Cell Biol 2024; 175:106648. [PMID: 39181502 DOI: 10.1016/j.biocel.2024.106648] [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: 05/01/2024] [Revised: 08/20/2024] [Accepted: 08/20/2024] [Indexed: 08/27/2024]
Abstract
Understanding the in situ structure, organization, and interactions of macromolecules is essential for elucidating their functions and mechanisms of action. Cellular cryo-electron tomography (cryo-ET) is a cutting-edge technique that reveals in situ molecular-resolution architectures of macromolecules in their lifelike states. It also provides insights into the three-dimensional distribution of macromolecules and their spatial relationships with various subcellular structures. Thus, cellular cryo-ET bridges the gap between structural biology and cell biology. With rapid advancements, this technique achieved substantial improvements in throughput, automation, and resolution. This review presents the fundamental principles and methodologies of cellular cryo-ET, highlighting recent developments in sample preparation, data collection, and image processing. We also discuss emerging trends and potential future directions. As cellular cryo-ET continues to develop, it is set to play an increasingly vital role in structural cell biology.
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Affiliation(s)
- Tianyu Zheng
- Department of Chemical Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China; Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen 518055, China
| | - Shujun Cai
- Department of Chemical Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China; Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen 518055, China.
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3
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Hirano S, Altae-Tran H, Kannan S, Macrae RK, Zhang F. Structural determinants of DNA cleavage by a CRISPR HNH-Cascade system. Mol Cell 2024; 84:3154-3162.e5. [PMID: 39111310 PMCID: PMC11459484 DOI: 10.1016/j.molcel.2024.07.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 07/08/2024] [Accepted: 07/25/2024] [Indexed: 08/25/2024]
Abstract
Canonical prokaryotic type I CRISPR-Cas adaptive immune systems contain a multicomponent effector complex called Cascade, which degrades large stretches of DNA via Cas3 helicase-nuclease activity. Recently, a highly precise subtype I-F1 CRISPR-Cas system (HNH-Cascade) was found that lacks Cas3, the absence of which is compensated for by the insertion of an HNH endonuclease domain in the Cas8 Cascade component. Here, we describe the cryo-EM structure of Selenomonas sp. HNH-Cascade (SsCascade) in complex with target DNA and characterize its mechanism of action. The Cascade scaffold is complemented by the HNH domain, creating a ring-like structure in which the unwound target DNA is precisely cleaved. This structure visualizes a unique hybrid of two extensible biological systems-Cascade, an evolutionary platform for programmable DNA effectors, and an HNH nuclease, an adaptive domain with a spectrum of enzymatic activity.
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Affiliation(s)
- Seiichi Hirano
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA; Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Cambridge, MA 02139, USA
| | - Han Altae-Tran
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA; Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Cambridge, MA 02139, USA
| | - Soumya Kannan
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA; Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Cambridge, MA 02139, USA
| | - Rhiannon K Macrae
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA; Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Cambridge, MA 02139, USA
| | - Feng Zhang
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA; Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Cambridge, MA 02139, USA.
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4
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Son Y, Kenny TC, Khan A, Birsoy K, Hite RK. Structural basis of lipid head group entry to the Kennedy pathway by FLVCR1. Nature 2024; 629:710-716. [PMID: 38693265 PMCID: PMC11188936 DOI: 10.1038/s41586-024-07374-4] [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: 09/28/2023] [Accepted: 04/02/2024] [Indexed: 05/03/2024]
Abstract
Phosphatidylcholine and phosphatidylethanolamine, the two most abundant phospholipids in mammalian cells, are synthesized de novo by the Kennedy pathway from choline and ethanolamine, respectively1-6. Despite the essential roles of these lipids, the mechanisms that enable the cellular uptake of choline and ethanolamine remain unknown. Here we show that the protein encoded by FLVCR1, whose mutation leads to the neurodegenerative syndrome posterior column ataxia and retinitis pigmentosa7-9, transports extracellular choline and ethanolamine into cells for phosphorylation by downstream kinases to initiate the Kennedy pathway. Structures of FLVCR1 in the presence of choline and ethanolamine reveal that both metabolites bind to a common binding site comprising aromatic and polar residues. Despite binding to a common site, FLVCR1 interacts in different ways with the larger quaternary amine of choline in and with the primary amine of ethanolamine. Structure-guided mutagenesis identified residues that are crucial for the transport of ethanolamine, but dispensable for choline transport, enabling functional separation of the entry points into the two branches of the Kennedy pathway. Altogether, these studies reveal how FLVCR1 is a high-affinity metabolite transporter that serves as the common origin for phospholipid biosynthesis by two branches of the Kennedy pathway.
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Affiliation(s)
- Yeeun Son
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- BCMB Allied Program, Weill Cornell Graduate School, New York, NY, USA
| | - Timothy C Kenny
- Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, New York, NY, USA
| | - Artem Khan
- Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, New York, NY, USA
| | - Kıvanç Birsoy
- Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, New York, NY, USA
| | - Richard K Hite
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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5
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Bay Y, Venskutonytė R, Frantsen SM, Thorsen TS, Musgaard M, Frydenvang K, Francotte P, Pirotte B, Biggin PC, Kristensen AS, Boesen T, Pickering DS, Gajhede M, Kastrup JS. Small-molecule positive allosteric modulation of homomeric kainate receptors GluK1-3: development of screening assays and insight into GluK3 structure. FEBS J 2024; 291:1506-1529. [PMID: 38145505 DOI: 10.1111/febs.17046] [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: 07/06/2023] [Revised: 10/20/2023] [Accepted: 12/22/2023] [Indexed: 12/27/2023]
Abstract
The kainate receptors GluK1-3 (glutamate receptor ionotropic, kainate receptors 1-3) belong to the family of ionotropic glutamate receptors and are essential for fast excitatory neurotransmission in the brain, and are associated with neurological and psychiatric diseases. How these receptors can be modulated by small-molecule agents is not well understood, especially for GluK3. We show that the positive allosteric modulator BPAM344 can be used to establish robust calcium-sensitive fluorescence-based assays to test agonists, antagonists, and positive allosteric modulators of GluK1-3. The half-maximal effective concentration (EC50) of BPAM344 for potentiating the response of 100 μm kainate was determined to be 26.3 μm for GluK1, 75.4 μm for GluK2, and 639 μm for GluK3. Domoate was found to be a potent agonist for GluK1 and GluK2, with an EC50 of 0.77 and 1.33 μm, respectively, upon co-application of 150 μm BPAM344. At GluK3, domoate acts as a very weak agonist or antagonist with a half-maximal inhibitory concentration (IC50) of 14.5 μm, in presence of 500 μm BPAM344 and 100 μm kainate for competition binding. Using H523A-mutated GluK3, we determined the first dimeric structure of the ligand-binding domain by X-ray crystallography, allowing location of BPAM344, as well as zinc-, sodium-, and chloride-ion binding sites at the dimer interface. Molecular dynamics simulations support the stability of the ion sites as well as the involvement of Asp761, Asp790, and Glu797 in the binding of zinc ions. Using electron microscopy, we show that, in presence of glutamate and BPAM344, full-length GluK3 adopts a dimer-of-dimers arrangement.
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Affiliation(s)
- Yasmin Bay
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Raminta Venskutonytė
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Stine M Frantsen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Thor S Thorsen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | | | - Karla Frydenvang
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Pierre Francotte
- Department of Medicinal Chemistry, Center for Interdisciplinary Research on Medicines (CIRM), University of Liège, Belgium
| | - Bernard Pirotte
- Department of Medicinal Chemistry, Center for Interdisciplinary Research on Medicines (CIRM), University of Liège, Belgium
| | | | - Anders S Kristensen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Thomas Boesen
- Danish Research Institute of Translational Neuroscience-DANDRITE, Nordic-EMBL Partnership for Molecular Medicine, Department of Molecular Biology and Genetics, Aarhus University, Denmark
| | - Darryl S Pickering
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Michael Gajhede
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Jette S Kastrup
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
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6
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Calise SJ, O’Neill AG, Burrell AL, Dickinson MS, Molfino J, Clarke C, Quispe J, Sokolov D, Buey RM, Kollman JM. Light-sensitive phosphorylation regulates retinal IMPDH1 activity and filament assembly. J Cell Biol 2024; 223:e202310139. [PMID: 38323936 PMCID: PMC10849882 DOI: 10.1083/jcb.202310139] [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: 10/27/2023] [Revised: 01/11/2024] [Accepted: 01/23/2024] [Indexed: 02/08/2024] Open
Abstract
Inosine monophosphate dehydrogenase (IMPDH) is the rate-limiting enzyme in guanosine triphosphate (GTP) synthesis and assembles into filaments in cells, which desensitizes the enzyme to feedback inhibition and boosts nucleotide production. The vertebrate retina expresses two splice variants IMPDH1(546) and IMPDH1(595). In bovine retinas, residue S477 is preferentially phosphorylated in the dark, but the effects on IMPDH1 activity and regulation are unclear. Here, we generated phosphomimetic mutants to investigate structural and functional consequences of S477 phosphorylation. The S477D mutation resensitized both variants to GTP inhibition but only blocked assembly of IMPDH1(595) filaments. Cryo-EM structures of both variants showed that S477D specifically blocks assembly of a high-activity assembly interface, still allowing assembly of low-activity IMPDH1(546) filaments. Finally, we discovered that S477D exerts a dominant-negative effect in cells, preventing endogenous IMPDH filament assembly. By modulating the structure and higher-order assembly of IMPDH, S477 phosphorylation acts as a mechanism for downregulating retinal GTP synthesis in the dark when nucleotide turnover is decreased.
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Affiliation(s)
- S. John Calise
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Audrey G. O’Neill
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Anika L. Burrell
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | | | - Josephine Molfino
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Charlie Clarke
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Joel Quispe
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - David Sokolov
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Rubén M. Buey
- Metabolic Engineering Group, Departamento de Microbiología y Genética, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
| | - Justin M. Kollman
- Department of Biochemistry, University of Washington, Seattle, WA, USA
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7
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Carrascosa JL. Characterization of Complexes and Supramolecular Structures by Electron Microscopy. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 3234:191-205. [PMID: 38507208 DOI: 10.1007/978-3-031-52193-5_13] [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
Recent advancements in cryo-electron microscopy (cryo-TEM) have enabled the determination of structures of macromolecular complexes at near-atomic resolution, establishing it as a pivotal tool in Structural Biology. This high resolution allows for the detection of ligands and substrates under physiological conditions. Enhancements in detectors and imaging devices, like phase plates, improve signal quality, facilitating the reconstruction of even smaller macromolecular complexes. The 100-kDa barrier has been surpassed, presenting new opportunities for pharmacological research and expanding the scope of crystallographic analyses in the pharmaceutical industry. Cryo-TEM produces vast data sets from minimal samples, and refined classification methods can identify different conformational states of macromolecular complexes, offering deeper insights into the functional characteristics of macromolecular systems. Additionally, cryo-TEM is paving the way for time-resolved microscopy, with rapid freezing techniques capturing snapshots of vital structural changes in biological complexes. Finally, in Structural Cell Biology, advanced cryo-TEM, through tomographic procedures, is revealing conformational changes related to the specific subcellular localization of macromolecular systems and their interactions within cells.
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Affiliation(s)
- José L Carrascosa
- Department of Structure of Macromolecules, Centro Nacional de Biotecnología (CNB, CSIC), Madrid, Spain.
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8
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Son Y, Kenny TC, Khan A, Birsoy K, Hite RK. Structural basis of lipid head group entry to the Kennedy pathway by FLVCR1. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.28.560019. [PMID: 37808796 PMCID: PMC10557757 DOI: 10.1101/2023.09.28.560019] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Phosphatidylcholine and phosphatidylethanolamine, the two most abundant phospholipids in mammalian cells, are synthesized de novo by the Kennedy pathway from choline and ethanolamine, respectively1-6. Despite the importance of these lipids, the mechanisms that enable the cellular uptake of choline and ethanolamine remain unknown. Here, we show that FLVCR1, whose mutation leads to the neurodegenerative syndrome PCARP7-9, transports extracellular choline and ethanolamine into cells for phosphorylation by downstream kinases to initiate the Kennedy pathway. Structures of FLVCR1 in the presence of choline and ethanolamine reveal that both metabolites bind to a common binding site comprised of aromatic and polar residues. Despite binding to a common site, the larger quaternary amine of choline interacts differently with FLVCR1 than does the primary amine of ethanolamine. Structure-guided mutagenesis identified residues that are critical for the transport of ethanolamine, while being dispensable for choline transport, enabling functional separation of the entry points into the two branches of the Kennedy pathway. Altogether, these studies reveal how FLCVR1 is a high-affinity metabolite transporter that serves as the common origin for phospholipid biosynthesis by two branches of the Kennedy pathway.
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Affiliation(s)
- Yeeun Son
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- BCMB Allied Program, Weill Cornell Graduate School, New York, NY, USA
| | - Timothy C. Kenny
- Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, New York, NY, USA
| | - Artem Khan
- Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, New York, NY, USA
| | - Kivanç Birsoy
- Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, New York, NY, USA
| | - Richard K. Hite
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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9
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Calise SJ, O’Neill AG, Burrell AL, Dickinson MS, Molfino J, Clarke C, Quispe J, Sokolov D, Buey RM, Kollman JM. Light-sensitive phosphorylation regulates enzyme activity and filament assembly of human IMPDH1 retinal splice variants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.21.558867. [PMID: 37790411 PMCID: PMC10542554 DOI: 10.1101/2023.09.21.558867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Inosine monophosphate dehydrogenase (IMPDH) is the rate-limiting enzyme in de novo guanosine triphosphate (GTP) synthesis and is controlled by feedback inhibition and allosteric regulation. IMPDH assembles into micron-scale filaments in cells, which desensitizes the enzyme to feedback inhibition by GTP and boosts nucleotide production. The vertebrate retina expresses two tissue-specific splice variants IMPDH1(546) and IMPDH1(595). IMPDH1(546) filaments adopt high and low activity conformations, while IMPDH1(595) filaments maintain high activity. In bovine retinas, residue S477 is preferentially phosphorylated in the dark, but the effects on IMPDH1 activity and regulation are unclear. Here, we generated phosphomimetic mutants to investigate structural and functional consequences of phosphorylation in IMPDH1 variants. The S477D mutation re-sensitized both variants to GTP inhibition, but only blocked assembly of IMPDH1(595) filaments and not IMPDH1(546) filaments. Cryo-EM structures of both variants showed that S477D specifically blocks assembly of the high activity assembly interface, still allowing assembly of low activity IMPDH1(546) filaments. Finally, we discovered that S477D exerts a dominant-negative effect in cells, preventing endogenous IMPDH filament assembly. By modulating the structure and higher-order assembly of IMPDH, phosphorylation at S477 acts as a mechanism for downregulating retinal GTP synthesis in the dark, when nucleotide turnover is decreased. Like IMPDH1, many other metabolic enzymes dynamically assemble filamentous polymers that allosterically regulate activity. Our work suggests that posttranslational modifications may be yet another layer of regulatory control to finely tune activity by modulating filament assembly in response to changing metabolic demands.
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Affiliation(s)
- S. John Calise
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Audrey G. O’Neill
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Anika L. Burrell
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | | | - Josephine Molfino
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Charlie Clarke
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Joel Quispe
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - David Sokolov
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Rubén M. Buey
- Metabolic Engineering Group, Departamento de Microbiología y Genética, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
| | - Justin M. Kollman
- Department of Biochemistry, University of Washington, Seattle, WA, USA
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10
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Cleeve P, Dierickx D, Naegele L, Kannachel R, Burne L, Buckley G, Gorelick S, Whisstock JC, de Marco A. OpenFIBSEM: A universal API for FIBSEM control. J Struct Biol 2023; 215:107967. [PMID: 37105276 DOI: 10.1016/j.jsb.2023.107967] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 04/19/2023] [Accepted: 04/20/2023] [Indexed: 04/29/2023]
Abstract
This paper introduces OpenFIBSEM, a universal API to control Focused Ion Beam Scanning Electron Microscopes (FIBSEM). OpenFIBSEM aims to improve the programmability and automation of electron microscopy workflows in structural biology research. The API is designed to be cross-platform, composable, and extendable: allowing users to use any portion of OpenFIBSEM to develop or integrate with other software tools. The package provides core functionality such as imaging, movement, milling, and manipulator control, as well as system calibration, alignment, and image analysis modules. Further, a library of reusable user interface components integrated with napari is provided, ensuring easy and efficient application development. OpenFIBSEM currently supports ThermoFisher and TESCAN hardware, with support for other manufacturers planned. To demonstrate the improved automation capabilities enabled by OpenFIBSEM, several example applications that are compatible with multiple hardware manufacturers are discussed. We argue that OpenFIBSEM provides the foundation for a cross-platform operating system and development ecosystem for FIBSEM systems. The API and applications are open-source and available on GitHub (https://github.com/DeMarcoLab/fibsem).
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Affiliation(s)
- Patrick Cleeve
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, 3800 Clayton, Victoria, Australia
| | - David Dierickx
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, 3800 Clayton, Victoria, Australia
| | - Lucile Naegele
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, 3800 Clayton, Victoria, Australia
| | - Rohit Kannachel
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, 3800 Clayton, Victoria, Australia
| | - Lachlan Burne
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, 3800 Clayton, Victoria, Australia
| | - Genevieve Buckley
- Ramaciotti Centre for Cryo-Electron Microscopy, Monash University, 3800 Clayton, Victoria, Australia
| | - Sergey Gorelick
- Monash Centre for Electron Microscopy, Monash University, 3800 Clayton, Victoria, Australia
| | - James C Whisstock
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, 3800 Clayton, Victoria, Australia; EMBL Australia, Monash University, 3800 Clayton, Victoria, Australia.
| | - Alex de Marco
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, 3800 Clayton, Victoria, Australia.
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11
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Tan ZY, Cai S, Noble AJ, Chen JK, Shi J, Gan L. Heterogeneous non-canonical nucleosomes predominate in yeast cells in situ. eLife 2023; 12:RP87672. [PMID: 37503920 PMCID: PMC10382156 DOI: 10.7554/elife.87672] [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] [Indexed: 07/29/2023] Open
Abstract
Nuclear processes depend on the organization of chromatin, whose basic units are cylinder-shaped complexes called nucleosomes. A subset of mammalian nucleosomes in situ (inside cells) resembles the canonical structure determined in vitro 25 years ago. Nucleosome structure in situ is otherwise poorly understood. Using cryo-electron tomography (cryo-ET) and 3D classification analysis of budding yeast cells, here we find that canonical nucleosomes account for less than 10% of total nucleosomes expected in situ. In a strain in which H2A-GFP is the sole source of histone H2A, class averages that resemble canonical nucleosomes both with and without GFP densities are found ex vivo (in nuclear lysates), but not in situ. These data suggest that the budding yeast intranuclear environment favors multiple non-canonical nucleosome conformations. Using the structural observations here and the results of previous genomics and biochemical studies, we propose a model in which the average budding yeast nucleosome's DNA is partially detached in situ.
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Affiliation(s)
- Zhi Yang Tan
- Department of Biological Sciences and Center for BioImaging Sciences, National University of SingaporeSingaporeSingapore
| | - Shujun Cai
- Department of Biological Sciences and Center for BioImaging Sciences, National University of SingaporeSingaporeSingapore
| | - Alex J Noble
- National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology CenterNew YorkUnited States
| | - Jon K Chen
- Department of Biological Sciences and Center for BioImaging Sciences, National University of SingaporeSingaporeSingapore
| | - Jian Shi
- Department of Biological Sciences and Center for BioImaging Sciences, National University of SingaporeSingaporeSingapore
| | - Lu Gan
- Department of Biological Sciences and Center for BioImaging Sciences, National University of SingaporeSingaporeSingapore
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12
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Abstract
Recent advances in cryo-electron microscopy have marked only the beginning of the potential of this technique. To bring structure into cell biology, the modality of cryo-electron tomography has fast developed into a bona fide in situ structural biology technique where structures are determined in their native environment, the cell. Nearly every step of the cryo-focused ion beam-assisted electron tomography (cryo-FIB-ET) workflow has been improved upon in the past decade, since the first windows were carved into cells, unveiling macromolecular networks in near-native conditions. By bridging structural and cell biology, cryo-FIB-ET is advancing our understanding of structure-function relationships in their native environment and becoming a tool for discovering new biology.
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Affiliation(s)
- Lindsey N Young
- Department of Molecular Biology, University of California, San Diego, La Jolla, California, USA;
| | - Elizabeth Villa
- Department of Molecular Biology, University of California, San Diego, La Jolla, California, USA;
- Howard Hughes Medical Institute, University of California, San Diego, La Jolla, California, USA
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13
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Raimondi A, Ilacqua N, Pellegrini L. Liver inter-organelle membrane contact sites revealed by serial section electron tomography. Methods Cell Biol 2023; 177:101-123. [PMID: 37451764 DOI: 10.1016/bs.mcb.2022.12.021] [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: 02/12/2023]
Abstract
Inter-organelle membrane contact sites (MCSs) are defined as areas of close proximity between the membranes of two organelles (10-80nm). They have been implicated in many physiological processes such as Ca++, lipids or small molecules transfer, organelles biogenesis or dynamic and have an important role in many cellular processes such as apoptosis, autophagy, and signaling. Since the distance and the extent of these contacts are in the nanometer range, high resolution techniques are ideal for imaging these structures. It is for this reason that transmission electron microscopy (TEM) has been considered the gold standard for MCSs visualization and the first technique that described them. However, often TEM analysis is limited to 2D lacking information on the 3D association between the organelles involved in MCSs. To fully describe the complex architecture of MSCs and to unveil their role in cellular physiology a 3D analysis is required. This chapter provides a method for the analysis of MCSs using serial section electron tomography (ssET), a technique able to reconstruct in 3D at nanometer resolution cellular and subcellular structures. By applying this procedure, it was possible to elucidate the role of the contacts between Endoplasmic Reticulum (ER) and other organelles in liver lipid metabolism.
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Affiliation(s)
- Andrea Raimondi
- Experimental Imaging Centre, IRCCS San Raffaele Scientific Institute, Milan, Italy.
| | - Nicolò Ilacqua
- Mitochondria Biology Laboratory, Brain Research Center, Quebec, QC, Canada; Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Laval University, Quebec, QC, Canada
| | - Luca Pellegrini
- Mitochondria Biology Laboratory, Brain Research Center, Quebec, QC, Canada; Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medicine, Laval University, Quebec, QC, Canada; Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada.
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14
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Bepler T, Borst AJ, Bouvette J, Cannone G, Chen S, Cheng A, Cheng A, Fan Q, Grollios F, Gupta H, Gupta M, Humphreys T, Kim PT, Kuang H, Li Y, Noble AJ, Punjani A, Rice WJ, Oscar S Sorzano C, Stagg SM, Strauss J, Yu L, Carragher B, Potter CS. Smart data collection for CryoEM. J Struct Biol 2022; 214:107913. [PMID: 36341954 DOI: 10.1016/j.jsb.2022.107913] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 09/29/2022] [Accepted: 10/23/2022] [Indexed: 11/06/2022]
Abstract
This report provides an overview of the discussions, presentations, and consensus thinking from the Workshop on Smart Data Collection for CryoEM held at the New York Structural Biology Center on April 6-7, 2022. The goal of the workshop was to address next generation data collection strategies that integrate machine learning and real-time processing into the workflow to reduce or eliminate the need for operator intervention.
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Affiliation(s)
| | - Andrew J Borst
- University of Washington, Institute for Protein Design, Seattle, WA, USA
| | - Jonathan Bouvette
- National Institute of Environmental Health Sciences, NIH, Durham, NC, USA
| | - Giuseppe Cannone
- Laboratory for Molecular Biology, Medical Research Council, Cambridge, England
| | - Songye Chen
- California Institute of Technology, Pasadena, CA, USA
| | - Anchi Cheng
- New York Structural Biology Center, New York, NY, USA
| | - Ao Cheng
- Northwestern University, Evanston, IL, USA
| | - Quanfu Fan
- MIT-IBM Watson AI Lab, Cambridge, MA, USA
| | | | - Harshit Gupta
- SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Meghna Gupta
- University of California at San Francisco, San Francisco, CA, USA
| | | | - Paul T Kim
- New York Structural Biology Center, New York, NY, USA
| | - Huihui Kuang
- New York Structural Biology Center, New York, NY, USA
| | - Yilai Li
- University of Michigan, Ann Arbor, MI, USA
| | - Alex J Noble
- New York Structural Biology Center, New York, NY, USA
| | | | - William J Rice
- New York University School of Medicine, New York, NY, USA
| | | | | | - Joshua Strauss
- University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Lingbo Yu
- ThermoFisher Scientific, Eindhoven, The Netherlands
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15
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Harrison JJEK, Passos DO, Bruhn JF, Bauman JD, Tuberty L, DeStefano JJ, Ruiz FX, Lyumkis D, Arnold E. Cryo-EM structure of the HIV-1 Pol polyprotein provides insights into virion maturation. SCIENCE ADVANCES 2022; 8:eabn9874. [PMID: 35857464 PMCID: PMC9258950 DOI: 10.1126/sciadv.abn9874] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 05/20/2022] [Indexed: 06/15/2023]
Abstract
Key proteins of retroviruses and other RNA viruses are translated and subsequently processed from polyprotein precursors by the viral protease (PR). Processing of the HIV Gag-Pol polyprotein yields the HIV structural proteins and enzymes. Structures of the mature enzymes PR, reverse transcriptase (RT), and integrase (IN) aided understanding of catalysis and design of antiretrovirals, but knowledge of the Pol precursor architecture and function before PR cleavage is limited. We developed a system to produce stable HIV-1 Pol and determined its cryo-electron microscopy structure. RT in Pol has a similar arrangement to the mature RT heterodimer, and its dimerization may draw together two PR monomers to activate proteolytic processing. HIV-1 thus may leverage the dimerization interfaces in Pol to regulate assembly and maturation of polyprotein precursors.
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Affiliation(s)
- Jerry Joe E. K. Harrison
- Center for Advanced Biotechnology and Medicine (CABM), Piscataway, NJ, USA
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, USA
- Department of Chemistry, University of Ghana, Legon, Ghana
| | | | - Jessica F. Bruhn
- The Salk Institute for Biological Studies, La Jolla, CA, USA
- NanoImaging Services, San Diego, CA, USA
| | - Joseph D. Bauman
- Center for Advanced Biotechnology and Medicine (CABM), Piscataway, NJ, USA
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, USA
| | - Lynda Tuberty
- Center for Advanced Biotechnology and Medicine (CABM), Piscataway, NJ, USA
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, USA
| | - Jeffrey J. DeStefano
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USA
- Maryland Pathogen Research Institute, University of Maryland, College Park, MD, USA
| | - Francesc Xavier Ruiz
- Center for Advanced Biotechnology and Medicine (CABM), Piscataway, NJ, USA
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, USA
| | - Dmitry Lyumkis
- The Salk Institute for Biological Studies, La Jolla, CA, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Eddy Arnold
- Center for Advanced Biotechnology and Medicine (CABM), Piscataway, NJ, USA
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, USA
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16
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Vallese F, Kim K, Yen LY, Johnston JD, Noble AJ, Calì T, Clarke OB. Architecture of the human erythrocyte ankyrin-1 complex. Nat Struct Mol Biol 2022; 29:706-718. [PMID: 35835865 PMCID: PMC10373098 DOI: 10.1038/s41594-022-00792-w] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 05/24/2022] [Indexed: 12/28/2022]
Abstract
The stability and shape of the erythrocyte membrane is provided by the ankyrin-1 complex, but how it tethers the spectrin-actin cytoskeleton to the lipid bilayer and the nature of its association with the band 3 anion exchanger and the Rhesus glycoproteins remains unknown. Here we present structures of ankyrin-1 complexes purified from human erythrocytes. We reveal the architecture of a core complex of ankyrin-1, the Rhesus proteins RhAG and RhCE, the band 3 anion exchanger, protein 4.2, glycophorin A and glycophorin B. The distinct T-shaped conformation of membrane-bound ankyrin-1 facilitates recognition of RhCE and, unexpectedly, the water channel aquaporin-1. Together, our results uncover the molecular details of ankyrin-1 association with the erythrocyte membrane, and illustrate the mechanism of ankyrin-mediated membrane protein clustering.
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Affiliation(s)
- Francesca Vallese
- Department of Anesthesiology, Columbia University Irving Medical Center, New York, NY, USA.,Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, USA.,Irving Institute for Clinical and Translational Research, Columbia University, New York, NY, USA
| | - Kookjoo Kim
- Department of Anesthesiology, Columbia University Irving Medical Center, New York, NY, USA.,Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, USA.,Irving Institute for Clinical and Translational Research, Columbia University, New York, NY, USA
| | - Laura Y Yen
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, USA
| | - Jake D Johnston
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, USA.,Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Alex J Noble
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Tito Calì
- Department of Biomedical Sciences, University of Padua, Padua, Italy.,Padua Neuroscience Center (PNC), University of Padua, Padua, Italy.,Study Center for Neurodegeneration (CESNE), University of Padua, Padua, Italy
| | - Oliver Biggs Clarke
- Department of Anesthesiology, Columbia University Irving Medical Center, New York, NY, USA. .,Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, USA. .,Irving Institute for Clinical and Translational Research, Columbia University, New York, NY, USA.
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17
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Adeno-Associated Virus Receptor-Binding: Flexible Domains and Alternative Conformations through Cryo-Electron Tomography of Adeno-Associated Virus 2 (AAV2) and AAV5 Complexes. J Virol 2022; 96:e0010622. [PMID: 35674430 PMCID: PMC9278096 DOI: 10.1128/jvi.00106-22] [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] [Indexed: 11/29/2022] Open
Abstract
Recombinant forms of adeno-associated virus (rAAV) are vectors of choice in the development of treatments for a number of genetic dispositions. Greater understanding of AAV’s molecular virology is needed to underpin needed improvements in efficiency and specificity. Recent advances have included identification of a near-universal entry receptor, AAVR, and structures detected by cryo-electron microscopy (EM) single particle analysis (SPA) that revealed, at high resolution, only the domains of AAVR most tightly bound to AAV. Here, cryogenic electron tomography (cryo-ET) is applied to reveal the neighboring domains of the flexible receptor. For AAV5, where the PKD1 domain is bound strongly, PKD2 is seen in three configurations extending away from the virus. AAV2 binds tightly to the PKD2 domain at a distinct site, and cryo-ET now reveals four configurations of PKD1, all different from that seen in AAV5. The AAV2 receptor complex also shows unmodeled features on the inner surface that appear to be an equilibrium alternate configuration. Other AAV structures start near the 5-fold axis, but now β-strand A is the minor conformer and, for the major conformer, partially ordered N termini near the 2-fold axis join the canonical capsid jellyroll fold at the βA-βB turn. The addition of cryo-ET is revealing unappreciated complexity that is likely relevant to viral entry and to the development of improved gene therapy vectors. IMPORTANCE With 150 clinical trials for 30 diseases under way, AAV is a leading gene therapy vector. Immunotoxicity at high doses used to overcome inefficient transduction has occasionally proven fatal and highlighted gaps in fundamental virology. AAV enters cells, interacting through distinct sites with different domains of the AAVR receptor, according to AAV clade. Single domains are resolved in structures by cryogenic electron microscopy. Here, the adjoining domains are revealed by cryo-electron tomography of AAV2 and AAV5 complexes. They are in flexible configurations interacting minimally with AAV, despite measurable dependence of AAV2 transduction on both domains.
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18
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Waffle Method: A general and flexible approach for improving throughput in FIB-milling. Nat Commun 2022; 13:1857. [PMID: 35387991 PMCID: PMC8987090 DOI: 10.1038/s41467-022-29501-3] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 03/17/2022] [Indexed: 12/29/2022] Open
Abstract
Cryo-FIB/SEM combined with cryo-ET has emerged from within the field of cryo-EM as the method for obtaining the highest resolution structural information of complex biological samples in-situ in native and non-native environments. However, challenges remain in conventional cryo-FIB/SEM workflows, including milling thick specimens with vitrification issues, specimens with preferred orientation, low-throughput when milling small and/or low concentration specimens, and specimens that distribute poorly across grid squares. Here we present a general approach called the ‘Waffle Method’ which leverages high-pressure freezing to address these challenges. We illustrate the mitigation of these challenges by applying the Waffle Method and cryo-ET to reveal the macrostructure of the polar tube in microsporidian spores in multiple complementary orientations, which was previously not possible due to preferred orientation. We demonstrate the broadness of the Waffle Method by applying it to three additional cellular samples and a single particle sample using a variety of cryo-FIB-milling hardware, with manual and automated approaches. We also present a unique and critical stress-relief gap designed specifically for waffled lamellae. We propose the Waffle Method as a way to achieve many advantages of cryo-liftout on the specimen grid while avoiding the long, challenging, and technically-demanding process required for cryo-liftout. Here the authors describe the Waffle Method, aimed at increasing the throughput of and solves several challenges present in cryo-FIB/SEM sample preparation for cryo-ET analysis — the highest-resolution method for obtaining 3D views of native biological specimens in-situ.
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19
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Calcraft T, Rosenthal PB. Cryogenic electron microscopy approaches that combine images and tilt series. Microscopy (Oxf) 2022; 71:i15-i22. [PMID: 35275182 PMCID: PMC8855521 DOI: 10.1093/jmicro/dfab053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 11/29/2021] [Accepted: 01/28/2022] [Indexed: 11/12/2022] Open
Abstract
Cryogenic electron microscopy can be widely applied to biological specimens from the molecular to the cellular scale. In single-particle analysis, 3D structures may be obtained in high resolution by averaging 2D images of single particles in random orientations. For pleomorphic specimens, structures may be obtained by recording the tilt series of a single example of the specimen and calculating tomograms. Where many copies of a single structure such as a protein or nucleic acid assembly are present within the tomogram, averaging of the sub-volumes (subtomogram averaging) has been successfully applied. The choice of data collection method for any given specimen may depend on the structural question of interest and is determined by the radiation sensitivity of the specimen. Here, we survey some recent developments on the use of hybrid methods for recording and analysing data from radiation-sensitive biological specimens. These include single-particle reconstruction from 2D images where additional views are recorded at a single tilt angle of the specimen and methods where image tilt series, initially used for tomogram reconstruction, are processed as individual single-particle images. There is a continuum of approaches now available to maximize structural information obtained from the specimen.
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Affiliation(s)
- Thomas Calcraft
- Structural Biology of Cells and Viruses Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
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20
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Burrell AL, Nie C, Said M, Simonet JC, Fernández-Justel D, Johnson MC, Quispe J, Buey RM, Peterson JR, Kollman JM. IMPDH1 retinal variants control filament architecture to tune allosteric regulation. Nat Struct Mol Biol 2022; 29:47-58. [PMID: 35013599 PMCID: PMC9044917 DOI: 10.1038/s41594-021-00706-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 11/23/2021] [Indexed: 01/06/2023]
Abstract
Inosine-5'-monophosphate dehydrogenase (IMPDH), a key regulatory enzyme in purine nucleotide biosynthesis, dynamically assembles filaments in response to changes in metabolic demand. Humans have two isoforms: IMPDH2 filaments reduce sensitivity to feedback inhibition, while IMPDH1 assembly remains uncharacterized. IMPDH1 plays a unique role in retinal metabolism, and point mutants cause blindness. Here, in a series of cryogenic-electron microscopy structures we show that human IMPDH1 assembles polymorphic filaments with different assembly interfaces in extended and compressed states. Retina-specific splice variants introduce structural elements that reduce sensitivity to GTP inhibition, including stabilization of the extended filament form. Finally, we show that IMPDH1 disease mutations fall into two classes: one disrupts GTP regulation and the other has no effect on GTP regulation or filament assembly. These findings provide a foundation for understanding the role of IMPDH1 in retinal function and disease and demonstrate the diverse mechanisms by which metabolic enzyme filaments are allosterically regulated.
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Affiliation(s)
- Anika L Burrell
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Chuankai Nie
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Meerit Said
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Jacqueline C Simonet
- Cancer Epigenetics and Signaling Program, Fox Chase Cancer Center, Philadelphia, PA, USA
- Department of Biology, Arcadia University, Glenside, PA, USA
| | - David Fernández-Justel
- Metabolic Engineering Group, Departamento de Microbiología y Genética, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
| | - Matthew C Johnson
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Department of Structural Biology, Genentech, South San Francisco, CA, USA
| | - Joel Quispe
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Rubén M Buey
- Metabolic Engineering Group, Departamento de Microbiología y Genética, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain
| | - Jeffrey R Peterson
- Cancer Epigenetics and Signaling Program, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Justin M Kollman
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
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21
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Solon AL, Tan Z, Schutt KL, Jepsen L, Haynes SE, Nesvizhskii AI, Sept D, Stumpff J, Ohi R, Cianfrocco MA. Kinesin-binding protein remodels the kinesin motor to prevent microtubule binding. SCIENCE ADVANCES 2021; 7:eabj9812. [PMID: 34797717 PMCID: PMC8604404 DOI: 10.1126/sciadv.abj9812] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 09/29/2021] [Indexed: 05/30/2023]
Abstract
Kinesins are regulated in space and time to ensure activation only in the presence of cargo. Kinesin-binding protein (KIFBP), which is mutated in Goldberg-Shprintzen syndrome, binds to and inhibits the catalytic motor heads of 8 of 45 kinesin superfamily members, but the mechanism remains poorly defined. Here, we used cryo–electron microscopy and cross-linking mass spectrometry to determine high-resolution structures of KIFBP alone and in complex with two mitotic kinesins, revealing structural remodeling of kinesin by KIFBP. We find that KIFBP remodels kinesin motors and blocks microtubule binding (i) via allosteric changes to kinesin and (ii) by sterically blocking access to the microtubule. We identified two regions of KIFBP necessary for kinesin binding and cellular regulation during mitosis. Together, this work further elucidates the molecular mechanism of KIFBP-mediated kinesin inhibition and supports a model in which structural rearrangement of kinesin motor domains by KIFBP abrogates motor protein activity.
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Affiliation(s)
- April L. Solon
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Zhenyu Tan
- Department of Biophysics, University of Michigan, Ann Arbor, MI, USA
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Katherine L. Schutt
- Department of Molecular Physiology and Biophysics, University of Vermont, Burlington, VT, USA
| | - Lauren Jepsen
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Sarah E. Haynes
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Alexey I. Nesvizhskii
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - David Sept
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Jason Stumpff
- Department of Molecular Physiology and Biophysics, University of Vermont, Burlington, VT, USA
| | - Ryoma Ohi
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Michael A. Cianfrocco
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA
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22
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Expression, purification and characterization of human proton-coupled oligopeptide transporter 1 hPEPT1. Protein Expr Purif 2021; 190:105990. [PMID: 34637915 DOI: 10.1016/j.pep.2021.105990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 09/27/2021] [Accepted: 10/05/2021] [Indexed: 11/22/2022]
Abstract
The human peptide transporter hPEPT1 (SLC15A1) is responsible for uptake of dietary di- and tripeptides and a number of drugs from the small intestine by utilizing the proton electrochemical gradient, and hence an important target for peptide-like drug design and drug delivery. hPEPT1 belongs to the ubiquitous major facilitator superfamily that all contain a 12TM core structure, with global conformational changes occurring during the transport cycle. Several bacterial homologues of these transporters have been characterized, providing valuable insight into the transport mechanism of this family. Here we report the overexpression and purification of recombinant hPEPT1 in a detergent-solubilized state. Thermostability profiling of hPEPT1 at different pH values revealed that hPEPT1 is more stable at pH 6 as compared to pH 7 and 8. Micro-scale thermophoresis (MST) confirmed that the purified hPEPT1 was able to bind di- and tripeptides respectively. To assess the in-solution oligomeric state of hPEPT1, negative stain electron microscopy was performed, demonstrating a predominantly monomeric state.
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23
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Wang Z, Zhang Q, Mim C. Coming of Age: Cryo-Electron Tomography as a Versatile Tool to Generate High-Resolution Structures at Cellular/Biological Interfaces. Int J Mol Sci 2021; 22:6177. [PMID: 34201105 PMCID: PMC8228724 DOI: 10.3390/ijms22126177] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 06/01/2021] [Accepted: 06/02/2021] [Indexed: 12/29/2022] Open
Abstract
Over the last few years, cryo electron microscopy has become the most important method in structural biology. While 80% of deposited maps are from single particle analysis, electron tomography has grown to become the second most important method. In particular sub-tomogram averaging has matured as a method, delivering structures between 2 and 5 Å from complexes in cells as well as in vitro complexes. While this resolution range is not standard, novel developments point toward a promising future. Here, we provide a guide for the workflow from sample to structure to gain insight into this emerging field.
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Affiliation(s)
| | | | - Carsten Mim
- Department of Biomedical Engineering and Health Systems, Royal Technical Institute (KTH), Hälsovägen 11C, 141 27 Huddinge, Sweden; (Z.W.); (Q.Z.)
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24
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Cheng A, Negro C, Bruhn JF, Rice WJ, Dallakyan S, Eng ET, Waterman DG, Potter CS, Carragher B. Leginon: New features and applications. Protein Sci 2021; 30:136-150. [PMID: 33030237 PMCID: PMC7737759 DOI: 10.1002/pro.3967] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 09/28/2020] [Accepted: 09/29/2020] [Indexed: 01/21/2023]
Abstract
Leginon is a system for automated data acquisition from a transmission electron microscope. Here we provide an updated summary of the overall Leginon architecture and an update of the current state of the package. We also highlight a few recent developments to provide some concrete examples and use cases.
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Affiliation(s)
- Anchi Cheng
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy CenterNew York Structural Biology CenterNew YorkNew YorkUSA
| | - Carl Negro
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy CenterNew York Structural Biology CenterNew YorkNew YorkUSA
| | | | - William J. Rice
- Cryo‐Electron Microscopy CoreNew York University School of MedicineNew YorkNew YorkUSA
- Department of Cell BiologyNew York University School of MedicineNew YorkNew YorkUSA
| | - Sargis Dallakyan
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy CenterNew York Structural Biology CenterNew YorkNew YorkUSA
| | - Edward T. Eng
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy CenterNew York Structural Biology CenterNew YorkNew YorkUSA
| | - David G. Waterman
- STFCRutherford Appleton LaboratoryDidcotUK
- CCP4, Research Complex at HarwellRutherford Appleton LaboratoryDidcotUK
| | - Clinton S. Potter
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy CenterNew York Structural Biology CenterNew YorkNew YorkUSA
- Department of Biochemistry and Molecular BiophysicsColumbia UniversityNew YorkNew YorkUSA
| | - Bridget Carragher
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy CenterNew York Structural Biology CenterNew YorkNew YorkUSA
- Department of Biochemistry and Molecular BiophysicsColumbia UniversityNew YorkNew YorkUSA
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25
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Vanrompay H, Skorikov A, Bladt E, Béché A, Freitag B, Verbeeck J, Bals S. Fast versus conventional HAADF-STEM tomography of nanoparticles: advantages and challenges. Ultramicroscopy 2020; 221:113191. [PMID: 33321424 DOI: 10.1016/j.ultramic.2020.113191] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 11/30/2020] [Accepted: 12/06/2020] [Indexed: 11/24/2022]
Abstract
HAADF-STEM tomography is a widely used experimental technique for analyzing nanometer-scale structures of a large variety of materials in three dimensions. It is especially useful for studying crystalline nanoparticles, where conventional TEM tomography suffers from diffraction-related artefacts. Unfortunately, the acquisition of a HAADF-STEM tilt series can easily take up one hour or more, depending on the complexity of the experiment. It is therefore challenging to investigate samples that do not withstand long electron beam illumination or to acquire a large number of tilt series during a single TEM experiment. The latter would facilitate obtaining more statistically representative 3D data, and enable performing dynamic in situ 3D characterizations with a finer time resolution. Various HAADF-STEM acquisition strategies have been proposed to accelerate the tomographic acquisition and reduce the required electron dose. These methods include tilting the holder continuously while acquiring a projection "movie" and a hybrid, incremental, methodology which combines the benefits of the conventional and continuous technique. However, until now an experimental evaluation of these techniques has been lacking. In this paper, the different acquisition strategies will be experimentally compared in terms of speed, resolution and electron dose. This evaluation will be performed based on experimental tilt series, acquired for various metallic nanoparticles with different shapes and sizes. We discuss the necessary data processing and provide a general guideline that can be used to determine the most optimal acquisition strategy for specific electron tomography experiments.
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Affiliation(s)
- Hans Vanrompay
- Electron Microscopy for Materials Science (EMAT), University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium; NANOlab Center of Excellence, University of Antwerp, Belgium
| | - Alexander Skorikov
- Electron Microscopy for Materials Science (EMAT), University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium; NANOlab Center of Excellence, University of Antwerp, Belgium
| | - Eva Bladt
- Electron Microscopy for Materials Science (EMAT), University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium; NANOlab Center of Excellence, University of Antwerp, Belgium
| | - Armand Béché
- Electron Microscopy for Materials Science (EMAT), University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium; NANOlab Center of Excellence, University of Antwerp, Belgium
| | - Bert Freitag
- Thermo Fisher Scientific, Achtseweg Noord 5, 5651 GG Eindhoven, The Netherlands
| | - Johan Verbeeck
- Electron Microscopy for Materials Science (EMAT), University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium; NANOlab Center of Excellence, University of Antwerp, Belgium
| | - Sara Bals
- Electron Microscopy for Materials Science (EMAT), University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium; NANOlab Center of Excellence, University of Antwerp, Belgium.
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26
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Basanta B, Chowdhury S, Lander GC, Grotjahn DA. A guided approach for subtomogram averaging of challenging macromolecular assemblies. J Struct Biol X 2020; 4:100041. [PMID: 33319208 PMCID: PMC7724198 DOI: 10.1016/j.yjsbx.2020.100041] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 10/13/2020] [Accepted: 11/18/2020] [Indexed: 11/20/2022] Open
Affiliation(s)
- Benjamin Basanta
- Department of Integrative Structural and Computational Biology, Scripps Research, HZ 175, 10550 N Torrey Pines Rd., La Jolla, CA 92037, United States
| | - Saikat Chowdhury
- Department of Biochemistry and Cell Biology, 144 Center for Molecular Medicine, Stony Brook University, Stony Brook, NY 11794, United States
| | - Gabriel C. Lander
- Department of Integrative Structural and Computational Biology, Scripps Research, HZ 175, 10550 N Torrey Pines Rd., La Jolla, CA 92037, United States
| | - Danielle A. Grotjahn
- Department of Integrative Structural and Computational Biology, Scripps Research, HZ 175, 10550 N Torrey Pines Rd., La Jolla, CA 92037, United States
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27
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Larsen AH, Johansen NT, Gajhede M, Arleth L, Midtgaard SR. Lipid-bound ApoE3 self-assemble into elliptical disc-shaped particles. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1863:183495. [PMID: 33189719 DOI: 10.1016/j.bbamem.2020.183495] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 10/14/2020] [Accepted: 10/26/2020] [Indexed: 11/29/2022]
Abstract
Apolipoproteins are vital to lipid metabolism and cholesterol transport in the human body. Here we present a structural study of the lipid-bound particles formed by ApoE3 in a full-length and a truncated version. The particles are formed with, respectively, POPC and DMPC and investigated by small-angle X-ray scattering and negative stain electron microscopy. We find that lipid-bound ApoE3 particles are elliptical, disc-shaped particles composed of a central lipid bilayer encircled by two amphipathic ApoE3 proteins. We went on to investigate a truncated form of ApoE3 containing only residue 80 to 255 (ApoE380-255), which is the central helical repeat segment of ApoE3. The lipid-bound ApoE380-255 particles are found to have the same morphology as the particles with full-length ApoE3. However, they are larger, and form more heterogeneous discoidal structures with four proteins per particle. This behavior is in contrast to ApoA1 where the highly similar helical repeat domain determines the size and stoichiometry of the formed particles both in the case of full-length and truncated ApoA1. Our data hence points towards different mechanisms for lipid bilayer structural modulation by ApoA1 and ApoE3 due to different roles of the non-repeat segments.
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Affiliation(s)
- Andreas Haahr Larsen
- University of Copenhagen, Niels Bohr Institute, Copenhagen, Denmark; University of Oxford, Department of Biochemistry, Oxford, United Kingdom.
| | | | - Michael Gajhede
- University of Copenhagen, Department of Drug Design and Pharmacology, Copenhagen, Denmark
| | - Lise Arleth
- University of Copenhagen, Niels Bohr Institute, Copenhagen, Denmark.
| | - Søren Roi Midtgaard
- University of Copenhagen, Niels Bohr Institute, Copenhagen, Denmark; Boston University School of Medicine, Department of Physiology and Biophysics, Boston, USA
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28
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Bepler T, Kelley K, Noble AJ, Berger B. Topaz-Denoise: general deep denoising models for cryoEM and cryoET. Nat Commun 2020; 11:5208. [PMID: 33060581 PMCID: PMC7567117 DOI: 10.1038/s41467-020-18952-1] [Citation(s) in RCA: 224] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 09/14/2020] [Indexed: 01/21/2023] Open
Abstract
Cryo-electron microscopy (cryoEM) is becoming the preferred method for resolving protein structures. Low signal-to-noise ratio (SNR) in cryoEM images reduces the confidence and throughput of structure determination during several steps of data processing, resulting in impediments such as missing particle orientations. Denoising cryoEM images can not only improve downstream analysis but also accelerate the time-consuming data collection process by allowing lower electron dose micrographs to be used for analysis. Here, we present Topaz-Denoise, a deep learning method for reliably and rapidly increasing the SNR of cryoEM images and cryoET tomograms. By training on a dataset composed of thousands of micrographs collected across a wide range of imaging conditions, we are able to learn models capturing the complexity of the cryoEM image formation process. The general model we present is able to denoise new datasets without additional training. Denoising with this model improves micrograph interpretability and allows us to solve 3D single particle structures of clustered protocadherin, an elongated particle with previously elusive views. We then show that low dose collection, enabled by Topaz-Denoise, improves downstream analysis in addition to reducing data collection time. We also present a general 3D denoising model for cryoET. Topaz-Denoise and pre-trained general models are now included in Topaz. We expect that Topaz-Denoise will be of broad utility to the cryoEM community for improving micrograph and tomogram interpretability and accelerating analysis.
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Affiliation(s)
- Tristan Bepler
- Computational and Systems Biology, MIT, Cambridge, MA, USA
- Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA, USA
| | - Kotaro Kelley
- National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Alex J Noble
- National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA.
| | - Bonnie Berger
- Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA, USA.
- Department of Mathematics, MIT, Cambridge, MA, USA.
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29
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Rossmann FM, Hug I, Sangermani M, Jenal U, Beeby M. In situ structure of the Caulobacter crescentus flagellar motor and visualization of binding of a CheY-homolog. Mol Microbiol 2020; 114:443-453. [PMID: 32449846 PMCID: PMC7534056 DOI: 10.1111/mmi.14525] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 04/30/2020] [Accepted: 05/04/2020] [Indexed: 12/30/2022]
Abstract
Bacterial flagellar motility is controlled by the binding of CheY proteins to the cytoplasmic switch complex of the flagellar motor, resulting in changes in swimming speed or direction. Despite its importance for motor function, structural information about the interaction between effector proteins and the motor are scarce. To address this gap in knowledge, we used electron cryotomography and subtomogram averaging to visualize such interactions inside Caulobacter crescentus cells. In C. crescentus, several CheY homologs regulate motor function for different aspects of the bacterial lifestyle. We used subtomogram averaging to image binding of the CheY family protein CleD to the cytoplasmic Cring switch complex, the control center of the flagellar motor. This unambiguously confirmed the orientation of the motor switch protein FliM and the binding of a member of the CheY protein family to the outside rim of the C ring. We also uncovered previously unknown structural elaborations of the alphaproteobacterial flagellar motor, including two novel periplasmic ring structures, and the stator ring harboring eleven stator units, adding to our growing catalog of bacterial flagellar diversity.
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Affiliation(s)
| | - Isabelle Hug
- Focal Area of Infection BiologyBiozentrum of the University of BaselBaselSwitzerland
| | - Matteo Sangermani
- Focal Area of Infection BiologyBiozentrum of the University of BaselBaselSwitzerland
| | - Urs Jenal
- Focal Area of Infection BiologyBiozentrum of the University of BaselBaselSwitzerland
| | - Morgan Beeby
- Department of Life SciencesImperial College LondonLondonUK
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30
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An ATP-dependent partner switch links flagellar C-ring assembly with gene expression. Proc Natl Acad Sci U S A 2020; 117:20826-20835. [PMID: 32788349 DOI: 10.1073/pnas.2006470117] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Bacterial flagella differ in their number and spatial arrangement. In many species, the MinD-type ATPase FlhG (also YlxH/FleN) is central to the numerical control of bacterial flagella, and its deletion in polarly flagellated bacteria typically leads to hyperflagellation. The molecular mechanism underlying this numerical control, however, remains enigmatic. Using the model species Shewanella putrefaciens, we show that FlhG links assembly of the flagellar C ring with the action of the master transcriptional regulator FlrA (named FleQ in other species). While FlrA and the flagellar C-ring protein FliM have an overlapping binding site on FlhG, their binding depends on the ATP-dependent dimerization state of FlhG. FliM interacts with FlhG independent of nucleotide binding, while FlrA exclusively interacts with the ATP-dependent FlhG dimer and stimulates FlhG ATPase activity. Our in vivo analysis of FlhG partner switching between FliM and FlrA reveals its mechanism in the numerical restriction of flagella, in which the transcriptional activity of FlrA is down-regulated through a negative feedback loop. Our study demonstrates another level of regulatory complexity underlying the spationumerical regulation of flagellar biogenesis and implies that flagellar assembly transcriptionally regulates the production of more initial building blocks.
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31
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Krintel C, Dorosz J, Larsen AH, Thorsen TS, Venskutonytė R, Mirza O, Gajhede M, Boesen T, Kastrup JS. Binding of a negative allosteric modulator and competitive antagonist can occur simultaneously at the ionotropic glutamate receptor GluA2. FEBS J 2020; 288:995-1007. [PMID: 32543078 DOI: 10.1111/febs.15455] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 05/25/2020] [Accepted: 06/12/2020] [Indexed: 11/26/2022]
Abstract
Ionotropic glutamate receptors are ligand-gated ion channels governing neurotransmission in the central nervous system. Three major types of antagonists are known for the AMPA-type receptor GluA2: competitive, noncompetitive (i.e., negative allosteric modulators; NAMs) used for treatment of epilepsy, and uncompetitive antagonists. We here report a 4.65 Å resolution X-ray structure of GluA2, revealing that four molecules of the competitive antagonist ZK200775 and four molecules of the NAM GYKI53655 are capable of binding at the same time. Using negative stain electron microscopy, we show that GYKI53655 alone or ZK200775/GYKI53655 in combination predominantly results in compact receptor forms. The agonist AMPA provides a mixed population of compact and bulgy shapes of GluA2 not impacted by addition of GYKI53655. Taken together, this suggests that the two different mechanisms of antagonism that lead to channel closure are independent and that the distribution between bulgy and compact receptors primarily depends on the ligand bound in the glutamate binding site. DATABASE: The atomic coordinates and structure factors from the crystal structure determination have been deposited in the Protein Data Bank under accession code https://doi.org/10.2210/pdb6RUQ/pdb. The electron microscopy 3D reconstruction volumes have been deposited in EMDB (EMD-4875: Apo; EMD-4920: ZK200775/GYKI53655; EMD-4921: AMPA compact; EMD-4922: AMPA/GYKI53655 bulgy; EMD-4923: GYKI53655; EMD-4924: AMPA bulgy; EMD-4925: AMPA/GYKI53655 compact).
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Affiliation(s)
- Christian Krintel
- Research Cluster on Molecular Neuroprotection, Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Jerzy Dorosz
- Research Cluster on Molecular Neuroprotection, Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Andreas Haahr Larsen
- Structural Biophysics, X-ray and Neutron Science, The Niels Bohr Institute, University of Copenhagen, Denmark
| | - Thor Seneca Thorsen
- Research Cluster on Molecular Neuroprotection, Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Raminta Venskutonytė
- Research Cluster on Molecular Neuroprotection, Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark.,Department of Experimental Medical Science, Lund University, Lund, 221 00, Sweden
| | - Osman Mirza
- Research Cluster on Molecular Neuroprotection, Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Michael Gajhede
- Research Cluster on Molecular Neuroprotection, Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Thomas Boesen
- Department of Molecular Biology and Genetics, Aarhus University, Denmark
| | - Jette Sandholm Kastrup
- Research Cluster on Molecular Neuroprotection, Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
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Waghwani HK, Uchida M, Fu CY, LaFrance B, Sharma J, McCoy K, Douglas T. Virus-Like Particles (VLPs) as a Platform for Hierarchical Compartmentalization. Biomacromolecules 2020; 21:2060-2072. [PMID: 32319761 DOI: 10.1021/acs.biomac.0c00030] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Hierarchically self-assembled structures are common in biology, but it is often challenging to design and fabricate synthetic analogs. The archetypal cell is defined by hierarchically organized multicompartmentalized structures with boundaries that delineate the interior from exterior environments and is an inspiration for complex functional materials. Here, we have demonstrated an approach to the design and construction of a nested protein cage system that can additionally incorporate the packing of other functional macromolecules and exhibit some of the features of a minimal synthetic cell-like material. We have demonstrated a strategy for controlled co-packaging of subcompartments, ferritin (Fn) cages, together with active cellobiose-hydrolyzing β-glycosidase enzyme macromolecules, CelB, inside the sequestered volume of the bacteriophage P22 capsid. Using controlled in vitro assembly, we were able to modulate the stoichiometry of Fn cages and CelB encapsulated inside the P22 to control the degree of compartmentalization. The co-encapsulated enzyme CelB showed catalytic activity even when packaged at high total macromolecular concentrations comparable to an intracellular environment. This approach could be used as a model to create synthetic protein-based protocells that can confine smaller functionalized proto-organelles and additional macromolecules to support a range of biochemical reactions.
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Affiliation(s)
- Hitesh Kumar Waghwani
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Masaki Uchida
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States.,Department of Chemistry, California State University Fresno, Fresno, California 93740, United States
| | - Chi-Yu Fu
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, United States.,Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, 115, Taiwan
| | - Benjamin LaFrance
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Jhanvi Sharma
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Kimberly McCoy
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Trevor Douglas
- Department of Chemistry, Indiana University, 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
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33
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Neutralizing Antibody Induction by HIV-1 Envelope Glycoprotein SOSIP Trimers on Iron Oxide Nanoparticles May Be Impaired by Mannose Binding Lectin. J Virol 2020; 94:JVI.01883-19. [PMID: 31852794 PMCID: PMC7158715 DOI: 10.1128/jvi.01883-19] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 12/12/2019] [Indexed: 01/23/2023] Open
Abstract
We covalently attached human immunodeficiency virus type 1 (HIV-1) Env SOSIP trimers to iron oxide nanoparticles (IO-NPs) to create a particulate immunogen for neutralizing antibody (NAb) induction. The attached trimers, ∼20 per particle, retained native-like antigenicity, judged by reactivity with NAbs and non-NAbs. Bivalent (BG505 and B41) trimer IO-NPs were made, as were IO-NPs displaying B41 trimers carrying a PADRE T-cell helper epitope (TCHE). We immunized mice with B41 soluble or IO-NP trimers after PADRE peptide priming. After two immunizations, IO-NP presentation and the TCHE tag independently and substantially increased anti-trimer antibody responses, but titer differences waned after two further doses. Notable and unexpected findings were that autologous NAbs to the N289 glycan hole epitope were consistently induced in mice given soluble but not IO-NP trimers. Various recombinant mannose binding lectins (MBLs) and MBLs in sera of both murine and human origin bound to soluble and IO-NP trimers. MBL binding occluded the autologous NAb epitope on the B41 IO-NP trimers, which may contribute to its poor immunogenicity. The exposure of a subset of broadly active NAb epitopes was also impaired by MBL binding, which could have substantial implications for the utility of trimer-bearing nanoparticles in general and perhaps also for soluble Env proteins.IMPORTANCE Recombinant trimeric SOSIP proteins are vaccine components intended to induce neutralizing antibodies (NAbs) that prevent cells from infection by human immunodeficiency virus type 1 (HIV-1). A way to increase the strength of antibody responses to these proteins is to present them on the surface of nanoparticles (NPs). We chemically attached about 20 SOSIP trimers to NPs made of iron oxide (IO). The resulting IO-NP trimers had appropriate properties when we studied them in the laboratory but, unexpectedly, were less able to induce NAbs than nonattached trimers when used to immunize mice. We found that mannose binding lectins, proteins naturally present in the serum of mice and other animals, bound strongly to the soluble and IO-NP trimers, blocking access to antibody epitopes in a way that may impede the development of NAb responses. These findings should influence how trimer-bearing NPs of various designs are made and used.
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34
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Family-wide Structural and Biophysical Analysis of Binding Interactions among Non-clustered δ-Protocadherins. Cell Rep 2020; 30:2655-2671.e7. [PMID: 32101743 PMCID: PMC7082078 DOI: 10.1016/j.celrep.2020.02.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Revised: 11/02/2019] [Accepted: 01/31/2020] [Indexed: 01/21/2023] Open
Abstract
Non-clustered δ1- and δ2-protocadherins, close relatives of clustered protocadherins, function in cell adhesion and motility and play essential roles in neural patterning. To understand the molecular interactions underlying these functions, we used solution biophysics to characterize binding of δ1- and δ2-protocadherins, determined crystal structures of ectodomain complexes from each family, and assessed ectodomain assembly in reconstituted intermembrane junctions by cryoelectron tomography (cryo-ET). Homophilic trans (cell-cell) interactions were preferred for all δ-protocadherins, with additional weaker heterophilic interactions observed exclusively within each subfamily. As expected, δ1- and δ2-protocadherin trans dimers formed through antiparallel EC1-EC4 interfaces, like clustered protocadherins. However, no ectodomain-mediated cis (same-cell) interactions were detectable in solution; consistent with this, cryo-ET of reconstituted junctions revealed dense assemblies lacking the characteristic order observed for clustered protocadherins. Our results define non-clustered protocadherin binding properties and their structural basis, providing a foundation for interpreting their functional roles in neural patterning.
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35
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Johnson MC, Kollman JM. Cryo-EM structures demonstrate human IMPDH2 filament assembly tunes allosteric regulation. eLife 2020; 9:e53243. [PMID: 31999252 PMCID: PMC7018514 DOI: 10.7554/elife.53243] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 01/29/2020] [Indexed: 02/06/2023] Open
Abstract
Inosine monophosphate dehydrogenase (IMPDH) mediates the first committed step in guanine nucleotide biosynthesis and plays important roles in cellular proliferation and the immune response. IMPDH reversibly polymerizes in cells and tissues in response to changes in metabolic demand. Self-assembly of metabolic enzymes is increasingly recognized as a general mechanism for regulating activity, typically by stabilizing specific conformations of an enzyme, but the regulatory role of IMPDH filaments has remained unclear. Here, we report a series of human IMPDH2 cryo-EM structures in both active and inactive conformations. The structures define the mechanism of filament assembly, and reveal how filament-dependent allosteric regulation of IMPDH2 makes the enzyme less sensitive to feedback inhibition, explaining why assembly occurs under physiological conditions that require expansion of guanine nucleotide pools. Tuning sensitivity to an allosteric inhibitor distinguishes IMPDH from other metabolic filaments, and highlights the diversity of regulatory outcomes that can emerge from self-assembly.
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Affiliation(s)
- Matthew C Johnson
- Department of BiochemistryUniversity of WashingtonSeattleUnited States
| | - Justin M Kollman
- Department of BiochemistryUniversity of WashingtonSeattleUnited States
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36
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Ng CT, Gan L. Investigating eukaryotic cells with cryo-ET. Mol Biol Cell 2020; 31:87-100. [PMID: 31935172 PMCID: PMC6960407 DOI: 10.1091/mbc.e18-05-0329] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 11/25/2019] [Accepted: 11/29/2019] [Indexed: 01/06/2023] Open
Abstract
The interior of eukaryotic cells is mysterious. How do the large communities of macromolecular machines interact with each other? How do the structures and positions of these nanoscopic entities respond to new stimuli? Questions like these can now be answered with the help of a method called electron cryotomography (cryo-ET). Cryo-ET will ultimately reveal the inner workings of a cell at the protein, secondary structure, and perhaps even side-chain levels. Combined with genetic or pharmacological perturbation, cryo-ET will allow us to answer previously unimaginable questions, such as how structure, biochemistry, and forces are related in situ. Because it bridges structural biology and cell biology, cryo-ET is indispensable for structural cell biology-the study of the 3-D macromolecular structure of cells. Here we discuss some of the key ideas, strategies, auxiliary techniques, and innovations that an aspiring structural cell biologist will consider when planning to ask bold questions.
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Affiliation(s)
- Cai Tong Ng
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore 117543
| | - Lu Gan
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore 117543
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37
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Kieuvongngam V, Olinares PDB, Palillo A, Oldham ML, Chait BT, Chen J. Structural basis of substrate recognition by a polypeptide processing and secretion transporter. eLife 2020; 9:51492. [PMID: 31934861 PMCID: PMC6959990 DOI: 10.7554/elife.51492] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 12/23/2019] [Indexed: 12/28/2022] Open
Abstract
The peptidase-containing ATP-binding cassette transporters (PCATs) are unique members of the ABC transporter family that proteolytically process and export peptides and proteins. Each PCAT contains two peptidase domains that cleave off the secretion signal, two transmembrane domains forming a translocation pathway, and two nucleotide-binding domains that hydrolyze ATP. Previously the crystal structures of a PCAT from Clostridium thermocellum (PCAT1) were determined in the absence and presence of ATP, revealing how ATP binding regulates the protease activity and access to the translocation pathway. However, how the substrate CtA, a 90-residue polypeptide, is recognized by PCAT1 remained elusive. To address this question, we determined the structure of the PCAT1-CtA complex by electron cryo-microscopy (cryo-EM) to 3.4 Å resolution. The structure shows that two CtAs are bound via their N-terminal leader peptides, but only one is positioned for cleavage and translocation. Based on these results, we propose a model of how substrate cleavage, ATP hydrolysis, and substrate translocation are coordinated in a transport cycle.
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Affiliation(s)
- Virapat Kieuvongngam
- Laboratory of Membrane Biophysics and Biology, The Rockefeller University, New York, United States
| | - Paul Dominic B Olinares
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, United States
| | - Anthony Palillo
- Laboratory of Membrane Biophysics and Biology, The Rockefeller University, New York, United States
| | - Michael L Oldham
- Laboratory of Membrane Biophysics and Biology, The Rockefeller University, New York, United States.,Howard Hughes Medical Institute, Chevy Chase, United States
| | - Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, United States
| | - Jue Chen
- Laboratory of Membrane Biophysics and Biology, The Rockefeller University, New York, United States.,Howard Hughes Medical Institute, Chevy Chase, United States
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38
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Jiang YF, Lin HL, Wang LJ, Hsu T, Fu CY. Coordinated organization of mitochondrial lamellar cristae and gain of COX function during mitochondrial maturation in Drosophila. Mol Biol Cell 2019; 31:18-26. [PMID: 31746672 PMCID: PMC6938269 DOI: 10.1091/mbc.e19-08-0450] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Mitochondrial cristae contain electron transport chain complexes and are distinct from the inner boundary membrane (IBM). While many details regarding the regulation of mitochondrial structure are known, the relationship between cristae structure and function during organelle development is not fully described. Here, we used serial-section tomography to characterize the formation of lamellar cristae in immature mitochondria during a period of dramatic mitochondrial development that occurs after Drosophila emergence as an adult. We found that the formation of lamellar cristae was associated with the gain of cytochrome c oxidase (COX) function, and the COX subunit, COX4, was localized predominantly to organized lamellar cristae. Interestingly, 3D tomography showed some COX-positive lamellar cristae were not connected to IBM. We hypothesize that some lamellar cristae may be organized by a vesicle germination process in the matrix, in addition to invagination of IBM. OXA1 protein, which mediates membrane insertion of COX proteins, was also localized to cristae and reticular structures isolated in the matrix additional to the IBM, suggesting that it may participate in the formation of vesicle germination-derived cristae. Overall, our study elaborates on how cristae morphogenesis and functional maturation are intricately associated. Our data support the vesicle germination and membrane invagination models of cristae formation.
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Affiliation(s)
- Yi-Fan Jiang
- Graduate Institute of Molecular and Comparative Pathobiology, School of Veterinary Medicine, National Taiwan University, Taipei 106, Taiwan
| | - Hsiang-Ling Lin
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 115, Taiwan
| | - Li-Jie Wang
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 115, Taiwan
| | - Tian Hsu
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 115, Taiwan
| | - Chi-Yu Fu
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 115, Taiwan
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Khayat R, Wen K, Alimova A, Gavrilov B, Katz A, Galarza JM, Gottlieb P. Structural characterization of the PCV2d virus-like particle at 3.3 Å resolution reveals differences to PCV2a and PCV2b capsids, a tetranucleotide, and an N-terminus near the icosahedral 3-fold axes. Virology 2019; 537:186-197. [PMID: 31505320 PMCID: PMC6958667 DOI: 10.1016/j.virol.2019.09.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 08/31/2019] [Accepted: 09/02/2019] [Indexed: 02/07/2023]
Abstract
Porcine circovirus 2 (PCV2) has a major impact on the swine industry. Eight PCV2 genotypes (a-h) have been identified using capsid sequence analysis. PCV2d has been designated as the emerging genotype. The cryo-electron microscopy molecular envelope of PCV2d virus-like particles identifies differences between PCV2a, b and d genotypes that accompany the emergence of PCV2b from PCV2a, and PCV2d from PCV2b. These differences indicate that sequence analysis of genotypes is insufficient, and that it is important to determine the PCV2 capsid structure as the virus evolves. Structure-based sequence comparison demonstrate that each genotype possesses a unique combination of amino acids located on the surface of the capsid that undergo substitution. We also demonstrate that the capsid N-terminus moves in response to increasing amount of nucleic acid packaged into the capsid. Furthermore, we model a tetranucleotide between the 5- and 2-fold axes of symmetry that appears to be responsible for capsid stability.
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Affiliation(s)
- Reza Khayat
- Department of Chemistry and Biochemistry, The City College of New York, New York, NY, 10031, USA; Graduate Program in Biochemistry, The Graduate Center of the City University of New York, New York, NY, 10016, USA.
| | - Ke Wen
- TechnoVax, Inc., 6 Westchester Plaza, Elmsford, NY, 10523, USA
| | | | - Boris Gavrilov
- Biologics Development, Huvepharma, 3A Nikolay Haytov Street, Sofia, 1113, Bulgaria
| | - Al Katz
- Department of Physics, City College of New York, New York, NY, 10031, USA
| | - Jose M Galarza
- TechnoVax, Inc., 6 Westchester Plaza, Elmsford, NY, 10523, USA
| | - Paul Gottlieb
- CUNY School of Medicine, City College of New York, NY, 10031, USA
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40
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Obr M, Schur FKM. Structural analysis of pleomorphic and asymmetric viruses using cryo-electron tomography and subtomogram averaging. Adv Virus Res 2019; 105:117-159. [PMID: 31522703 DOI: 10.1016/bs.aivir.2019.07.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Describing the protein interactions that form pleomorphic and asymmetric viruses represents a considerable challenge to most structural biology techniques, including X-ray crystallography and single particle cryo-electron microscopy. Obtaining a detailed understanding of these interactions is nevertheless important, considering the number of relevant human pathogens that do not follow strict icosahedral or helical symmetry. Cryo-electron tomography and subtomogram averaging methods provide structural insights into complex biological environments and are well suited to go beyond structures of perfectly symmetric viruses. This chapter discusses recent developments showing that cryo-ET and subtomogram averaging can provide high-resolution insights into hitherto unknown structural features of pleomorphic and asymmetric virus particles. It also describes how these methods have significantly added to our understanding of retrovirus capsid assemblies in immature and mature viruses. Additional examples of irregular viruses and their associated proteins, whose structures have been studied via cryo-ET and subtomogram averaging, further support the versatility of these methods.
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Affiliation(s)
- Martin Obr
- Institute of Science and Technology Austria (IST Austria), Klosterneuburg, Austria
| | - Florian K M Schur
- Institute of Science and Technology Austria (IST Austria), Klosterneuburg, Austria.
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41
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Dhindwal S, Feng S, Khayat R. The Arginines in the N-Terminus of the Porcine Circovirus 2 Virus-like Particles Are Responsible for Disrupting the Membranes at Neutral and Acidic pH. J Mol Biol 2019; 431:3261-3274. [PMID: 31173778 PMCID: PMC6697213 DOI: 10.1016/j.jmb.2019.05.044] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 05/21/2019] [Accepted: 05/27/2019] [Indexed: 12/23/2022]
Abstract
Non-enveloped viruses that are endocytosed employ numerous mechanisms to disrupt endosomal membranes for escape into the cellular cytoplasm. These include the use of amphipathic helices or sheets, hydrophobic loops, myristoylated peptides, and proteins with phospholipase activity. Some mechanisms result in immediate deterioration of the endosome, while others form pores in the membrane causing osmolysis to disrupt the endosome and allow viral escape. We describe an additional mechanism by a non-enveloped virus to disrupt endosomal membranes. Porcine circovirus 2 (PCV2) possesses a 41-amino acid arginine-rich motif (ARM) at the N-terminus of its capsid protein that appears to be in the interior of the virus-like particle (VLP). Using in vitro membrane disruption assays, we demonstrate that PCV2 VLP, unassembled capsid, and ARM peptide possess the ability to disrupt endosomal-like membranes, whereas VLP lacking the ARM sequence does not possess this capability. Membrane disruption by VLP is insensitive to pH, but unassembled capsid protein and ARM peptide exhibit diminished activity at low pH. Our liposome disruption assays, circular dichroism, and intrinsic tryptophan fluorescence assays allow us to propose a model for PCV2-endosomal membrane interaction wherein the ARM peptide externalizes from the capsid, its C-terminus (amino acids 28-40) anchors into the membrane, and the arginine-rich N-terminus (amino acids 1-27) drives membrane disruption. To our knowledge, this is the first example of a non-enveloped virus using the arginines of an ARM to disrupt membranes. Also, this is the first example of such study for the Circoviridae family of viruses.
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Affiliation(s)
- Sonali Dhindwal
- Department of Chemistry and Biochemistry, The City College of New York, New York, NY 10031, USA
| | - Shanshan Feng
- Department of Chemistry and Biochemistry, The City College of New York, New York, NY 10031, USA; Graduate Program in Biochemistry, The Graduate Center of the City University of New York, New York, NY 10016, USA
| | - Reza Khayat
- Department of Chemistry and Biochemistry, The City College of New York, New York, NY 10031, USA; Graduate Program in Biochemistry, The Graduate Center of the City University of New York, New York, NY 10016, USA.
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Abstract
For automated acquisition of tilt series for electron tomography, software needs to handle complications such as movements of the sample in x/y and z, increased projected thickness at high tilt, specimen drift, etc. In addition, many applications require special functionality such as low dose acquisition, automated sequential (batch) tomography, or montage tomography. After reviewing how these difficulties can be addressed and a closer look at what advanced acquisition strategies are employed in biosciences, this chapter introduces acquisition software both developed in academia as well as by hardware vendors. It covers the hardware requirements and compatibility, the functional principle and workflow implemented, as well as what advanced functions are supported by the individual programs.
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Affiliation(s)
- Guenter P Resch
- Nexperion e.U.-Solutions for Electron Microscopy, Vienna, Austria.
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43
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Gan L, Ng CT, Chen C, Cai S. A collection of yeast cellular electron cryotomography data. Gigascience 2019; 8:giz077. [PMID: 31247098 PMCID: PMC6596884 DOI: 10.1093/gigascience/giz077] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Revised: 05/09/2019] [Accepted: 06/10/2019] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Cells are powered by a large set of macromolecular complexes, which work together in a crowded environment. The in situ mechanisms of these complexes are unclear because their 3D distribution, organization, and interactions are largely unknown. Electron cryotomography (cryo-ET) can address these knowledge gaps because it produces cryotomograms-3D images that reveal biological structure at ∼4-nm resolution. Cryo-ET uses no fixation, dehydration, staining, or plastic embedment, so cellular features are visualized in a life-like, frozen-hydrated state. To study chromatin and mitotic machinery in situ, we subjected yeast cells to genetic and chemical perturbations, cryosectioned them, and then imaged the cells by cryo-ET. FINDINGS Here we share >1,000 cryo-ET raw datasets of cryosectioned budding yeast Saccharomyces cerevisiaecollected as part of previously published studies. These data will be valuable to cell biologists who are interested in the nanoscale organization of yeasts and of eukaryotic cells in general. All the unpublished tilt series and a subset of corresponding cryotomograms have been deposited in the EMPIAR resource for the community to use freely. To improve tilt series discoverability, we have uploaded metadata and preliminary notes to publicly accessible Google Sheets, EMPIAR, and GigaDB. CONCLUSIONS Cellular cryo-ET data can be mined to obtain new cell-biological, structural, and 3D statistical insights in situ. These data contain structures not visible in traditional electron-microscopy data. Template matching and subtomogram averaging of known macromolecular complexes can reveal their 3D distributions and low-resolution structures. Furthermore, these data can serve as testbeds for high-throughput image-analysis pipelines, as training sets for feature-recognition software, for feasibility analysis when planning new structural-cell-biology projects, and as practice data for students.
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Affiliation(s)
- Lu Gan
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543
| | - Cai Tong Ng
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543
| | - Chen Chen
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543
| | - Shujun Cai
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543
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44
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Meyer NL, Hu G, Davulcu O, Xie Q, Noble AJ, Yoshioka C, Gingerich DS, Trzynka A, David L, Stagg SM, Chapman MS. Structure of the gene therapy vector, adeno-associated virus with its cell receptor, AAVR. eLife 2019; 8:e44707. [PMID: 31115336 PMCID: PMC6561701 DOI: 10.7554/elife.44707] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Accepted: 05/22/2019] [Indexed: 11/26/2022] Open
Abstract
Adeno-associated virus (AAV) vectors are preeminent in emerging clinical gene therapies. Generalizing beyond the most tractable genetic diseases will require modulation of cell specificity and immune neutralization. Interactions of AAV with its cellular receptor, AAVR, are key to understanding cell-entry and trafficking with the rigor needed to engineer tissue-specific vectors. Cryo-electron tomography shows ordered binding of part of the flexible receptor to the viral surface, with distal domains in multiple conformations. Regions of the virus and receptor in close physical proximity can be identified by cross-linking/mass spectrometry. Cryo-electron microscopy with a two-domain receptor fragment reveals the interactions at 2.4 Å resolution. AAVR binds between AAV's spikes on a plateau that is conserved, except in one clade whose structure is AAVR-incompatible. AAVR's footprint overlaps the epitopes of several neutralizing antibodies, prompting a re-evaluation of neutralization mechanisms. The structure provides a roadmap for experimental probing and manipulation of viral-receptor interactions.
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Affiliation(s)
- Nancy L Meyer
- Department of Biochemistry and Molecular BiologyOregon Health and Science UniversityPortlandUnited States
| | - Guiqing Hu
- Institute Molecular BiophysicsFlorida State UniversityTallahasseeUnited States
| | - Omar Davulcu
- Department of Biochemistry and Molecular BiologyOregon Health and Science UniversityPortlandUnited States
| | - Qing Xie
- Department of Biochemistry and Molecular BiologyOregon Health and Science UniversityPortlandUnited States
| | - Alex J Noble
- Institute Molecular BiophysicsFlorida State UniversityTallahasseeUnited States
| | - Craig Yoshioka
- OHSU Center for Spatial Systems BiomedicinePortlandUnited States
| | - Drew S Gingerich
- OHSU Center for Spatial Systems BiomedicinePortlandUnited States
| | - Andrew Trzynka
- Department of Biochemistry and Molecular BiologyOregon Health and Science UniversityPortlandUnited States
| | - Larry David
- Department of Biochemistry and Molecular BiologyOregon Health and Science UniversityPortlandUnited States
| | - Scott M Stagg
- Institute Molecular BiophysicsFlorida State UniversityTallahasseeUnited States
- Department of Chemistry and BiochemistryFlorida State UniversityTallahasseeUnited States
| | - Michael Stewart Chapman
- Department of Biochemistry and Molecular BiologyOregon Health and Science UniversityPortlandUnited States
- Department of BiochemistryUniversity of MissouriColumbiaUnited States
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45
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Schur FK. Toward high-resolution in situ structural biology with cryo-electron tomography and subtomogram averaging. Curr Opin Struct Biol 2019; 58:1-9. [PMID: 31005754 DOI: 10.1016/j.sbi.2019.03.018] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 03/08/2019] [Accepted: 03/12/2019] [Indexed: 01/03/2023]
Abstract
Cryo-electron tomography (cryo-ET) provides unprecedented insights into the molecular constituents of biological environments. In combination with an image processing method called subtomogram averaging (STA), detailed 3D structures of biological molecules can be obtained in large, irregular macromolecular assemblies or in situ, without the need for purification. The contextual meta-information these methods also provide, such as a protein's location within its native environment, can then be combined with functional data. This allows the derivation of a detailed view on the physiological or pathological roles of proteins from the molecular to cellular level. Despite their tremendous potential in in situ structural biology, cryo-ET and STA have been restricted by methodological limitations, such as the low obtainable resolution. Exciting progress now allows one to reach unprecedented resolutions in situ, ranging in optimal cases beyond the nanometer barrier. Here, I review current frontiers and future challenges in routinely determining high-resolution structures in in situ environments using cryo-ET and STA.
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Affiliation(s)
- Florian Km Schur
- Institute of Science and Technology Austria, Am Campus 1, A-3400 Klosterneuburg, Austria.
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46
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Influenza Virus-Liposome Fusion Studies Using Fluorescence Dequenching and Cryo-electron Tomography. Methods Mol Biol 2019; 1836:261-279. [PMID: 30151578 DOI: 10.1007/978-1-4939-8678-1_13] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
Influenza virus enters host cells by fusion of viral and endosomal membranes mediated by the influenza hemagglutinin (HA). The pathway of HA-catalyzed fusion has been widely investigated in influenza virus membrane fusion with liposomes. In this chapter we describe methodology for studying the virus-liposome fusion system using a combination of fluorescence dequenching assays and cryo-electron tomography (cryo-ET). In particular, the fluorescence dequenching is used to monitor the efficiency of membrane fusion between whole influenza viruses labeled with a lipophilic dye (DiD) in the membrane and liposomes labeled with a water-soluble dye (sulforhodamine B). By simultaneously monitoring the two fluorescent signals, we can determine the relative time scales of liposomal content leakage or transfer vs. lipid merging. In addition, cryo-ET offers a means of imaging three-dimensional snapshots of different stages of virus-liposome fusion such as prefusion, fusion intermediates, and postfusion.
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47
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Brasch J, Goodman KM, Noble AJ, Rapp M, Mannepalli S, Bahna F, Dandey VP, Bepler T, Berger B, Maniatis T, Potter CS, Carragher B, Honig B, Shapiro L. Visualization of clustered protocadherin neuronal self-recognition complexes. Nature 2019; 569:280-283. [PMID: 30971825 DOI: 10.1038/s41586-019-1089-3] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 03/07/2019] [Indexed: 11/09/2022]
Abstract
Neurite self-recognition and avoidance are fundamental properties of all nervous systems1. These processes facilitate dendritic arborization2,3, prevent formation of autapses4 and allow free interaction among non-self neurons1,2,4,5. Avoidance among self neurites is mediated by stochastic cell-surface expression of combinations of about 60 isoforms of α-, β- and γ-clustered protocadherin that provide mammalian neurons with single-cell identities1,2,4-13. Avoidance is observed between neurons that express identical protocadherin repertoires2,5, and single-isoform differences are sufficient to prevent self-recognition10. Protocadherins form isoform-promiscuous cis dimers and isoform-specific homophilic trans dimers10,14-20. Although these interactions have previously been characterized in isolation15,17-20, structures of full-length protocadherin ectodomains have not been determined, and how these two interfaces engage in self-recognition between neuronal surfaces remains unknown. Here we determine the molecular arrangement of full-length clustered protocadherin ectodomains in single-isoform self-recognition complexes, using X-ray crystallography and cryo-electron tomography. We determine the crystal structure of the clustered protocadherin γB4 ectodomain, which reveals a zipper-like lattice that is formed by alternating cis and trans interactions. Using cryo-electron tomography, we show that clustered protocadherin γB6 ectodomains tethered to liposomes spontaneously assemble into linear arrays at membrane contact sites, in a configuration that is consistent with the assembly observed in the crystal structure. These linear assemblies pack against each other as parallel arrays to form larger two-dimensional structures between membranes. Our results suggest that the formation of ordered linear assemblies by clustered protocadherins represents the initial self-recognition step in neuronal avoidance, and thus provide support for the isoform-mismatch chain-termination model of protocadherin-mediated self-recognition, which depends on these linear chains11.
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Affiliation(s)
- Julia Brasch
- Zuckerman Mind, Brain and Behavior Institute, Columbia University, New York, NY, USA.,Simons Electron Microscopy Center, New York Structural Biology Center, The National Resource for Automated Molecular Microscopy, New York, NY, USA.,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Kerry M Goodman
- Zuckerman Mind, Brain and Behavior Institute, Columbia University, New York, NY, USA.,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Alex J Noble
- Simons Electron Microscopy Center, New York Structural Biology Center, The National Resource for Automated Molecular Microscopy, New York, NY, USA
| | - Micah Rapp
- Zuckerman Mind, Brain and Behavior Institute, Columbia University, New York, NY, USA.,Simons Electron Microscopy Center, New York Structural Biology Center, The National Resource for Automated Molecular Microscopy, New York, NY, USA.,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Seetha Mannepalli
- Zuckerman Mind, Brain and Behavior Institute, Columbia University, New York, NY, USA.,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Fabiana Bahna
- Zuckerman Mind, Brain and Behavior Institute, Columbia University, New York, NY, USA.,Howard Hughes Medical Institute, Columbia University, New York, NY, USA.,Department of Systems Biology, Columbia University, New York, NY, USA
| | - Venkata P Dandey
- Simons Electron Microscopy Center, New York Structural Biology Center, The National Resource for Automated Molecular Microscopy, New York, NY, USA
| | - Tristan Bepler
- Computational and Systems Biology, MIT, Cambridge, MA, USA.,Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA, USA
| | - Bonnie Berger
- Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA, USA.,Department of Mathematics, MIT, Cambridge, MA, USA
| | - Tom Maniatis
- Zuckerman Mind, Brain and Behavior Institute, Columbia University, New York, NY, USA.,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Clinton S Potter
- Simons Electron Microscopy Center, New York Structural Biology Center, The National Resource for Automated Molecular Microscopy, New York, NY, USA.,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Bridget Carragher
- Simons Electron Microscopy Center, New York Structural Biology Center, The National Resource for Automated Molecular Microscopy, New York, NY, USA.,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Barry Honig
- Zuckerman Mind, Brain and Behavior Institute, Columbia University, New York, NY, USA. .,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA. .,Howard Hughes Medical Institute, Columbia University, New York, NY, USA. .,Department of Systems Biology, Columbia University, New York, NY, USA. .,Department of Medicine, Columbia University, New York, NY, USA.
| | - Lawrence Shapiro
- Zuckerman Mind, Brain and Behavior Institute, Columbia University, New York, NY, USA. .,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA. .,Department of Systems Biology, Columbia University, New York, NY, USA.
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48
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Dorosz J, Kristensen LH, Aduri NG, Mirza O, Lousen R, Bucciarelli S, Mehta V, Sellés-Baiget S, Solbak SMØ, Bach A, Mesa P, Hernandez PA, Montoya G, Nguyen TTTN, Rand KD, Boesen T, Gajhede M. Molecular architecture of the Jumonji C family histone demethylase KDM5B. Sci Rep 2019; 9:4019. [PMID: 30858420 PMCID: PMC6411775 DOI: 10.1038/s41598-019-40573-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 02/19/2019] [Indexed: 12/02/2022] Open
Abstract
The full length human histone 3 lysine 4 demethylase KDM5B (PLU-1/Jarid1B) has been studied using Hydrogen/Deuterium exchange mass spectrometry, homology modelling, sequence analysis, small angle X-ray scattering and electron microscopy. This first structure on an intact multi-domain Jumonji histone demethylase reveal that the so-called PLU region, in the central region of KDM5B, has a curved α-helical three-dimensional structure, that acts as a rigid linker between the catalytic core and a region comprising four α-helices, a loop comprising the PHD2 domain, two large intrinsically disordered loops and the PHD3 domain in close proximity. The dumbbell shaped and curved KDM5B architecture observed by electron microscopy is complementary to the nucleosome surface and has a striking overall similarity to that of the functionally related KDM1A/CoREST complex. This could suggest that there are similarities between the demethylation mechanisms employed by the two histone 3 lysine 4 demethylases at the molecular level.
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Affiliation(s)
- Jerzy Dorosz
- Biostructural Research, Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, 2100, Copenhagen, Denmark
| | - Line Hyltoft Kristensen
- Biostructural Research, Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, 2100, Copenhagen, Denmark
| | - Nanda G Aduri
- Biostructural Research, Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, 2100, Copenhagen, Denmark
| | - Osman Mirza
- Biostructural Research, Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, 2100, Copenhagen, Denmark
| | - Rikke Lousen
- Biostructural Research, Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, 2100, Copenhagen, Denmark
| | - Saskia Bucciarelli
- Biostructural Research, Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, 2100, Copenhagen, Denmark
| | - Ved Mehta
- Biostructural Research, Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, 2100, Copenhagen, Denmark
| | - Selene Sellés-Baiget
- Biostructural Research, Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, 2100, Copenhagen, Denmark
| | - Sara Marie Øie Solbak
- Medicinal Chemistry Research, Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, 2100, Copenhagen, Denmark
| | - Anders Bach
- Medicinal Chemistry Research, Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, 2100, Copenhagen, Denmark
| | - Pablo Mesa
- Protein Structure & Function Programme, Macromolecular Crystallography Group, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, Copenhagen, 2200, Denmark
| | - Pablo Alcon Hernandez
- Protein Structure & Function Programme, Macromolecular Crystallography Group, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, Copenhagen, 2200, Denmark
| | - Guillermo Montoya
- Protein Structure & Function Programme, Macromolecular Crystallography Group, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, Copenhagen, 2200, Denmark
| | - Tam T T N Nguyen
- Department of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100, Copenhagen, Denmark
| | - Kasper D Rand
- Department of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100, Copenhagen, Denmark
| | - Thomas Boesen
- Interdisciplinary Nanoscience Center, Aarhus University, Gustav Wieds Vej 14, 8000, Aarhus, Denmark
| | - Michael Gajhede
- Biostructural Research, Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, 2100, Copenhagen, Denmark.
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49
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de Ruiter MV, Klem R, Luque D, Cornelissen JJLM, Castón JR. Structural nanotechnology: three-dimensional cryo-EM and its use in the development of nanoplatforms for in vitro catalysis. NANOSCALE 2019; 11:4130-4146. [PMID: 30793729 DOI: 10.1039/c8nr09204d] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The organization of enzymes into different subcellular compartments is essential for correct cell function. Protein-based cages are a relatively recently discovered subclass of structurally dynamic cellular compartments that can be mimicked in the laboratory to encapsulate enzymes. These synthetic structures can then be used to improve our understanding of natural protein-based cages, or as nanoreactors in industrial catalysis, metabolic engineering, and medicine. Since the function of natural protein-based cages is related to their three-dimensional structure, it is important to determine this at the highest possible resolution if viable nanoreactors are to be engineered. Cryo-electron microscopy (cryo-EM) is ideal for undertaking such analyses within a feasible time frame and at near-native conditions. This review describes how three-dimensional cryo-EM is used in this field and discusses its advantages. An overview is also given of the nanoreactors produced so far, their structure, function, and applications.
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Affiliation(s)
- Mark V de Ruiter
- Department of Biomolecular Nanotechnology, MESA+ Institute for Nanotechnology, University of Twente, 7500 AE Enschede, The Netherlands.
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50
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Chreifi G, Chen S, Metskas LA, Kaplan M, Jensen GJ. Rapid tilt-series acquisition for electron cryotomography. J Struct Biol 2019; 205:163-169. [PMID: 30639925 PMCID: PMC6389375 DOI: 10.1016/j.jsb.2018.12.008] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Revised: 12/18/2018] [Accepted: 12/20/2018] [Indexed: 11/30/2022]
Abstract
Using a new Titan Krios stage equipped with a single-axis holder, we developed two methods to accelerate the collection of tilt-series. We demonstrate a continuous-tilting method that can record a tilt-series in seconds, but with loss of details finer than ∼4 nm. We also demonstrate a fast-incremental method that can record a tilt-series several-fold faster than current methods and with similar resolution. We characterize the utility of both methods in real biological electron cryotomography workflows. We identify opportunities for further improvements in hardware and software and speculate on the impact such advances could have on structural biology.
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Affiliation(s)
- Georges Chreifi
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, United States
| | - Songye Chen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, United States; Beckman Institute, California Institute of Technology, Pasadena, CA 91125, United States
| | - Lauren Ann Metskas
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, United States; Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125, United States
| | - Mohammed Kaplan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, United States
| | - Grant J Jensen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, United States; Beckman Institute, California Institute of Technology, Pasadena, CA 91125, United States; Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125, United States.
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