1
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Takahashi K, Lee Y, Fago A, Bautista NM, Storz JF, Kawamoto A, Kurisu G, Nishizawa T, Tame JRH. The unique allosteric property of crocodilian haemoglobin elucidated by cryo-EM. Nat Commun 2024; 15:6505. [PMID: 39090102 PMCID: PMC11294572 DOI: 10.1038/s41467-024-49947-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Accepted: 06/25/2024] [Indexed: 08/04/2024] Open
Abstract
The principal effect controlling the oxygen affinity of vertebrate haemoglobins (Hbs) is the allosteric switch between R and T forms with relatively high and low oxygen affinity respectively. Uniquely among jawed vertebrates, crocodilians possess Hb that shows a profound drop in oxygen affinity in the presence of bicarbonate ions. This allows them to stay underwater for extended periods by consuming almost all the oxygen present in the blood-stream, as metabolism releases carbon dioxide, whose conversion to bicarbonate and hydrogen ions is catalysed by carbonic anhydrase. Despite the apparent universal utility of bicarbonate as an allosteric regulator of Hb, this property evolved only in crocodilians. We report here the molecular structures of both human and a crocodilian Hb in the deoxy and liganded states, solved by cryo-electron microscopy. We reveal the precise interactions between two bicarbonate ions and the crocodilian protein at symmetry-related sites found only in the T state. No other known effector of vertebrate Hbs binds anywhere near these sites.
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Affiliation(s)
- Katsuya Takahashi
- Graduate School of Medical Life Science, Yokohama City University, Suehiro 1-7-29, Yokohama, 230-0045, Japan
| | - Yongchan Lee
- Graduate School of Medical Life Science, Yokohama City University, Suehiro 1-7-29, Yokohama, 230-0045, Japan
| | - Angela Fago
- Department of Biology, Aarhus University, C. F. Møllers Alle 3, Aarhus, DK-8000, Aarhus C, Denmark
| | - Naim M Bautista
- School of Biological Sciences, University of Nebraska, 1104 T St., Lincoln, NE 68588-0118, NE, USA
| | - Jay F Storz
- School of Biological Sciences, University of Nebraska, 1104 T St., Lincoln, NE 68588-0118, NE, USA
| | - Akihiro Kawamoto
- Institute for Protein Research, Osaka University, 3-2, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Genji Kurisu
- Institute for Protein Research, Osaka University, 3-2, Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Tomohiro Nishizawa
- Graduate School of Medical Life Science, Yokohama City University, Suehiro 1-7-29, Yokohama, 230-0045, Japan.
| | - Jeremy R H Tame
- Graduate School of Medical Life Science, Yokohama City University, Suehiro 1-7-29, Yokohama, 230-0045, Japan.
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2
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Falk M, Tobiasson V, Bock A, Hansen C, Ynnerman A. A Visual Environment for Data Driven Protein Modeling and Validation. IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS 2024; 30:5063-5073. [PMID: 37327104 PMCID: PMC11273209 DOI: 10.1109/tvcg.2023.3286582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
In structural biology, validation and verification of new atomic models are crucial and necessary steps which limit the production of reliable molecular models for publications and databases. An atomic model is the result of meticulous modeling and matching and is evaluated using a variety of metrics that provide clues to improve and refine the model so it fits our understanding of molecules and physical constraints. In cryo electron microscopy (cryo-EM) the validation is also part of an iterative modeling process in which there is a need to judge the quality of the model during the creation phase. A shortcoming is that the process and results of the validation are rarely communicated using visual metaphors. This work presents a visual framework for molecular validation. The framework was developed in close collaboration with domain experts in a participatory design process. Its core is a novel visual representation based on 2D heatmaps that shows all available validation metrics in a linear fashion, presenting a global overview of the atomic model and provide domain experts with interactive analysis tools. Additional information stemming from the underlying data, such as a variety of local quality measures, is used to guide the user's attention toward regions of higher relevance. Linked with the heatmap is a three-dimensional molecular visualization providing the spatial context of the structures and chosen metrics. Additional views of statistical properties of the structure are included in the visual framework. We demonstrate the utility of the framework and its visual guidance with examples from cryo-EM.
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3
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Gustavsson E, Grünewald K, Elias P, Hällberg BM. Dynamics of the Herpes simplex virus DNA polymerase holoenzyme during DNA synthesis and proof-reading revealed by Cryo-EM. Nucleic Acids Res 2024; 52:7292-7304. [PMID: 38806233 PMCID: PMC11229320 DOI: 10.1093/nar/gkae374] [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: 11/01/2023] [Revised: 04/16/2024] [Accepted: 04/25/2024] [Indexed: 05/30/2024] Open
Abstract
Herpes simplex virus 1 (HSV-1), a double-stranded DNA virus, replicates using seven essential proteins encoded by its genome. Among these, the UL30 DNA polymerase, complexed with the UL42 processivity factor, orchestrates leading and lagging strand replication of the 152 kb viral genome. UL30 polymerase is a prime target for antiviral therapy, and resistance to current drugs can arise in immunocompromised individuals. Using electron cryo-microscopy (cryo-EM), we unveil the dynamic changes of the UL30/UL42 complex with DNA in three distinct states. First, a pre-translocation state with an open fingers domain ready for nucleotide incorporation. Second, a halted elongation state where the fingers close, trapping dATP in the dNTP pocket. Third, a DNA-editing state involving significant conformational changes to allow DNA realignment for exonuclease activity. Additionally, the flexible UL30 C-terminal domain interacts with UL42, forming an extended positively charged surface binding to DNA, thereby enhancing processive synthesis. These findings highlight substantial structural shifts in the polymerase and its DNA interactions during replication, offering insights for future antiviral drug development.
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Affiliation(s)
- Emil Gustavsson
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
- Centre for Structural Systems Biology, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, Building 15, 22607 Hamburg, Germany
| | - Kay Grünewald
- Centre for Structural Systems Biology, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, Building 15, 22607 Hamburg, Germany
- Leibniz-Institute of Virology, Martinistraße 52, 20251 Hamburg, Germany
- Department of Chemistry, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Per Elias
- Institute of Biomedicine, Department of Medical Biochemistry and Cell Biology, Sahlgrenska Academy, University of Gothenburg, Box 440, 405 30 Gothenburg, Sweden
| | - B Martin Hällberg
- Department of Cell and Molecular Biology, Karolinska Institutet, 171 77 Stockholm, Sweden
- Centre for Structural Systems Biology, Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, Building 15, 22607 Hamburg, Germany
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4
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Calcraft T, Stanke-Scheffler N, Nans A, Lindemann D, Taylor IA, Rosenthal PB. Integrated cryoEM structure of a spumaretrovirus reveals cross-kingdom evolutionary relationships and the molecular basis for assembly and virus entry. Cell 2024:S0092-8674(24)00657-3. [PMID: 39013471 DOI: 10.1016/j.cell.2024.06.017] [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: 11/02/2023] [Revised: 02/26/2024] [Accepted: 06/11/2024] [Indexed: 07/18/2024]
Abstract
Foamy viruses (FVs) are an ancient lineage of retroviruses, with an evolutionary history spanning over 450 million years. Vector systems based on Prototype Foamy Virus (PFV) are promising candidates for gene and oncolytic therapies. Structural studies of PFV contribute to the understanding of the mechanisms of FV replication, cell entry and infection, and retroviral evolution. Here we combine cryoEM and cryoET to determine high-resolution in situ structures of the PFV icosahedral capsid (CA) and envelope glycoprotein (Env), including its type III transmembrane anchor and membrane-proximal external region (MPER), and show how they are organized in an integrated structure of assembled PFV particles. The atomic models reveal an ancient retroviral capsid architecture and an unexpected relationship between Env and other class 1 fusion proteins of the Mononegavirales. Our results represent the de novo structure determination of an assembled retrovirus particle.
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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
| | - Nicole Stanke-Scheffler
- Institute of Medical Microbiology and Virology, University Hospital and Medical Faculty "Carl Gustav Carus", Technische Universität Dresden, Fetscherstr. 74, 01307 Dresden, Germany; Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, 01307 Dresden, Germany
| | - Andrea Nans
- Structural Biology Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Dirk Lindemann
- Institute of Medical Microbiology and Virology, University Hospital and Medical Faculty "Carl Gustav Carus", Technische Universität Dresden, Fetscherstr. 74, 01307 Dresden, Germany; Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, 01307 Dresden, Germany.
| | - Ian A Taylor
- Macromolecular Structure Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
| | - Peter B Rosenthal
- Structural Biology of Cells and Viruses Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
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5
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Kobayashi TA, Shimada H, Sano FK, Itoh Y, Enoki S, Okada Y, Kusakizako T, Nureki O. Dimeric transport mechanism of human vitamin C transporter SVCT1. Nat Commun 2024; 15:5569. [PMID: 38956111 PMCID: PMC11219872 DOI: 10.1038/s41467-024-49899-2] [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: 05/31/2023] [Accepted: 06/20/2024] [Indexed: 07/04/2024] Open
Abstract
Vitamin C plays important roles as a cofactor in many enzymatic reactions and as an antioxidant against oxidative stress. As some mammals including humans cannot synthesize vitamin C de novo from glucose, its uptake from dietary sources is essential, and is mediated by the sodium-dependent vitamin C transporter 1 (SVCT1). Despite its physiological significance in maintaining vitamin C homeostasis, the structural basis of the substrate transport mechanism remained unclear. Here, we report the cryo-EM structures of human SVCT1 in different states at 2.5-3.5 Å resolutions. The binding manner of vitamin C together with two sodium ions reveals the counter ion-dependent substrate recognition mechanism. Furthermore, comparisons of the inward-open and occluded structures support a transport mechanism combining elevator and distinct rotational motions. Our results demonstrate the molecular mechanism of vitamin C transport with its underlying conformational cycle, potentially leading to future industrial and medical applications.
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Affiliation(s)
- Takaaki A Kobayashi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Hiroto Shimada
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
- Research Division, Chugai Pharmaceutical Co., Ltd., Kanagawa, Japan
| | - Fumiya K Sano
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Yuzuru Itoh
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Sawako Enoki
- Department of Physics, and Universal Biology Institute (UBI), Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Yasushi Okada
- Department of Physics, and Universal Biology Institute (UBI), Graduate School of Science, The University of Tokyo, Tokyo, Japan
- Department of Cell Biology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Laboratory for Cell Polarity Regulation, RIKEN Center for Biosystems Dynamics Research (BDR), Osaka, Japan
- International Research Center for Neurointelligence (WPI-IRCN), The University of Tokyo, Tokyo, Japan
| | - Tsukasa Kusakizako
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.
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6
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Yadav S, Vinothkumar KR. Factors affecting macromolecule orientations in thin films formed in cryo-EM. Acta Crystallogr D Struct Biol 2024; 80:535-550. [PMID: 38935342 PMCID: PMC11220838 DOI: 10.1107/s2059798324005229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 06/01/2024] [Indexed: 06/28/2024] Open
Abstract
The formation of a vitrified thin film embedded with randomly oriented macromolecules is an essential prerequisite for cryogenic sample electron microscopy. Most commonly, this is achieved using the plunge-freeze method first described nearly 40 years ago. Although this is a robust method, the behaviour of different macromolecules shows great variation upon freezing and often needs to be optimized to obtain an isotropic, high-resolution reconstruction. For a macromolecule in such a film, the probability of encountering the air-water interface in the time between blotting and freezing and adopting preferred orientations is very high. 3D reconstruction using preferentially oriented particles often leads to anisotropic and uninterpretable maps. Currently, there are no general solutions to this prevalent issue, but several approaches largely focusing on sample preparation with the use of additives and novel grid modifications have been attempted. In this study, the effect of physical and chemical factors on the orientations of macromolecules was investigated through an analysis of selected well studied macromolecules, and important parameters that determine the behaviour of proteins on cryo-EM grids were revealed. These insights highlight the nature of the interactions that cause preferred orientations and can be utilized to systematically address orientation bias for any given macromolecule and to provide a framework to design small-molecule additives to enhance sample stability and behaviour.
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Affiliation(s)
- Swati Yadav
- National Centre for Biological SciencesTata Institute of Fundamental ResearchGKVK Post, Bellary RoadBengaluru560 065India
| | - Kutti R. Vinothkumar
- National Centre for Biological SciencesTata Institute of Fundamental ResearchGKVK Post, Bellary RoadBengaluru560 065India
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7
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Lawson CL, Kryshtafovych A, Pintilie GD, Burley SK, Černý J, Chen VB, Emsley P, Gobbi A, Joachimiak A, Noreng S, Prisant MG, Read RJ, Richardson JS, Rohou AL, Schneider B, Sellers BD, Shao C, Sourial E, Williams CI, Williams CJ, Yang Y, Abbaraju V, Afonine PV, Baker ML, Bond PS, Blundell TL, Burnley T, Campbell A, Cao R, Cheng J, Chojnowski G, Cowtan KD, DiMaio F, Esmaeeli R, Giri N, Grubmüller H, Hoh SW, Hou J, Hryc CF, Hunte C, Igaev M, Joseph AP, Kao WC, Kihara D, Kumar D, Lang L, Lin S, Maddhuri Venkata Subramaniya SR, Mittal S, Mondal A, Moriarty NW, Muenks A, Murshudov GN, Nicholls RA, Olek M, Palmer CM, Perez A, Pohjolainen E, Pothula KR, Rowley CN, Sarkar D, Schäfer LU, Schlicksup CJ, Schröder GF, Shekhar M, Si D, Singharoy A, Sobolev OV, Terashi G, Vaiana AC, Vedithi SC, Verburgt J, Wang X, Warshamanage R, Winn MD, Weyand S, Yamashita K, Zhao M, Schmid MF, Berman HM, Chiu W. Outcomes of the EMDataResource cryo-EM Ligand Modeling Challenge. Nat Methods 2024; 21:1340-1348. [PMID: 38918604 DOI: 10.1038/s41592-024-02321-7] [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: 01/14/2024] [Accepted: 05/24/2024] [Indexed: 06/27/2024]
Abstract
The EMDataResource Ligand Model Challenge aimed to assess the reliability and reproducibility of modeling ligands bound to protein and protein-nucleic acid complexes in cryogenic electron microscopy (cryo-EM) maps determined at near-atomic (1.9-2.5 Å) resolution. Three published maps were selected as targets: Escherichia coli beta-galactosidase with inhibitor, SARS-CoV-2 virus RNA-dependent RNA polymerase with covalently bound nucleotide analog and SARS-CoV-2 virus ion channel ORF3a with bound lipid. Sixty-one models were submitted from 17 independent research groups, each with supporting workflow details. The quality of submitted ligand models and surrounding atoms were analyzed by visual inspection and quantification of local map quality, model-to-map fit, geometry, energetics and contact scores. A composite rather than a single score was needed to assess macromolecule+ligand model quality. These observations lead us to recommend best practices for assessing cryo-EM structures of liganded macromolecules reported at near-atomic resolution.
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Affiliation(s)
- Catherine L Lawson
- RCSB Protein Data Bank and Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.
| | | | - Grigore D Pintilie
- Departments of Bioengineering and of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - Stephen K Burley
- RCSB Protein Data Bank and Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
- RCSB Protein Data Bank and San Diego Supercomputer Center, University of California San Diego, La Jolla, CA, USA
| | - Jiří Černý
- Institute of Biotechnology, Czech Academy of Sciences, Vestec, Czech Republic
| | - Vincent B Chen
- Department of Biochemistry, Duke University, Durham, NC, USA
| | - Paul Emsley
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Alberto Gobbi
- Discovery Chemistry, Genentech Inc., San Francisco, CA, USA
- , Berlin, Germany
| | - Andrzej Joachimiak
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL, USA
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Sigrid Noreng
- Structural Biology, Genentech Inc., South San Francisco, CA, USA
- Protein Science, Septerna, South San Francisco, CA, USA
| | | | - Randy J Read
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | | | - Alexis L Rohou
- Structural Biology, Genentech Inc., South San Francisco, CA, USA
| | - Bohdan Schneider
- Institute of Biotechnology, Czech Academy of Sciences, Vestec, Czech Republic
| | - Benjamin D Sellers
- Discovery Chemistry, Genentech Inc., San Francisco, CA, USA
- Computational Chemistry, Vilya, South San Francisco, CA, USA
| | - Chenghua Shao
- RCSB Protein Data Bank and Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | | | | | | | - Ying Yang
- Structural Biology, Genentech Inc., South San Francisco, CA, USA
| | - Venkat Abbaraju
- RCSB Protein Data Bank and Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Pavel V Afonine
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Matthew L Baker
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Paul S Bond
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK
| | - Tom L Blundell
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Tom Burnley
- Scientific Computing Department, UKRI Science and Technology Facilities Council, Research Complex at Harwell, Didcot, UK
| | - Arthur Campbell
- Center for Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Renzhi Cao
- Department of Computer Science, Pacific Lutheran University, Tacoma, WA, USA
| | - Jianlin Cheng
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, USA
| | | | - K D Cowtan
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK
| | - Frank DiMaio
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Reza Esmaeeli
- Department of Chemistry and Quantum Theory Project, University of Florida, Gainesville, FL, USA
| | - Nabin Giri
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, USA
| | - Helmut Grubmüller
- Theoretical and Computational Biophysics Department, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Soon Wen Hoh
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK
| | - Jie Hou
- Department of Computer Science, Saint Louis University, St. Louis, MO, USA
| | - Corey F Hryc
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Carola Hunte
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine and CIBSS-Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Maxim Igaev
- Theoretical and Computational Biophysics Department, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Agnel P Joseph
- Scientific Computing Department, UKRI Science and Technology Facilities Council, Research Complex at Harwell, Didcot, UK
| | - Wei-Chun Kao
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine and CIBSS-Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | - Daisuke Kihara
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
- Department of Computer Science, Purdue University, West Lafayette, IN, USA
| | - Dilip Kumar
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
- Trivedi School of Biosciences, Ashoka University, Sonipat, India
| | - Lijun Lang
- Department of Chemistry and Quantum Theory Project, University of Florida, Gainesville, FL, USA
- The Chinese University of Hong Kong, Hong Kong, China
| | - Sean Lin
- Division of Computing & Software Systems, University of Washington, Bothell, WA, USA
| | | | - Sumit Mittal
- Biodesign Institute, Arizona State University, Tempe, AZ, USA
- School of Advanced Sciences and Languages, VIT Bhopal University, Bhopal, India
| | - Arup Mondal
- Department of Chemistry and Quantum Theory Project, University of Florida, Gainesville, FL, USA
- National Renewable Energy Laboratory (NREL), Golden, CO, USA
| | - Nigel W Moriarty
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Andrew Muenks
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, USA
| | | | - Robert A Nicholls
- MRC Laboratory of Molecular Biology, Cambridge, UK
- Scientific Computing Department, UKRI Science and Technology Facilities Council, Research Complex at Harwell, Didcot, UK
| | - Mateusz Olek
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK
- Electron Bio-Imaging Centre, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Colin M Palmer
- Scientific Computing Department, UKRI Science and Technology Facilities Council, Research Complex at Harwell, Didcot, UK
| | - Alberto Perez
- Department of Chemistry and Quantum Theory Project, University of Florida, Gainesville, FL, USA
| | - Emmi Pohjolainen
- Theoretical and Computational Biophysics Department, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Karunakar R Pothula
- Institute of Biological Information Processing (IBI-7, Structural Biochemistry) and Jülich Centre for Structural Biology (JuStruct), Forschungszentrum Jülich, Jülich, Germany
| | | | - Daipayan Sarkar
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
- Biodesign Institute, Arizona State University, Tempe, AZ, USA
- MSU-DOE Plant Research Laboratory, East Lansing, MI, USA
- School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
| | - Luisa U Schäfer
- Institute of Biological Information Processing (IBI-7, Structural Biochemistry) and Jülich Centre for Structural Biology (JuStruct), Forschungszentrum Jülich, Jülich, Germany
| | - Christopher J Schlicksup
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Gunnar F Schröder
- Institute of Biological Information Processing (IBI-7, Structural Biochemistry) and Jülich Centre for Structural Biology (JuStruct), Forschungszentrum Jülich, Jülich, Germany
- Physics Department, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Mrinal Shekhar
- Center for Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Dong Si
- Division of Computing & Software Systems, University of Washington, Bothell, WA, USA
| | | | - Oleg V Sobolev
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Genki Terashi
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Andrea C Vaiana
- Theoretical and Computational Biophysics Department, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Nature's Toolbox (NTx), Rio Rancho, NM, USA
| | | | - Jacob Verburgt
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Xiao Wang
- Department of Computer Science, Purdue University, West Lafayette, IN, USA
| | | | - Martyn D Winn
- Scientific Computing Department, UKRI Science and Technology Facilities Council, Research Complex at Harwell, Didcot, UK
| | - Simone Weyand
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | | | - Minglei Zhao
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Michael F Schmid
- Division of Cryo-EM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Helen M Berman
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Wah Chiu
- Departments of Bioengineering and of Microbiology and Immunology, Stanford University, Stanford, CA, USA.
- Division of Cryo-EM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA, USA.
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8
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Kimanius D, Jamali K, Wilkinson ME, Lövestam S, Velazhahan V, Nakane T, Scheres SHW. Data-driven regularization lowers the size barrier of cryo-EM structure determination. Nat Methods 2024; 21:1216-1221. [PMID: 38862790 PMCID: PMC11239489 DOI: 10.1038/s41592-024-02304-8] [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: 10/27/2023] [Accepted: 05/08/2024] [Indexed: 06/13/2024]
Abstract
Macromolecular structure determination by electron cryo-microscopy (cryo-EM) is limited by the alignment of noisy images of individual particles. Because smaller particles have weaker signals, alignment errors impose size limitations on its applicability. Here, we explore how image alignment is improved by the application of deep learning to exploit prior knowledge about biological macromolecular structures that would otherwise be difficult to express mathematically. We train a denoising convolutional neural network on pairs of half-set reconstructions from the electron microscopy data bank (EMDB) and use this denoiser as an alternative to a commonly used smoothness prior. We demonstrate that this approach, which we call Blush regularization, yields better reconstructions than do existing algorithms, in particular for data with low signal-to-noise ratios. The reconstruction of a protein-nucleic acid complex with a molecular weight of 40 kDa, which was previously intractable, illustrates that denoising neural networks will expand the applicability of cryo-EM structure determination for a wide range of biological macromolecules.
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Affiliation(s)
- Dari Kimanius
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, UK.
- CZ Imaging Institute, Redwood City, CA, USA.
| | - Kiarash Jamali
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, UK
| | - Max E Wilkinson
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Howard Hughes Medical Institute, Cambridge, MA, USA
| | - Sofia Lövestam
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, UK
| | - Vaithish Velazhahan
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, UK
- School of Medicine, Stanford University, Stanford, CA, USA
| | - Takanori Nakane
- Institute for Protein Research, Osaka University, Suita-shi, Osaka, Japan
| | - Sjors H W Scheres
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, UK.
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9
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Arseni D, Nonaka T, Jacobsen MH, Murzin AG, Cracco L, Peak-Chew SY, Garringer HJ, Kawakami I, Suzuki H, Onaya M, Saito Y, Murayama S, Geula C, Vidal R, Newell KL, Mesulam M, Ghetti B, Hasegawa M, Ryskeldi-Falcon B. Heteromeric amyloid filaments of ANXA11 and TDP-43 in FTLD-TDP Type C. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.25.600403. [PMID: 38979278 PMCID: PMC11230283 DOI: 10.1101/2024.06.25.600403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Neurodegenerative diseases are characterised by the abnormal filamentous assembly of specific proteins in the central nervous system 1 . Human genetic studies established a causal role for protein assembly in neurodegeneration 2 . However, the underlying molecular mechanisms remain largely unknown, which is limiting progress in developing clinical tools for these diseases. Recent advances in electron cryo-microscopy (cryo-EM) have enabled the structures of the protein filaments to be determined from patient brains 1 . All diseases studied to date have been characterised by the self-assembly of a single intracellular protein in homomeric amyloid filaments, including that of TAR DNA-binding protein 43 (TDP-43) in amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration with TDP-43 inclusions (FTLD-TDP) Types A and B 3,4 . Here, we used cryo-EM to determine filament structures from the brains of individuals with FTLD-TDP Type C, one of the most common forms of sporadic FTLD-TDP. Unexpectedly, the structures revealed that a second protein, annexin A11 (ANXA11), co-assembles with TDP-43 in heteromeric amyloid filaments. The ordered filament fold is formed by TDP-43 residues G282/284-N345 and ANXA11 residues L39-L74 from their respective low-complexity domains (LCDs). Regions of TDP-43 and ANXA11 previously implicated in protein-protein interactions form an extensive hydrophobic interface at the centre of the filament fold. Immunoblots of the filaments revealed that the majority of ANXA11 exists as a ∼22 kDa N-terminal fragment (NTF) lacking the annexin core domain. Immunohistochemistry of brain sections confirmed the co-localisation of ANXA11 and TDP-43 in inclusions, redefining the histopathology of FTLD-TDP Type C. This work establishes a central role for ANXA11 in FTLD-TDP Type C. The unprecedented formation of heteromeric amyloid filaments in human brain revises our understanding of amyloid assembly and may be of significance for the pathogenesis of neurodegenerative diseases.
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10
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Hussein R, Graça A, Forsman J, Aydin AO, Hall M, Gaetcke J, Chernev P, Wendler P, Dobbek H, Messinger J, Zouni A, Schröder WP. Cryo-electron microscopy reveals hydrogen positions and water networks in photosystem II. Science 2024; 384:1349-1355. [PMID: 38900892 DOI: 10.1126/science.adn6541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 05/16/2024] [Indexed: 06/22/2024]
Abstract
Photosystem II starts the photosynthetic electron transport chain that converts solar energy into chemical energy and thus sustains life on Earth. It catalyzes two chemical reactions: water oxidation to molecular oxygen and plastoquinone reduction. Coupling of electron and proton transfer is crucial for efficiency; however, the molecular basis of these processes remains speculative owing to uncertain water binding sites and the lack of experimentally determined hydrogen positions. We thus collected high-resolution cryo-electron microscopy data of fully hydrated photosystem II from the thermophilic cyanobacterium Thermosynechococcus vestitus to a final resolution of 1.71 angstroms. The structure reveals several previously undetected partially occupied water binding sites and more than half of the hydrogen and proton positions. This clarifies the pathways of substrate water binding and plastoquinone B protonation.
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Affiliation(s)
- Rana Hussein
- Humboldt-Universität zu Berlin, Department of Biology, D 10099 Berlin, Germany
| | - André Graça
- Department of Chemistry, Umeå University, SE 90187 Umeå, Sweden
- Molecular Biomimetics, Department of Chemistry- Ångström Laboratory, Uppsala University, SE 75120 Uppsala, Sweden
| | - Jack Forsman
- Department of Chemistry, Umeå University, SE 90187 Umeå, Sweden
| | - A Orkun Aydin
- Molecular Biomimetics, Department of Chemistry- Ångström Laboratory, Uppsala University, SE 75120 Uppsala, Sweden
| | - Michael Hall
- Department of Chemistry, Umeå University, SE 90187 Umeå, Sweden
| | - Julia Gaetcke
- Humboldt-Universität zu Berlin, Department of Biology, D 10099 Berlin, Germany
| | - Petko Chernev
- Molecular Biomimetics, Department of Chemistry- Ångström Laboratory, Uppsala University, SE 75120 Uppsala, Sweden
| | - Petra Wendler
- Institute of Biochemistry and Biology, Department of Biochemistry, University of Potsdam, Karl-Liebknecht Strasse 24-25, D 14476, Potsdam-Golm, Germany
| | - Holger Dobbek
- Humboldt-Universität zu Berlin, Department of Biology, D 10099 Berlin, Germany
| | - Johannes Messinger
- Molecular Biomimetics, Department of Chemistry- Ångström Laboratory, Uppsala University, SE 75120 Uppsala, Sweden
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Sweden
| | - Athina Zouni
- Humboldt-Universität zu Berlin, Department of Biology, D 10099 Berlin, Germany
| | - Wolfgang P Schröder
- Department of Chemistry, Umeå University, SE 90187 Umeå, Sweden
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Sweden
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11
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Karimullina E, Guo Y, Khan HM, Emde T, Quade B, Leo RD, Otwinowski Z, Tieleman Peter D, Borek D, Savchenko A. Structural architecture of TolQ-TolR inner membrane protein complex from opportunistic pathogen Acinetobacter baumannii. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.19.599759. [PMID: 38948712 PMCID: PMC11212960 DOI: 10.1101/2024.06.19.599759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Gram-negative bacteria harness the proton motive force (PMF) within their inner membrane (IM) to uphold the integrity of their cell envelope, an indispensable aspect for both division and survival. The IM TolQ-TolR complex is the essential part of the Tol-Pal system, serving as a conduit for PMF energy transfer to the outer membrane. Here we present cryo-EM reconstructions of Acinetobacter baumannii TolQ in apo and TolR- bound forms at atomic resolution. The apo TolQ configuration manifests as a symmetric pentameric pore, featuring a trans-membrane funnel leading towards a cytoplasmic chamber. In contrast, the TolQ-TolR complex assumes a proton non-permeable stance, characterized by the TolQ pentamer's flexure to accommodate the TolR dimer, where two protomers undergo a translation-based relationship. Our structure-guided analysis and simulations support the rotor-stator mechanism of action, wherein the rotation of the TolQ pentamer harmonizes with the TolR protomers' interplay. These findings broaden our mechanistic comprehension of molecular stator units empowering critical functions within the Gram-negative bacterial cell envelope. Teaser Apo TolQ and TolQ-TolR structures depict structural rearrangements required for cell envelope organization in bacterial cell division.
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12
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Handa S, Biswas T, Chakraborty J, Ghosh G, Paul BG, Ghosh P. Structural Requirements for Reverse Transcription by a Diversity-generating Retroelement. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.23.563531. [PMID: 37961358 PMCID: PMC10634737 DOI: 10.1101/2023.10.23.563531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Diversity-generating retroelements (DGRs) create massive protein sequence variation in ecologically diverse microbes. Variation occurs during reverse transcription of a protein-encoding RNA template coupled to misincorporation at adenosines. In the prototypical Bordetella bacteriophage DGR, the template must be surrounded by upstream and downstream RNA segments for cDNA synthesis by the reverse transcriptase bRT and associated protein Avd. The function of the surrounding RNA was unknown. Cryo-EM revealed that this RNA enveloped bRT and lay over barrel-shaped Avd, forming an intimate ribonucleoprotein (RNP). An abundance of essential interactions between RNA structural elements and bRT-Avd precisely positioned an RNA homoduplex for initiation of cDNA synthesis by cis -priming. Our results explain how the surrounding RNA primes cDNA synthesis, promotes processivity, terminates polymerization, and strictly limits mutagenesis to select proteins through mechanisms that are likely conserved in DGRs from distant taxa.
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13
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von Kügelgen A, Cassidy CK, van Dorst S, Pagani LL, Batters C, Ford Z, Löwe J, Alva V, Stansfeld PJ, Bharat TAM. Membraneless channels sieve cations in ammonia-oxidizing marine archaea. Nature 2024; 630:230-236. [PMID: 38811725 PMCID: PMC11153153 DOI: 10.1038/s41586-024-07462-5] [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: 01/13/2023] [Accepted: 04/24/2024] [Indexed: 05/31/2024]
Abstract
Nitrosopumilus maritimus is an ammonia-oxidizing archaeon that is crucial to the global nitrogen cycle1,2. A critical step for nitrogen oxidation is the entrapment of ammonium ions from a dilute marine environment at the cell surface and their subsequent channelling to the cell membrane of N. maritimus. Here we elucidate the structure of the molecular machinery responsible for this process, comprising the surface layer (S-layer), using electron cryotomography and subtomogram averaging from cells. We supplemented our in situ structure of the ammonium-binding S-layer array with a single-particle electron cryomicroscopy structure, revealing detailed features of this immunoglobulin-rich and glycan-decorated S-layer. Biochemical analyses showed strong ammonium binding by the cell surface, which was lost after S-layer disassembly. Sensitive bioinformatic analyses identified similar S-layers in many ammonia-oxidizing archaea, with conserved sequence and structural characteristics. Moreover, molecular simulations and structure determination of ammonium-enriched specimens enabled us to examine the cation-binding properties of the S-layer, revealing how it concentrates ammonium ions on its cell-facing side, effectively acting as a multichannel sieve on the cell membrane. This in situ structural study illuminates the biogeochemically essential process of ammonium binding and channelling, common to many marine microorganisms that are fundamental to the nitrogen cycle.
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Affiliation(s)
- Andriko von Kügelgen
- Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, UK
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - C Keith Cassidy
- Department of Physics and Astronomy, University of Missouri-Columbia, Columbia, MO, USA
| | - Sofie van Dorst
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Lennart L Pagani
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Christopher Batters
- Protein and Nucleic Acid Chemistry Division, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Zephyr Ford
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Jan Löwe
- Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Vikram Alva
- Department of Protein Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Phillip J Stansfeld
- School of Life Sciences and Department of Chemistry, University of Warwick, Coventry, UK
| | - Tanmay A M Bharat
- Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, UK.
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14
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Kimanius D, Schwab J. Confronting heterogeneity in cryogenic electron microscopy data: Innovative strategies and future perspectives with data-driven methods. Curr Opin Struct Biol 2024; 86:102815. [PMID: 38657561 DOI: 10.1016/j.sbi.2024.102815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 02/26/2024] [Accepted: 03/26/2024] [Indexed: 04/26/2024]
Abstract
The surge in the influx of data from cryogenic electron microscopy (cryo-EM) experiments has intensified the demand for robust algorithms capable of autonomously managing structurally heterogeneous datasets. This presents a wealth of exciting opportunities from a data science viewpoint, inspiring the development of numerous innovative, application-specific methods, many of which leverage contemporary data-driven techniques. However, addressing the challenges posed by heterogeneous datasets remains a paramount yet unresolved issue in the field. Here, we explore the subtleties of this challenge and the array of strategies devised to confront it. We pinpoint the shortcomings of existing methodologies and deliberate on prospective avenues for improvement. Specifically, our discussion focuses on strategies to mitigate model overfitting and manage data noise, as well as the effects of constraints, priors, and invariances on the optimization process.
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Affiliation(s)
- Dari Kimanius
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK; CZ Imaging Institute, 3400 Bridge Parkway, Redwood City, CA 94065, USA.
| | - Johannes Schwab
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
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15
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Warren AL, Lankri D, Cunningham MJ, Serrano IC, Parise LF, Kruegel AC, Duggan P, Zilberg G, Capper MJ, Havel V, Russo SJ, Sames D, Wacker D. Structural pharmacology and therapeutic potential of 5-methoxytryptamines. Nature 2024; 630:237-246. [PMID: 38720072 PMCID: PMC11152992 DOI: 10.1038/s41586-024-07403-2] [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: 02/14/2023] [Accepted: 04/09/2024] [Indexed: 06/07/2024]
Abstract
Psychedelic substances such as lysergic acid diethylamide (LSD) and psilocybin show potential for the treatment of various neuropsychiatric disorders1-3. These compounds are thought to mediate their hallucinogenic and therapeutic effects through the serotonin (5-hydroxytryptamine (5-HT)) receptor 5-HT2A (ref. 4). However, 5-HT1A also plays a part in the behavioural effects of tryptamine hallucinogens5, particularly 5-methoxy-N,N-dimethyltryptamine (5-MeO-DMT), a psychedelic found in the toxin of Colorado River toads6. Although 5-HT1A is a validated therapeutic target7,8, little is known about how psychedelics engage 5-HT1A and which effects are mediated by this receptor. Here we map the molecular underpinnings of 5-MeO-DMT pharmacology through five cryogenic electron microscopy (cryo-EM) structures of 5-HT1A, systematic medicinal chemistry, receptor mutagenesis and mouse behaviour. Structure-activity relationship analyses of 5-methoxytryptamines at both 5-HT1A and 5-HT2A enable the characterization of molecular determinants of 5-HT1A signalling potency, efficacy and selectivity. Moreover, we contrast the structural interactions and in vitro pharmacology of 5-MeO-DMT and analogues to the pan-serotonergic agonist LSD and clinically used 5-HT1A agonists. We show that a 5-HT1A-selective 5-MeO-DMT analogue is devoid of hallucinogenic-like effects while retaining anxiolytic-like and antidepressant-like activity in socially defeated animals. Our studies uncover molecular aspects of 5-HT1A-targeted psychedelics and therapeutics, which may facilitate the future development of new medications for neuropsychiatric disorders.
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MESH Headings
- Animals
- Humans
- Male
- Mice
- 5-Methoxytryptamine/analogs & derivatives
- 5-Methoxytryptamine/chemistry
- 5-Methoxytryptamine/pharmacology
- 5-Methoxytryptamine/therapeutic use
- Anti-Anxiety Agents/chemistry
- Anti-Anxiety Agents/pharmacology
- Anti-Anxiety Agents/therapeutic use
- Antidepressive Agents/chemistry
- Antidepressive Agents/pharmacology
- Antidepressive Agents/therapeutic use
- Cryoelectron Microscopy
- Hallucinogens
- Lysergic Acid Diethylamide/chemistry
- Lysergic Acid Diethylamide/pharmacology
- Methoxydimethyltryptamines/chemistry
- Methoxydimethyltryptamines/pharmacology
- Methoxydimethyltryptamines/therapeutic use
- Models, Molecular
- Receptor, Serotonin, 5-HT1A/chemistry
- Receptor, Serotonin, 5-HT1A/genetics
- Receptor, Serotonin, 5-HT1A/metabolism
- Receptor, Serotonin, 5-HT1A/ultrastructure
- Receptor, Serotonin, 5-HT2A/chemistry
- Receptor, Serotonin, 5-HT2A/genetics
- Receptor, Serotonin, 5-HT2A/metabolism
- Receptor, Serotonin, 5-HT2A/ultrastructure
- Serotonin Receptor Agonists/chemistry
- Serotonin Receptor Agonists/pharmacology
- Serotonin Receptor Agonists/therapeutic use
- Structure-Activity Relationship
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Affiliation(s)
- Audrey L Warren
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - David Lankri
- Department of Chemistry, Columbia University, New York, NY, USA
| | | | - Inis C Serrano
- Department of Chemistry, Columbia University, New York, NY, USA
| | - Lyonna F Parise
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | | | - Gregory Zilberg
- Zuckerman Institute of Mind, Brain, Behavior, Columbia University, New York, NY, USA
| | - Michael J Capper
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Vaclav Havel
- Department of Chemistry, Columbia University, New York, NY, USA
| | - Scott J Russo
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Dalibor Sames
- Department of Chemistry, Columbia University, New York, NY, USA.
- Zuckerman Institute of Mind, Brain, Behavior, Columbia University, New York, NY, USA.
| | - Daniel Wacker
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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16
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Hiraizumi M, Perry NT, Durrant MG, Soma T, Nagahata N, Okazaki S, Athukoralage JS, Isayama Y, Pai JJ, Pawluk A, Konermann S, Yamashita K, Hsu PD, Nishimasu H. Structural mechanism of bridge RNA-guided recombination. Nature 2024; 630:994-1002. [PMID: 38926616 PMCID: PMC11208158 DOI: 10.1038/s41586-024-07570-2] [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: 11/27/2023] [Accepted: 05/15/2024] [Indexed: 06/28/2024]
Abstract
Insertion sequence (IS) elements are the simplest autonomous transposable elements found in prokaryotic genomes1. We recently discovered that IS110 family elements encode a recombinase and a non-coding bridge RNA (bRNA) that confers modular specificity for target DNA and donor DNA through two programmable loops2. Here we report the cryo-electron microscopy structures of the IS110 recombinase in complex with its bRNA, target DNA and donor DNA in three different stages of the recombination reaction cycle. The IS110 synaptic complex comprises two recombinase dimers, one of which houses the target-binding loop of the bRNA and binds to target DNA, whereas the other coordinates the bRNA donor-binding loop and donor DNA. We uncovered the formation of a composite RuvC-Tnp active site that spans the two dimers, positioning the catalytic serine residues adjacent to the recombination sites in both target and donor DNA. A comparison of the three structures revealed that (1) the top strands of target and donor DNA are cleaved at the composite active sites to form covalent 5'-phosphoserine intermediates, (2) the cleaved DNA strands are exchanged and religated to create a Holliday junction intermediate, and (3) this intermediate is subsequently resolved by cleavage of the bottom strands. Overall, this study reveals the mechanism by which a bispecific RNA confers target and donor DNA specificity to IS110 recombinases for programmable DNA recombination.
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Affiliation(s)
- Masahiro Hiraizumi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Nicholas T Perry
- Arc Institute, Palo Alto, CA, USA
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- San Francisco Graduate Program in Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | | | - Teppei Soma
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Naoto Nagahata
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Sae Okazaki
- Structural Biology Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | | | - Yukari Isayama
- Structural Biology Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | | | | | - Silvana Konermann
- Arc Institute, Palo Alto, CA, USA
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Keitaro Yamashita
- Structural Biology Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Patrick D Hsu
- Arc Institute, Palo Alto, CA, USA.
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA.
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA.
| | - Hiroshi Nishimasu
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan.
- Structural Biology Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan.
- Inamori Research Institute for Science, Kyoto, Japan.
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17
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Goto S, Tsutsumi A, Lee Y, Hosojima M, Kabasawa H, Komochi K, Nagatoishi S, Takemoto K, Tsumoto K, Nishizawa T, Kikkawa M, Saito A. Cryo-EM structures elucidate the multiligand receptor nature of megalin. Proc Natl Acad Sci U S A 2024; 121:e2318859121. [PMID: 38771880 PMCID: PMC11145282 DOI: 10.1073/pnas.2318859121] [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: 10/30/2023] [Accepted: 04/19/2024] [Indexed: 05/23/2024] Open
Abstract
Megalin (low-density lipoprotein receptor-related protein 2) is a giant glycoprotein of about 600 kDa, mediating the endocytosis of more than 60 ligands, including those of proteins, peptides, and drug compounds [S. Goto, M. Hosojima, H. Kabasawa, A. Saito, Int. J. Biochem. Cell Biol. 157, 106393 (2023)]. It is expressed predominantly in renal proximal tubule epithelial cells, as well as in the brain, lungs, eyes, inner ear, thyroid gland, and placenta. Megalin is also known to mediate the endocytosis of toxic compounds, particularly those that cause renal and hearing disorders [Y. Hori et al., J. Am. Soc. Nephrol. 28, 1783-1791 (2017)]. Genetic megalin deficiency causes Donnai-Barrow syndrome/facio-oculo-acoustico-renal syndrome in humans. However, it is not known how megalin interacts with such a wide variety of ligands and plays pathological roles in various organs. In this study, we elucidated the dimeric architecture of megalin, purified from rat kidneys, using cryoelectron microscopy. The maps revealed the densities of endogenous ligands bound to various regions throughout the dimer, elucidating the multiligand receptor nature of megalin. We also determined the structure of megalin in complex with receptor-associated protein, a molecular chaperone for megalin. The results will facilitate further studies on the pathophysiology of megalin-dependent multiligand endocytic pathways in multiple organs and will also be useful for the development of megalin-targeted drugs for renal and hearing disorders, Alzheimer's disease [B. V. Zlokovic et al., Proc. Natl. Acad. Sci. U.S.A. 93, 4229-4234 (1996)], and other illnesses.
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Affiliation(s)
- Sawako Goto
- Department of Applied Molecular Medicine, Kidney Research Center, Niigata University Graduate School of Medical and Dental Sciences, Niigata City951-8510, Japan
| | - Akihisa Tsutsumi
- Department of Cell Biology and Anatomy, Graduate School of Medicine, The University of Tokyo, Tokyo113-0033, Japan
| | - Yongchan Lee
- Department of the Biological Membrane Dynamics, Graduate School of Medical Life Science, Yokohama City University, Yokohama230-0045, Japan
| | - Michihiro Hosojima
- Department of Clinical Nutrition Science, Kidney Research Center, Niigata University Graduate School of Medical and Dental Sciences, Niigata City951-8510, Japan
| | - Hideyuki Kabasawa
- Department of Clinical Nutrition Science, Kidney Research Center, Niigata University Graduate School of Medical and Dental Sciences, Niigata City951-8510, Japan
| | - Koichi Komochi
- Department of Clinical Nutrition Science, Kidney Research Center, Niigata University Graduate School of Medical and Dental Sciences, Niigata City951-8510, Japan
| | - Satoru Nagatoishi
- Medical Device Development and Regulation Research Center, School of Engineering, The University of Tokyo, Tokyo113-8656, Japan
| | - Kazuya Takemoto
- Department of Applied Molecular Medicine, Kidney Research Center, Niigata University Graduate School of Medical and Dental Sciences, Niigata City951-8510, Japan
| | - Kouhei Tsumoto
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo113-8656, Japan
| | - Tomohiro Nishizawa
- Department of the Biological Membrane Dynamics, Graduate School of Medical Life Science, Yokohama City University, Yokohama230-0045, Japan
| | - Masahide Kikkawa
- Department of Cell Biology and Anatomy, Graduate School of Medicine, The University of Tokyo, Tokyo113-0033, Japan
| | - Akihiko Saito
- Department of Applied Molecular Medicine, Kidney Research Center, Niigata University Graduate School of Medical and Dental Sciences, Niigata City951-8510, Japan
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18
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Koller TO, Berger MJ, Morici M, Paternoga H, Bulatov T, Di Stasi A, Dang T, Mainz A, Raulf K, Crowe-McAuliffe C, Scocchi M, Mardirossian M, Beckert B, Vázquez-Laslop N, Mankin A, Süssmuth RD, Wilson DN. Paenilamicins from the honey bee pathogen Paenibacillus larvae are context-specific translocation inhibitors of protein synthesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.21.595107. [PMID: 38826346 PMCID: PMC11142091 DOI: 10.1101/2024.05.21.595107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
The paenilamicins are a group of hybrid non-ribosomal peptide-polyketide compounds produced by the honey bee pathogen Paenibacillus larvae that display activity against Gram-positive pathogens, such as Staphylococcus aureus. While paenilamicins have been shown to inhibit protein synthesis, their mechanism of action has remained unclear. Here, we have determined structures of the paenilamicin PamB2 stalled ribosomes, revealing a unique binding site on the small 30S subunit located between the A- and P-site tRNAs. In addition to providing a precise description of interactions of PamB2 with the ribosome, the structures also rationalize the resistance mechanisms utilized by P. larvae. We could further demonstrate that PamB2 interferes with the translocation of mRNA and tRNAs through the ribosome during translation elongation, and that this inhibitory activity is influenced by the presence of modifications at position 37 of the A-site tRNA. Collectively, our study defines the paenilamicins as a new class of context-specific translocation inhibitors.
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Affiliation(s)
- Timm O. Koller
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Max J. Berger
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Martino Morici
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Helge Paternoga
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Timur Bulatov
- Institut für Chemie, Technische Universität Berlin, 10623 Berlin, Germany
| | - Adriana Di Stasi
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy
| | - Tam Dang
- Institut für Chemie, Technische Universität Berlin, 10623 Berlin, Germany
| | - Andi Mainz
- Institut für Chemie, Technische Universität Berlin, 10623 Berlin, Germany
| | - Karoline Raulf
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Caillan Crowe-McAuliffe
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Marco Scocchi
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy
| | - Mario Mardirossian
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy
| | - Bertrand Beckert
- Dubochet Center for Imaging (DCI) at EPFL, EPFL SB IPHYS DCI, Lausanne, Switzerland
| | - Nora Vázquez-Laslop
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL 60607
| | - Alexander Mankin
- Center for Biomolecular Sciences, University of Illinois at Chicago, Chicago, IL 60607
| | | | - Daniel N. Wilson
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
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19
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Hamaguchi-Suzuki N, Adachi N, Moriya T, Yasuda S, Kawasaki M, Suzuki K, Ogasawara S, Anzai N, Senda T, Murata T. Cryo-EM structure of P-glycoprotein bound to triple elacridar inhibitor molecules. Biochem Biophys Res Commun 2024; 709:149855. [PMID: 38579618 DOI: 10.1016/j.bbrc.2024.149855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 03/27/2024] [Indexed: 04/07/2024]
Abstract
P-glycoprotein (P-gp) is an ATP-binding cassette transporter known for its roles in expelling xenobiotic compounds from cells and contributing to cellular drug resistance through multidrug efflux. This mechanism is particularly problematic in cancer cells, where it diminishes the therapeutic efficacy of anticancer drugs. P-gp inhibitors, such as elacridar, have been developed to circumvent the decrease in drug efficacy due to P-gp efflux. An earlier study reported the cryo-EM structure of human P-gp-Fab (MRK-16) complex bound by two elacridar molecules, at a resolution of 3.6 Å. In this study, we have obtained a higher resolution (2.5 Å) structure of the P-gp- Fab (UIC2) complex bound by three elacridar molecules. This finding, which exposes a larger space for compound-binding sites than previously acknowledged, has significant implications for the development of more selective inhibitors and enhances our understanding of the compound recognition mechanism of P-gp.
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Affiliation(s)
- Norie Hamaguchi-Suzuki
- Department of Pharmacology, Chiba University Graduate School of Medicine, 1-8-1 Inohana, Chuo, Chiba, 260-8670, Japan; Department of Chemistry, Graduate School of Science, Chiba University, 1-33 Yayoi-cho, Inage, Chiba, 263-8522, Japan
| | - Naruhiko Adachi
- Structure Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1, Oho, Tsukuba, 305-0801, Japan; Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8577, Japan
| | - Toshio Moriya
- Structure Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1, Oho, Tsukuba, 305-0801, Japan
| | - Satoshi Yasuda
- Department of Chemistry, Graduate School of Science, Chiba University, 1-33 Yayoi-cho, Inage, Chiba, 263-8522, Japan; Membrane Protein Research Center, Chiba University, 1-33 Yayoi-cho, Inage, Chiba, 263-8522, Japan
| | - Masato Kawasaki
- Structure Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1, Oho, Tsukuba, 305-0801, Japan
| | - Kano Suzuki
- Department of Chemistry, Graduate School of Science, Chiba University, 1-33 Yayoi-cho, Inage, Chiba, 263-8522, Japan; Membrane Protein Research Center, Chiba University, 1-33 Yayoi-cho, Inage, Chiba, 263-8522, Japan
| | - Satoshi Ogasawara
- Department of Chemistry, Graduate School of Science, Chiba University, 1-33 Yayoi-cho, Inage, Chiba, 263-8522, Japan; Membrane Protein Research Center, Chiba University, 1-33 Yayoi-cho, Inage, Chiba, 263-8522, Japan
| | - Naohiko Anzai
- Department of Pharmacology, Chiba University Graduate School of Medicine, 1-8-1 Inohana, Chuo, Chiba, 260-8670, Japan
| | - Toshiya Senda
- Structure Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1, Oho, Tsukuba, 305-0801, Japan
| | - Takeshi Murata
- Department of Chemistry, Graduate School of Science, Chiba University, 1-33 Yayoi-cho, Inage, Chiba, 263-8522, Japan; Membrane Protein Research Center, Chiba University, 1-33 Yayoi-cho, Inage, Chiba, 263-8522, Japan.
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20
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Qi C, Kobayashi R, Kawakatsu S, Kametani F, Scheres SHW, Goedert M, Hasegawa M. Tau filaments with the chronic traumatic encephalopathy fold in a case of vacuolar tauopathy with VCP mutation D395G. Acta Neuropathol 2024; 147:86. [PMID: 38758288 PMCID: PMC7616110 DOI: 10.1007/s00401-024-02741-x] [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: 04/01/2024] [Revised: 05/09/2024] [Accepted: 05/09/2024] [Indexed: 05/18/2024]
Abstract
Dominantly inherited mutation D395G in the gene encoding valosin-containing protein causes vacuolar tauopathy, a type of behavioural-variant frontotemporal dementia, with marked vacuolation and abundant filamentous tau inclusions made of all six brain isoforms. Here we report that tau inclusions were concentrated in layers II/III of the frontotemporal cortex in a case of vacuolar tauopathy. By electron cryomicroscopy, tau filaments had the chronic traumatic encephalopathy (CTE) fold. Tau inclusions of vacuolar tauopathy share this cortical location and the tau fold with CTE, subacute sclerosing panencephalitis and amyotrophic lateral sclerosis/parkinsonism-dementia complex, which are believed to be environmentally induced. Vacuolar tauopathy is the first inherited disease with the CTE tau fold.
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Affiliation(s)
- Chao Qi
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Ryota Kobayashi
- Department of Psychiatry, Yamagata University School of Medicine, Yamagata, Japan
| | - Shinobu Kawakatsu
- Department of Neuropsychiatry, Aizu Medical Center, Fukushima Medical University, Aizuwakamatsu, Japan
| | - Fuyuki Kametani
- Department of Brain and Neurosciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Sjors H W Scheres
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.
| | - Michel Goedert
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.
| | - Masato Hasegawa
- Department of Brain and Neurosciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan.
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21
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Schneider S, Brandina I, Peter D, Lagad S, Fraudeau A, Portell-Montserrat J, Tholen J, Zhao J, Galej WP. Structure of the human 20S U5 snRNP. Nat Struct Mol Biol 2024; 31:752-756. [PMID: 38467877 PMCID: PMC11102862 DOI: 10.1038/s41594-024-01250-5] [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: 08/11/2023] [Accepted: 02/14/2024] [Indexed: 03/13/2024]
Abstract
The 20S U5 small nuclear ribonucleoprotein particle (snRNP) is a 17-subunit RNA-protein complex and a precursor of the U4/U6.U5 tri-snRNP, the major building block of the precatalytic spliceosome. CD2BP2 is a hallmark protein of the 20S U5 snRNP, absent from the mature tri-snRNP. Here we report a high-resolution cryogenic electron microscopy structure of the 20S U5 snRNP, shedding light on the mutually exclusive interfaces utilized during tri-snRNP assembly and the role of the CD2BP2 in facilitating this process.
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Affiliation(s)
- Sarah Schneider
- European Molecular Biology Laboratory, EMBL Grenoble, Grenoble, France
| | - Irina Brandina
- European Molecular Biology Laboratory, EMBL Grenoble, Grenoble, France
| | - Daniel Peter
- European Molecular Biology Laboratory, EMBL Grenoble, Grenoble, France
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | - Sonal Lagad
- European Molecular Biology Laboratory, EMBL Grenoble, Grenoble, France
| | | | - Júlia Portell-Montserrat
- European Molecular Biology Laboratory, EMBL Grenoble, Grenoble, France
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
| | - Jonas Tholen
- European Molecular Biology Laboratory, EMBL Grenoble, Grenoble, France
- Department of Structural Biology, Genentech Inc., South San Francisco, CA, USA
| | - Jiangfeng Zhao
- European Molecular Biology Laboratory, EMBL Grenoble, Grenoble, France
| | - Wojciech P Galej
- European Molecular Biology Laboratory, EMBL Grenoble, Grenoble, France.
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22
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Qi C, Lövestam S, Murzin AG, Peak-Chew S, Franco C, Bogdani M, Latimer C, Murrell JR, Cullinane PW, Jaunmuktane Z, Bird TD, Ghetti B, Scheres SH, Goedert M. Tau filaments with the Alzheimer fold in cases with MAPT mutations V337M and R406W. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.29.591661. [PMID: 38746388 PMCID: PMC11092478 DOI: 10.1101/2024.04.29.591661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Frontotemporal dementia (FTD) and Alzheimer's disease are the most common forms of early-onset dementia. Dominantly inherited mutations in MAPT, the microtubule-associated protein tau gene, cause FTD and parkinsonism linked to chromosome 17 (FTDP-17). Individuals with FTDP-17 develop abundant filamentous tau inclusions in brain cells. Here we used electron cryo-microscopy to determine the structures of tau filaments from the brains of individuals with MAPT mutations V337M and R406W. Both mutations gave rise to tau filaments with the Alzheimer fold, which consisted of paired helical filaments in all V337M and R406W cases and of straight filaments in two V337M cases. We also identified a new assembly of the Alzheimer fold into triple tau filaments in a V337M case. Filaments assembled from recombinant tau(297-391) with mutation V337M had the Alzheimer fold and showed an increased rate of assembly.
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Affiliation(s)
- Chao Qi
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | | | | | | | | | - Marika Bogdani
- Departments of Neurology and Pathology, University of Washington, Seattle, USA
- Veterans Administration Puget Sound Health Care System, Seattle, USA
| | - Caitlin Latimer
- Departments of Neurology and Pathology, University of Washington, Seattle, USA
- Veterans Administration Puget Sound Health Care System, Seattle, USA
| | - Jill R. Murrell
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, USA
- Department of Pathology and Laboratory Medicine, Children’s Hospital of the University of Pennsylvania, Philadelphia, USA
| | - Patrick W. Cullinane
- Department of Clinical and Movement Neurosciences, Queen Square Institute of Neurology, University College, London UK
- Queen Square Brain Bank for Neurological Disorders, Institute of Neurology, University College, London, UK
| | - Zane Jaunmuktane
- Department of Clinical and Movement Neurosciences, Queen Square Institute of Neurology, University College, London UK
- Queen Square Brain Bank for Neurological Disorders, Institute of Neurology, University College, London, UK
| | - Thomas D. Bird
- Departments of Neurology and Pathology, University of Washington, Seattle, USA
- Veterans Administration Puget Sound Health Care System, Seattle, USA
| | - Bernardino Ghetti
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, USA
| | - Sjors H.W. Scheres
- MRC Laboratory of Molecular Biology, Cambridge, UK
- These authors jointly supervised this work: Sjors H.W. Scheres, Michel Goedert
| | - Michel Goedert
- MRC Laboratory of Molecular Biology, Cambridge, UK
- These authors jointly supervised this work: Sjors H.W. Scheres, Michel Goedert
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23
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Rauscher R, Eggers C, Dimitrova-Paternoga L, Shankar V, Rosina A, Cristodero M, Paternoga H, Wilson DN, Leidel SA, Polacek N. Evolving precision: rRNA expansion segment 7S modulates translation velocity and accuracy in eukaryal ribosomes. Nucleic Acids Res 2024; 52:4021-4036. [PMID: 38324474 DOI: 10.1093/nar/gkae067] [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: 08/20/2023] [Revised: 01/16/2024] [Accepted: 01/22/2024] [Indexed: 02/09/2024] Open
Abstract
Ribosome-enhanced translational miscoding of the genetic code causes protein dysfunction and loss of cellular fitness. During evolution, open reading frame length increased, necessitating mechanisms for enhanced translation fidelity. Indeed, eukaryal ribosomes are more accurate than bacterial counterparts, despite their virtually identical, conserved active centers. During the evolution of eukaryotic organisms ribosome expansions at the rRNA and protein level occurred, which potentially increases the options for translation regulation and cotranslational events. Here we tested the hypothesis that ribosomal RNA expansions can modulate the core function of the ribosome, faithful protein synthesis. We demonstrate that a short expansion segment present in all eukaryotes' small subunit, ES7S, is crucial for accurate protein synthesis as its presence adjusts codon-specific velocities and guarantees high levels of cognate tRNA selection. Deletion of ES7S in yeast enhances mistranslation and causes protein destabilization and aggregation, dramatically reducing cellular fitness. Removal of ES7S did not alter ribosome architecture but altered the structural dynamics of inter-subunit bridges thus affecting A-tRNA selection. Exchanging the yeast ES7S sequence with the human ES7S increases accuracy whereas shortening causes the opposite effect. Our study demonstrates that ES7S provided eukaryal ribosomes with higher accuracy without perturbing the structurally conserved decoding center.
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Affiliation(s)
- Robert Rauscher
- Department for Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Cristian Eggers
- Department for Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Lyudmila Dimitrova-Paternoga
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Vaishnavi Shankar
- Department for Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Alessia Rosina
- Department for Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Marina Cristodero
- Department for Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Helge Paternoga
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Daniel N Wilson
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Sebastian A Leidel
- Department for Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Norbert Polacek
- Department for Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
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24
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Yamagata A, Ito K, Suzuki T, Dohmae N, Terada T, Shirouzu M. Structural basis for antiepileptic drugs and botulinum neurotoxin recognition of SV2A. Nat Commun 2024; 15:3027. [PMID: 38637505 PMCID: PMC11026379 DOI: 10.1038/s41467-024-47322-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 03/26/2024] [Indexed: 04/20/2024] Open
Abstract
More than one percent of people have epilepsy worldwide. Levetiracetam (LEV) is a successful new-generation antiepileptic drug (AED), and its derivative, brivaracetam (BRV), shows improved efficacy. Synaptic vesicle glycoprotein 2a (SV2A), a putative membrane transporter in the synaptic vesicles (SVs), has been identified as a target of LEV and BRV. SV2A also serves as a receptor for botulinum neurotoxin (BoNT), which is the most toxic protein and has paradoxically emerged as a potent reagent for therapeutic and cosmetic applications. Nevertheless, no structural analysis on AEDs and BoNT recognition by full-length SV2A has been available. Here we describe the cryo-electron microscopy structures of the full-length SV2A in complex with the BoNT receptor-binding domain, BoNT/A2 HC, and either LEV or BRV. The large fourth luminal domain of SV2A binds to BoNT/A2 HC through protein-protein and protein-glycan interactions. LEV and BRV occupy the putative substrate-binding site in an outward-open conformation. A propyl group in BRV creates additional contacts with SV2A, explaining its higher binding affinity than that of LEV, which was further supported by label-free spectral shift assay. Numerous LEV derivatives have been developed as AEDs and positron emission tomography (PET) tracers for neuroimaging. Our work provides a structural framework for AEDs and BoNT recognition of SV2A and a blueprint for the rational design of additional AEDs and PET tracers.
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Affiliation(s)
- Atsushi Yamagata
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, Japan.
| | - Kaori Ito
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, Japan
| | - Takehiro Suzuki
- Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, Japan
| | - Naoshi Dohmae
- Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, Japan
| | - Tohru Terada
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, Japan
| | - Mikako Shirouzu
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, Japan
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25
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Sauer PV, Cupellini L, Sutter M, Bondanza M, Domínguez Martin MA, Kirst H, Bína D, Koh AF, Kotecha A, Greber BJ, Nogales E, Polívka7 T, Mennucci B, Kerfeld CA. Structural and quantum chemical basis for OCP-mediated quenching of phycobilisomes. SCIENCE ADVANCES 2024; 10:eadk7535. [PMID: 38578996 PMCID: PMC10997198 DOI: 10.1126/sciadv.adk7535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 03/04/2024] [Indexed: 04/07/2024]
Abstract
Cyanobacteria use large antenna complexes called phycobilisomes (PBSs) for light harvesting. However, intense light triggers non-photochemical quenching, where the orange carotenoid protein (OCP) binds to PBS, dissipating excess energy as heat. The mechanism of efficiently transferring energy from phycocyanobilins in PBS to canthaxanthin in OCP remains insufficiently understood. Using cryo-electron microscopy, we unveiled the OCP-PBS complex structure at 1.6- to 2.1-angstrom resolution, showcasing its inherent flexibility. Using multiscale quantum chemistry, we disclosed the quenching mechanism. Identifying key protein residues, we clarified how canthaxanthin's transition dipole moment in its lowest-energy dark state becomes large enough for efficient energy transfer from phycocyanobilins. Our energy transfer model offers a detailed understanding of the atomic determinants of light harvesting regulation and antenna architecture in cyanobacteria.
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Affiliation(s)
- Paul V. Sauer
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
| | - Lorenzo Cupellini
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, I-56124 Pisa, Italy
| | - Markus Sutter
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Mattia Bondanza
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, I-56124 Pisa, Italy
| | - María Agustina Domínguez Martin
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Henning Kirst
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - David Bína
- Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic
- Biology Centre of the Czech Academy of Sciences, Ceske Budejovice, Czech Republic
| | | | | | - Basil J. Greber
- Division of Structural Biology, The Institute of Cancer Research, London SW7 3RP, UK
| | - Eva Nogales
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Molecular and Cellular Biology, University of California, Berkeley, CA 94720, USA
| | - Tomáš Polívka7
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, I-56124 Pisa, Italy
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic
- Biology Centre of the Czech Academy of Sciences, Ceske Budejovice, Czech Republic
- Thermo Fisher Scientific, Eindhoven, Netherlands
- Division of Structural Biology, The Institute of Cancer Research, London SW7 3RP, UK
- Department of Molecular and Cellular Biology, University of California, Berkeley, CA 94720, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, I-56124 Pisa, Italy
| | - Cheryl A. Kerfeld
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
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26
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Jamali K, Käll L, Zhang R, Brown A, Kimanius D, Scheres SHW. Automated model building and protein identification in cryo-EM maps. Nature 2024; 628:450-457. [PMID: 38408488 PMCID: PMC11006616 DOI: 10.1038/s41586-024-07215-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 02/19/2024] [Indexed: 02/28/2024]
Abstract
Interpreting electron cryo-microscopy (cryo-EM) maps with atomic models requires high levels of expertise and labour-intensive manual intervention in three-dimensional computer graphics programs1,2. Here we present ModelAngelo, a machine-learning approach for automated atomic model building in cryo-EM maps. By combining information from the cryo-EM map with information from protein sequence and structure in a single graph neural network, ModelAngelo builds atomic models for proteins that are of similar quality to those generated by human experts. For nucleotides, ModelAngelo builds backbones with similar accuracy to those built by humans. By using its predicted amino acid probabilities for each residue in hidden Markov model sequence searches, ModelAngelo outperforms human experts in the identification of proteins with unknown sequences. ModelAngelo will therefore remove bottlenecks and increase objectivity in cryo-EM structure determination.
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Affiliation(s)
| | - Lukas Käll
- Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Rui Zhang
- Washington University in St Louis, St Louis, MO, USA
| | - Alan Brown
- Blavatnik Institute, Harvard Medical School, Boston, MA, USA
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27
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Morici M, Gabrielli S, Fujiwara K, Paternoga H, Beckert B, Bock LV, Chiba S, Wilson DN. RAPP-containing arrest peptides induce translational stalling by short circuiting the ribosomal peptidyltransferase activity. Nat Commun 2024; 15:2432. [PMID: 38503735 PMCID: PMC10951233 DOI: 10.1038/s41467-024-46761-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 01/24/2024] [Indexed: 03/21/2024] Open
Abstract
Arrest peptides containing RAPP (ArgAlaProPro) motifs have been discovered in both Gram-positive and Gram-negative bacteria, where they are thought to regulate expression of important protein localization machinery components. Here we determine cryo-EM structures of ribosomes stalled on RAPP arrest motifs in both Bacillus subtilis and Escherichia coli. Together with molecular dynamics simulations, our structures reveal that the RAPP motifs allow full accommodation of the A-site tRNA, but prevent the subsequent peptide bond from forming. Our data support a model where the RAP in the P-site interacts and stabilizes a single hydrogen atom on the Pro-tRNA in the A-site, thereby preventing an optimal geometry for the nucleophilic attack required for peptide bond formation to occur. This mechanism to short circuit the ribosomal peptidyltransferase activity is likely to operate for the majority of other RAPP-like arrest peptides found across diverse bacterial phylogenies.
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Affiliation(s)
- Martino Morici
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146, Hamburg, Germany
| | - Sara Gabrielli
- Theoretical and Computational Biophysics Department, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Keigo Fujiwara
- Faculty of Life Sciences and Institute for Protein Dynamics, Kyoto Sangyo University, Kamigamo, Motoyama, Kita-ku, Kyoto, 603-8555, Japan
| | - Helge Paternoga
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146, Hamburg, Germany
| | - Bertrand Beckert
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146, Hamburg, Germany
| | - Lars V Bock
- Theoretical and Computational Biophysics Department, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Shinobu Chiba
- Faculty of Life Sciences and Institute for Protein Dynamics, Kyoto Sangyo University, Kamigamo, Motoyama, Kita-ku, Kyoto, 603-8555, Japan.
| | - Daniel N Wilson
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146, Hamburg, Germany.
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28
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Gersteuer F, Morici M, Gabrielli S, Fujiwara K, Safdari HA, Paternoga H, Bock LV, Chiba S, Wilson DN. The SecM arrest peptide traps a pre-peptide bond formation state of the ribosome. Nat Commun 2024; 15:2431. [PMID: 38503753 PMCID: PMC10951299 DOI: 10.1038/s41467-024-46762-2] [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: 10/30/2023] [Accepted: 03/07/2024] [Indexed: 03/21/2024] Open
Abstract
Nascent polypeptide chains can induce translational stalling to regulate gene expression. This is exemplified by the E. coli secretion monitor (SecM) arrest peptide that induces translational stalling to regulate expression of the downstream encoded SecA, an ATPase that co-operates with the SecYEG translocon to facilitate insertion of proteins into or through the cytoplasmic membrane. Here we present the structure of a ribosome stalled during translation of the full-length E. coli SecM arrest peptide at 2.0 Å resolution. The structure reveals that SecM arrests translation by stabilizing the Pro-tRNA in the A-site, but in a manner that prevents peptide bond formation with the SecM-peptidyl-tRNA in the P-site. By employing molecular dynamic simulations, we also provide insight into how a pulling force on the SecM nascent chain can relieve the SecM-mediated translation arrest. Collectively, the mechanisms determined here for SecM arrest and relief are also likely to be applicable for a variety of other arrest peptides that regulate components of the protein localization machinery identified across a wide range of bacteria lineages.
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Affiliation(s)
- Felix Gersteuer
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146, Hamburg, Germany
| | - Martino Morici
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146, Hamburg, Germany
| | - Sara Gabrielli
- Theoretical and Computational Biophysics Department, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Keigo Fujiwara
- Faculty of Life Sciences and Institute for Protein Dynamics, Kyoto Sangyo University, Kamigamo, Motoyama, Kita-ku, Kyoto, 603-8555, Japan
| | - Haaris A Safdari
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146, Hamburg, Germany
| | - Helge Paternoga
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146, Hamburg, Germany
| | - Lars V Bock
- Theoretical and Computational Biophysics Department, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Shinobu Chiba
- Faculty of Life Sciences and Institute for Protein Dynamics, Kyoto Sangyo University, Kamigamo, Motoyama, Kita-ku, Kyoto, 603-8555, Japan
| | - Daniel N Wilson
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146, Hamburg, Germany.
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29
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Watanabe S, Kise Y, Yonezawa K, Inoue M, Shimizu N, Nureki O, Inaba K. Structure of full-length ERGIC-53 in complex with MCFD2 for cargo transport. Nat Commun 2024; 15:2404. [PMID: 38493152 PMCID: PMC10944485 DOI: 10.1038/s41467-024-46747-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 03/07/2024] [Indexed: 03/18/2024] Open
Abstract
ERGIC-53 transports certain subsets of newly synthesized secretory proteins and membrane proteins from the endoplasmic reticulum to the Golgi apparatus. Despite numerous structural and functional studies since its identification, the overall architecture and mechanism of action of ERGIC-53 remain unclear. Here we present cryo-EM structures of full-length ERGIC-53 in complex with its functional partner MCFD2. These structures reveal that ERGIC-53 exists as a homotetramer, not a homohexamer as previously suggested, and comprises a four-leaf clover-like head and a long stalk composed of three sets of four-helix coiled-coil followed by a transmembrane domain. 3D variability analysis visualizes the flexible motion of the long stalk and local plasticity of the head region. Notably, MCFD2 is shown to possess a Zn2+-binding site in its N-terminal lid, which appears to modulate cargo binding. Altogether, distinct mechanisms of cargo capture and release by ERGIC- 53 via the stalk bending and metal binding are proposed.
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Affiliation(s)
- Satoshi Watanabe
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, Miyagi, 980-8577, Japan.
- Department of Molecular and Chemical Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, 980-8577, Japan.
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, Miyagi, 980-8578, Japan.
| | - Yoshiaki Kise
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Kento Yonezawa
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki, 305-0801, Japan
- Center for Digital Green-innovation, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
| | - Mariko Inoue
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, Miyagi, 980-8577, Japan
| | - Nobutaka Shimizu
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki, 305-0801, Japan
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Kenji Inaba
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, Miyagi, 980-8577, Japan.
- Department of Molecular and Chemical Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, 980-8577, Japan.
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, Miyagi, 980-8578, Japan.
- Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan.
- Core Research for Evolutional Science and Technology (CREST), Japan Agency for Medical Research and Development (AMED), Tokyo, Japan.
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30
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Cushing VI, Koh AF, Feng J, Jurgaityte K, Bondke A, Kroll SHB, Barbazanges M, Scheiper B, Bahl AK, Barrett AGM, Ali S, Kotecha A, Greber BJ. High-resolution cryo-EM of the human CDK-activating kinase for structure-based drug design. Nat Commun 2024; 15:2265. [PMID: 38480681 PMCID: PMC10937634 DOI: 10.1038/s41467-024-46375-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 02/23/2024] [Indexed: 03/17/2024] Open
Abstract
Rational design of next-generation therapeutics can be facilitated by high-resolution structures of drug targets bound to small-molecule inhibitors. However, application of structure-based methods to macromolecules refractory to crystallization has been hampered by the often-limiting resolution and throughput of cryogenic electron microscopy (cryo-EM). Here, we use high-resolution cryo-EM to determine structures of the CDK-activating kinase, a master regulator of cell growth and division, in its free and nucleotide-bound states and in complex with 15 inhibitors at up to 1.8 Å resolution. Our structures provide detailed insight into inhibitor interactions and networks of water molecules in the active site of cyclin-dependent kinase 7 and provide insights into the mechanisms contributing to inhibitor selectivity, thereby providing the basis for rational design of next-generation therapeutics. These results establish a methodological framework for the use of high-resolution cryo-EM in structure-based drug design.
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Affiliation(s)
- Victoria I Cushing
- The Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London, SW3 6JB, UK
| | - Adrian F Koh
- Materials and Structural Analysis Division, Thermo Fisher Scientific, Achtseweg Noord 5, 5651, Eindhoven, The Netherlands
| | - Junjie Feng
- The Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London, SW3 6JB, UK
| | - Kaste Jurgaityte
- Division of Cancer, Department of Surgery & Cancer, Imperial College London, Hammersmith Hospital Campus, London, UK
| | | | | | - Marion Barbazanges
- Department of Chemistry, Imperial College London, London, UK
- Institut Parisien de Chimie Moléculaire, Sorbonne Université, CNRS, 4 Place Jussieu, 75252, Paris Cedex 05, France
| | - Bodo Scheiper
- Department of Chemistry, Imperial College London, London, UK
| | - Ash K Bahl
- Carrick Therapeutics, Nova UCD, Bellfield Innovation Park, Dublin 4, Ireland
| | | | - Simak Ali
- Division of Cancer, Department of Surgery & Cancer, Imperial College London, Hammersmith Hospital Campus, London, UK.
| | - Abhay Kotecha
- Materials and Structural Analysis Division, Thermo Fisher Scientific, Achtseweg Noord 5, 5651, Eindhoven, The Netherlands.
| | - Basil J Greber
- The Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London, SW3 6JB, UK.
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31
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Kato K, Hamaguchi T, Kumazawa M, Nakajima Y, Ifuku K, Hirooka S, Hirose Y, Miyagishima SY, Suzuki T, Kawakami K, Dohmae N, Yonekura K, Shen JR, Nagao R. The structure of PSI-LHCI from Cyanidium caldarium provides evolutionary insights into conservation and diversity of red-lineage LHCs. Proc Natl Acad Sci U S A 2024; 121:e2319658121. [PMID: 38442179 PMCID: PMC10945839 DOI: 10.1073/pnas.2319658121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 01/31/2024] [Indexed: 03/07/2024] Open
Abstract
Light-harvesting complexes (LHCs) are diversified among photosynthetic organisms, and the structure of the photosystem I-LHC (PSI-LHCI) supercomplex has been shown to be variable depending on the species of organisms. However, the structural and evolutionary correlations of red-lineage LHCs are unknown. Here, we determined a 1.92-Å resolution cryoelectron microscopic structure of a PSI-LHCI supercomplex isolated from the red alga Cyanidium caldarium RK-1 (NIES-2137), which is an important taxon in the Cyanidiophyceae. We subsequently investigated the correlations of PSI-LHCIs from different organisms through structural comparisons and phylogenetic analysis. The PSI-LHCI structure obtained shows five LHCI subunits surrounding a PSI-monomer core. The five LHCIs are composed of two Lhcr1s, two Lhcr2s, and one Lhcr3. Phylogenetic analysis of LHCs bound to PSI in the red-lineage algae showed clear orthology of LHCs between C. caldarium and Cyanidioschyzon merolae, whereas no orthologous relationships were found between C. caldarium Lhcr1-3 and LHCs in other red-lineage PSI-LHCI structures. These findings provide evolutionary insights into conservation and diversity of red-lineage LHCs associated with PSI.
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Affiliation(s)
- Koji Kato
- Division of Photosynthesis and Structural Biology, Research Institute for Interdisciplinary Science, and Graduate School of Natural Science and Technology, Okayama University, Okayama700-8530, Japan
| | - Tasuku Hamaguchi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Miyagi980-8577, Japan
- Biostructural Mechanism Laboratory, RIKEN SPring-8 Center, Hyogo679-5148, Japan
| | - Minoru Kumazawa
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto606-8502, Japan
| | - Yoshiki Nakajima
- Division of Photosynthesis and Structural Biology, Research Institute for Interdisciplinary Science, and Graduate School of Natural Science and Technology, Okayama University, Okayama700-8530, Japan
| | - Kentaro Ifuku
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto606-8502, Japan
| | - Shunsuke Hirooka
- Department of Gene Function and Phenomics, National Institute of Genetics, Shizuoka411-8540, Japan
| | - Yuu Hirose
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, Aichi441-8580, Japan
| | - Shin-ya Miyagishima
- Department of Gene Function and Phenomics, National Institute of Genetics, Shizuoka411-8540, Japan
- Department of Genetics, The Graduate University for Advanced Studies (SOKENDAI), Shizuoka411-8540, Japan
| | - Takehiro Suzuki
- Biomolecular Characterization Unit, Technology Platform Division, RIKEN Center for Sustainable Resource Science, Saitama351-0198, Japan
| | - Keisuke Kawakami
- Biostructural Mechanism Laboratory, RIKEN SPring-8 Center, Hyogo679-5148, Japan
| | - Naoshi Dohmae
- Biomolecular Characterization Unit, Technology Platform Division, RIKEN Center for Sustainable Resource Science, Saitama351-0198, Japan
| | - Koji Yonekura
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Miyagi980-8577, Japan
- Biostructural Mechanism Laboratory, RIKEN SPring-8 Center, Hyogo679-5148, Japan
| | - Jian-Ren Shen
- Division of Photosynthesis and Structural Biology, Research Institute for Interdisciplinary Science, and Graduate School of Natural Science and Technology, Okayama University, Okayama700-8530, Japan
| | - Ryo Nagao
- Department of Applied Life Sciences, Faculty of Agriculture, Shizuoka University, Shizuoka422-8529, Japan
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32
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DaRosa PA, Penchev I, Gumbin SC, Scavone F, Wąchalska M, Paulo JA, Ordureau A, Peter JJ, Kulathu Y, Harper JW, Becker T, Beckmann R, Kopito RR. UFM1 E3 ligase promotes recycling of 60S ribosomal subunits from the ER. Nature 2024; 627:445-452. [PMID: 38383785 DOI: 10.1038/s41586-024-07073-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 01/15/2024] [Indexed: 02/23/2024]
Abstract
Reversible modification of target proteins by ubiquitin and ubiquitin-like proteins (UBLs) is widely used by eukaryotic cells to control protein fate and cell behaviour1. UFM1 is a UBL that predominantly modifies a single lysine residue on a single ribosomal protein, uL24 (also called RPL26), on ribosomes at the cytoplasmic surface of the endoplasmic reticulum (ER)2,3. UFM1 conjugation (UFMylation) facilitates the rescue of 60S ribosomal subunits (60S) that are released after ribosome-associated quality-control-mediated splitting of ribosomes that stall during co-translational translocation of secretory proteins into the ER3,4. Neither the molecular mechanism by which the UFMylation machinery achieves such precise target selection nor how this ribosomal modification promotes 60S rescue is known. Here we show that ribosome UFMylation in vivo occurs on free 60S and we present sequential cryo-electron microscopy snapshots of the heterotrimeric UFM1 E3 ligase (E3(UFM1)) engaging its substrate uL24. E3(UFM1) binds the L1 stalk, empty transfer RNA-binding sites and the peptidyl transferase centre through carboxy-terminal domains of UFL1, which results in uL24 modification more than 150 Å away. After catalysing UFM1 transfer, E3(UFM1) remains stably bound to its product, UFMylated 60S, forming a C-shaped clamp that extends all the way around the 60S from the transfer RNA-binding sites to the polypeptide tunnel exit. Our structural and biochemical analyses suggest a role for E3(UFM1) in post-termination release and recycling of the large ribosomal subunit from the ER membrane.
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Affiliation(s)
- Paul A DaRosa
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Ivan Penchev
- Department of Biochemistry, Gene Center, University of Munich, Munich, Germany
| | | | | | - Magda Wąchalska
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Alban Ordureau
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
- Cell Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Joshua J Peter
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit (MRC-PPU), School of Life Sciences, University of Dundee, Dundee, UK
| | - Yogesh Kulathu
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit (MRC-PPU), School of Life Sciences, University of Dundee, Dundee, UK
| | - J Wade Harper
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Thomas Becker
- Department of Biochemistry, Gene Center, University of Munich, Munich, Germany
| | - Roland Beckmann
- Department of Biochemistry, Gene Center, University of Munich, Munich, Germany.
| | - Ron R Kopito
- Department of Biology, Stanford University, Stanford, CA, USA.
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33
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Hernandez-Gonzalez M, Calcraft T, Nans A, Rosenthal PB, Way M. Palisade structure in intact vaccinia virions. mBio 2024; 15:e0313423. [PMID: 38171004 PMCID: PMC10865856 DOI: 10.1128/mbio.03134-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 11/30/2023] [Indexed: 01/05/2024] Open
Abstract
Vaccinia virus assembly in the cytoplasm of infected cells involves the formation of a biconcave viral core inside the maturing viral particle. The boundary of the core is defined by a pseudohexagonal palisade layer, composed of trimers projecting from an inner wall. To understand the assembly of this complex core architecture, we obtained a subnanometer structure of the palisade trimer by cryo-electron tomography and subtomogram averaging of purified intact virions. Using AlphaFold2 structure predictions, we determined that the palisade is formed from trimers of the proteolytically processed form of the viral protein A10. In addition, we found that each A10 protomer associates with an α-helix (residues 24-66) of A4. Cellular localization assays outside the context of infection demonstrate that the A4 N-terminus is necessary and sufficient to interact with A10. The interaction between A4 and A10 provides insights into how the palisade layer might become tightly associated with the viral membrane during virion maturation. Reconstruction of the palisade layer reveals that, despite local hexagonal ordering, the A10/A4 trimers are widely spaced, suggesting that additional components organize the lattice. This spacing would, however, allow the adoption of the characteristic biconcave shape of the viral core. Finally, we also found that the palisade incorporates multiple copies of a hexameric portal structure. We suggest that these portals are formed by E6, a viral protein that is essential for virion assembly and required to release viral mRNA from the core early in infection.IMPORTANCEPoxviruses such as variola virus (smallpox) and monkeypox cause diseases in humans. Other poxviruses, including vaccinia and modified vaccinia Ankara, are used as vaccine vectors. Given their importance, a greater structural understanding of poxvirus virions is needed. We now performed cryo-electron tomography of purified intact vaccinia virions to study the structure of the palisade, a protein lattice that defines the viral core boundary. We identified the main viral proteins that form the palisade and their interaction surfaces and provided new insights into the organization of the viral core.
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Affiliation(s)
- Miguel Hernandez-Gonzalez
- Cellular Signalling and Cytoskeletal Function Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Thomas Calcraft
- Structural Biology of Cells and Viruses Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Andrea Nans
- Structural Biology Science Technology Platform, The Francis Crick Institute, London, United Kingdom
| | - Peter B. Rosenthal
- Structural Biology of Cells and Viruses Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Michael Way
- Cellular Signalling and Cytoskeletal Function Laboratory, The Francis Crick Institute, London, United Kingdom
- Department of Infectious Disease, Imperial College, London, United Kingdom
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34
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Izume T, Kawahara R, Uwamizu A, Chen L, Yaginuma S, Omi J, Kawana H, Hou F, Sano FK, Tanaka T, Kobayashi K, Okamoto HH, Kise Y, Ohwada T, Aoki J, Shihoya W, Nureki O. Structural basis for lysophosphatidylserine recognition by GPR34. Nat Commun 2024; 15:902. [PMID: 38326347 PMCID: PMC10850092 DOI: 10.1038/s41467-024-45046-z] [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: 12/27/2022] [Accepted: 01/12/2024] [Indexed: 02/09/2024] Open
Abstract
GPR34 is a recently identified G-protein coupled receptor, which has an immunomodulatory role and recognizes lysophosphatidylserine (LysoPS) as a putative ligand. Here, we report cryo-electron microscopy structures of human GPR34-Gi complex bound with one of two ligands bound: either the LysoPS analogue S3E-LysoPS, or M1, a derivative of S3E-LysoPS in which oleic acid is substituted with a metabolically stable aromatic fatty acid surrogate. The ligand-binding pocket is laterally open toward the membrane, allowing lateral entry of lipidic agonists into the cavity. The amine and carboxylate groups of the serine moiety are recognized by the charged residue cluster. The acyl chain of S3E-LysoPS is bent and fits into the L-shaped hydrophobic pocket in TM4-5 gap, and the aromatic fatty acid surrogate of M1 fits more appropriately. Molecular dynamics simulations further account for the LysoPS-regioselectivity of GPR34. Thus, using a series of structural and physiological experiments, we provide evidence that chemically unstable 2-acyl LysoPS is the physiological ligand for GPR34. Overall, we anticipate the present structures will pave the way for development of novel anticancer drugs that specifically target GPR34.
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Affiliation(s)
- Tamaki Izume
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Ryo Kawahara
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Akiharu Uwamizu
- Department of Health Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Luying Chen
- Department of Organic and Medicinal Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Shun Yaginuma
- Department of Health Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Jumpei Omi
- Department of Health Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Hiroki Kawana
- Department of Health Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Fengjue Hou
- Department of Health Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Fumiya K Sano
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Tatsuki Tanaka
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Kazuhiro Kobayashi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Hiroyuki H Okamoto
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Yoshiaki Kise
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Tomohiko Ohwada
- Department of Organic and Medicinal Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
| | - Junken Aoki
- Department of Health Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
| | - Wataru Shihoya
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan.
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan.
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35
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Dimitrova-Paternoga L, Kasvandik S, Beckert B, Granneman S, Tenson T, Wilson DN, Paternoga H. Structural basis of ribosomal 30S subunit degradation by RNase R. Nature 2024; 626:1133-1140. [PMID: 38326618 PMCID: PMC10901742 DOI: 10.1038/s41586-024-07027-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 01/04/2024] [Indexed: 02/09/2024]
Abstract
Protein synthesis is a major energy-consuming process of the cell that requires the controlled production1-3 and turnover4,5 of ribosomes. Although the past few years have seen major advances in our understanding of ribosome biogenesis, structural insight into the degradation of ribosomes has been lacking. Here we present native structures of two distinct small ribosomal 30S subunit degradation intermediates associated with the 3' to 5' exonuclease ribonuclease R (RNase R). The structures reveal that RNase R binds at first to the 30S platform to facilitate the degradation of the functionally important anti-Shine-Dalgarno sequence and the decoding-site helix 44. RNase R then encounters a roadblock when it reaches the neck region of the 30S subunit, and this is overcome by a major structural rearrangement of the 30S head, involving the loss of ribosomal proteins. RNase R parallels this movement and relocates to the decoding site by using its N-terminal helix-turn-helix domain as an anchor. In vitro degradation assays suggest that head rearrangement poses a major kinetic barrier for RNase R, but also indicate that the enzyme alone is sufficient for complete degradation of 30S subunits. Collectively, our results provide a mechanistic basis for the degradation of 30S mediated by RNase R, and reveal that RNase R targets orphaned 30S subunits using a dynamic mechanism involving an anchored switching of binding sites.
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Affiliation(s)
| | - Sergo Kasvandik
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Bertrand Beckert
- Dubochet Center for Imaging (DCI) at EPFL, EPFL SB IPHYS DCI, Lausanne, Switzerland
| | - Sander Granneman
- Centre for Engineering Biology (SynthSys), University of Edinburgh, Edinburgh, UK
| | - Tanel Tenson
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Daniel N Wilson
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany.
| | - Helge Paternoga
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Hamburg, Germany.
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36
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Lawson CL, Kryshtafovych A, Pintilie GD, Burley SK, Černý J, Chen VB, Emsley P, Gobbi A, Joachimiak A, Noreng S, Prisant M, Read RJ, Richardson JS, Rohou AL, Schneider B, Sellers BD, Shao C, Sourial E, Williams CI, Williams CJ, Yang Y, Abbaraju V, Afonine PV, Baker ML, Bond PS, Blundell TL, Burnley T, Campbell A, Cao R, Cheng J, Chojnowski G, Cowtan KD, DiMaio F, Esmaeeli R, Giri N, Grubmüller H, Hoh SW, Hou J, Hryc CF, Hunte C, Igaev M, Joseph AP, Kao WC, Kihara D, Kumar D, Lang L, Lin S, Maddhuri Venkata Subramaniya SR, Mittal S, Mondal A, Moriarty NW, Muenks A, Murshudov GN, Nicholls RA, Olek M, Palmer CM, Perez A, Pohjolainen E, Pothula KR, Rowley CN, Sarkar D, Schäfer LU, Schlicksup CJ, Schröder GF, Shekhar M, Si D, Singharoy A, Sobolev OV, Terashi G, Vaiana AC, Vedithi SC, Verburgt J, Wang X, Warshamanage R, Winn MD, Weyand S, Yamashita K, Zhao M, Schmid MF, Berman HM, Chiu W. Outcomes of the EMDataResource Cryo-EM Ligand Modeling Challenge. RESEARCH SQUARE 2024:rs.3.rs-3864137. [PMID: 38343795 PMCID: PMC10854310 DOI: 10.21203/rs.3.rs-3864137/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/18/2024]
Abstract
The EMDataResource Ligand Model Challenge aimed to assess the reliability and reproducibility of modeling ligands bound to protein and protein/nucleic-acid complexes in cryogenic electron microscopy (cryo-EM) maps determined at near-atomic (1.9-2.5 Å) resolution. Three published maps were selected as targets: E. coli beta-galactosidase with inhibitor, SARS-CoV-2 RNA-dependent RNA polymerase with covalently bound nucleotide analog, and SARS-CoV-2 ion channel ORF3a with bound lipid. Sixty-one models were submitted from 17 independent research groups, each with supporting workflow details. We found that (1) the quality of submitted ligand models and surrounding atoms varied, as judged by visual inspection and quantification of local map quality, model-to-map fit, geometry, energetics, and contact scores, and (2) a composite rather than a single score was needed to assess macromolecule+ligand model quality. These observations lead us to recommend best practices for assessing cryo-EM structures of liganded macromolecules reported at near-atomic resolution.
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Affiliation(s)
- Catherine L. Lawson
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | | | - Grigore D. Pintilie
- Departments of Bioengineering and of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - Stephen K. Burley
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
- Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ USA
- San Diego Supercomputer Center, University of California San Diego, La Jolla, CA USA
| | - Jiří Černý
- Institute of Biotechnology, Czech Academy of Sciences, Vestec, CZ
| | | | - Paul Emsley
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Alberto Gobbi
- Discovery Chemistry, Genentech Inc, South San Francisco, USA
| | - Andrzej Joachimiak
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL, USA
| | - Sigrid Noreng
- Structural Biology, Genentech Inc, South San Francisco, USA
| | | | - Randy J. Read
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | | | | | - Bohdan Schneider
- Institute of Biotechnology, Czech Academy of Sciences, Vestec, CZ
| | | | - Chenghua Shao
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | | | | | | | - Ying Yang
- Structural Biology, Genentech Inc, South San Francisco, USA
| | - Venkat Abbaraju
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Pavel V. Afonine
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Matthew L. Baker
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Paul S. Bond
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK
| | - Tom L. Blundell
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Tom Burnley
- Scientific Computing Department, UKRI Science and Technology Facilities Council, Research Complex at Harwell, Didcot, UK
| | - Arthur Campbell
- Center for Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Renzhi Cao
- Department of Computer Science, Pacific Lutheran University, Tacoma, WA, USA
| | - Jianlin Cheng
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, USA
| | | | - Kevin D. Cowtan
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK
| | - Frank DiMaio
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Reza Esmaeeli
- Department of Chemistry and Quantum Theory Project, University of Florida, Gainesville, FL, USA
| | - Nabin Giri
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, USA
| | - Helmut Grubmüller
- Theoretical and Computational Biophysics Department, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Soon Wen Hoh
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK
| | - Jie Hou
- Department of Computer Science, Saint Louis University, St. Louis, MO, USA
| | - Corey F. Hryc
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Carola Hunte
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine and CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Maxim Igaev
- Theoretical and Computational Biophysics Department, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Agnel P. Joseph
- Scientific Computing Department, UKRI Science and Technology Facilities Council, Research Complex at Harwell, Didcot, UK
| | - Wei-Chun Kao
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine and CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Daisuke Kihara
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
- Department of Computer Science, Purdue University, West Lafayette, IN, USA
| | - Dilip Kumar
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Lijun Lang
- Department of Chemistry and Quantum Theory Project, University of Florida, Gainesville, FL, USA
| | - Sean Lin
- Division of Computing & Software Systems, University of Washington, Bothell, WA, USA
| | | | - Sumit Mittal
- Biodesign Institute, Arizona State University, Tempe, AZ, USA
- School of Advanced Sciences and Languages, VIT Bhopal University, Bhopal, India
| | - Arup Mondal
- Department of Chemistry and Quantum Theory Project, University of Florida, Gainesville, FL, USA
| | - Nigel W. Moriarty
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Andrew Muenks
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, USA
| | | | | | - Mateusz Olek
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK
- Electron Bio-Imaging Centre, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Colin M. Palmer
- Scientific Computing Department, UKRI Science and Technology Facilities Council, Research Complex at Harwell, Didcot, UK
| | - Alberto Perez
- Department of Chemistry and Quantum Theory Project, University of Florida, Gainesville, FL, USA
| | - Emmi Pohjolainen
- Theoretical and Computational Biophysics Department, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Karunakar R. Pothula
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry) and Jülich Centre for Structural Biology (JuStruct), Forschungszentrum Jülich, Jülich, Germany
| | | | - Daipayan Sarkar
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
- Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Luisa U. Schäfer
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry) and Jülich Centre for Structural Biology (JuStruct), Forschungszentrum Jülich, Jülich, Germany
| | - Christopher J. Schlicksup
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Gunnar F. Schröder
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry) and Jülich Centre for Structural Biology (JuStruct), Forschungszentrum Jülich, Jülich, Germany
- Physics Department, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Mrinal Shekhar
- Center for Development of Therapeutics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Dong Si
- Division of Computing & Software Systems, University of Washington, Bothell, WA, USA
| | | | - Oleg V. Sobolev
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Genki Terashi
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Andrea C. Vaiana
- Theoretical and Computational Biophysics Department, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Nature’s Toolbox (NTx), Rio Rancho, NM, USA
| | | | - Jacob Verburgt
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Xiao Wang
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | | | - Martyn D. Winn
- Scientific Computing Department, UKRI Science and Technology Facilities Council, Research Complex at Harwell, Didcot, UK
| | - Simone Weyand
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | | | - Minglei Zhao
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Michael F. Schmid
- Division of Cryo-EM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Helen M. Berman
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Wah Chiu
- Departments of Bioengineering and of Microbiology and Immunology, Stanford University, Stanford, CA, USA
- Division of Cryo-EM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
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37
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Zilberg G, Parpounas AK, Warren AL, Yang S, Wacker D. Molecular basis of human trace amine-associated receptor 1 activation. Nat Commun 2024; 15:108. [PMID: 38168118 PMCID: PMC10762035 DOI: 10.1038/s41467-023-44601-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 12/21/2023] [Indexed: 01/05/2024] Open
Abstract
The human trace amine-associated receptor 1 (hTAAR1, hTA1) is a key regulator of monoaminergic neurotransmission and the actions of psychostimulants. Despite preclinical research demonstrating its tractability as a drug target, its molecular mechanisms of activation remain unclear. Moreover, poorly understood pharmacological differences between rodent and human TA1 complicate the translation of findings from preclinical disease models into novel pharmacotherapies. To elucidate hTA1's mechanisms on the molecular scale and investigate the underpinnings of its divergent pharmacology from rodent orthologs, we herein report the structure of the human TA1 receptor in complex with a Gαs heterotrimer. Our structure reveals shared structural elements with other TAARs, as well as with its closest monoaminergic orthologue, the serotonin receptor 5-HT4R. We further find that a single mutation dramatically shifts the selectivity of hTA1 towards that of its rodent orthologues, and report on the effects of substituting residues to those found in serotonin and dopamine receptors. Strikingly, we also discover that the atypical antipsychotic medication and pan-monoaminergic antagonist asenapine potently and efficaciously activates hTA1. Together our studies provide detailed insight into hTA1 structure and function, contrast its molecular pharmacology with that of related receptors, and uncover off-target activities of monoaminergic drugs at hTA1.
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Affiliation(s)
- Gregory Zilberg
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
| | - Alexandra K Parpounas
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Audrey L Warren
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Shifan Yang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Daniel Wacker
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
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38
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Hiraizumi M, Akashi T, Murasaki K, Kishida H, Kumanomidou T, Torimoto N, Nureki O, Miyaguchi I. Transport and inhibition mechanism of the human SGLT2-MAP17 glucose transporter. Nat Struct Mol Biol 2024; 31:159-169. [PMID: 38057552 PMCID: PMC10803289 DOI: 10.1038/s41594-023-01134-0] [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: 01/10/2023] [Accepted: 09/22/2023] [Indexed: 12/08/2023]
Abstract
Sodium-glucose cotransporter 2 (SGLT2) is imporant in glucose reabsorption. SGLT2 inhibitors suppress renal glucose reabsorption, therefore reducing blood glucose levels in patients with type 2 diabetes. We and others have developed several SGLT2 inhibitors starting from phlorizin, a natural product. Using cryo-electron microscopy, we present the structures of human (h)SGLT2-MAP17 complexed with five natural or synthetic inhibitors. The four synthetic inhibitors (including canagliflozin) bind the transporter in the outward conformations, while phlorizin binds it in the inward conformation. The phlorizin-hSGLT2 interaction exhibits biphasic kinetics, suggesting that phlorizin alternately binds to the extracellular and intracellular sides. The Na+-bound outward-facing and unbound inward-open structures of hSGLT2-MAP17 suggest that the MAP17-associated bundle domain functions as a scaffold, with the hash domain rotating around the Na+-binding site. Thus, Na+ binding stabilizes the outward-facing conformation, and its release promotes state transition to inward-open conformation, exhibiting a role of Na+ in symport mechanism. These results provide structural evidence for the Na+-coupled alternating-access mechanism proposed for the transporter family.
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Affiliation(s)
- Masahiro Hiraizumi
- Discovery Technology Laboratories Sohyaku Innovative Research Division, Mitsubishi Tanabe Pharma, Yokohama, Japan.
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan.
| | - Tomoya Akashi
- DMPK Research Laboratories Sohyaku Innovative Research Division, Mitsubishi Tanabe Pharma, Yokohama, Japan
| | - Kouta Murasaki
- Discovery Technology Laboratories Sohyaku Innovative Research Division, Mitsubishi Tanabe Pharma, Yokohama, Japan
| | - Hiroyuki Kishida
- Discovery Technology Laboratories Sohyaku Innovative Research Division, Mitsubishi Tanabe Pharma, Yokohama, Japan
| | - Taichi Kumanomidou
- Discovery Technology Laboratories Sohyaku Innovative Research Division, Mitsubishi Tanabe Pharma, Yokohama, Japan
| | - Nao Torimoto
- Discovery Technology Laboratories Sohyaku Innovative Research Division, Mitsubishi Tanabe Pharma, Yokohama, Japan
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.
| | - Ikuko Miyaguchi
- Discovery Technology Laboratories Sohyaku Innovative Research Division, Mitsubishi Tanabe Pharma, Yokohama, Japan.
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39
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Tetter S, Arseni D, Murzin AG, Buhidma Y, Peak-Chew SY, Garringer HJ, Newell KL, Vidal R, Apostolova LG, Lashley T, Ghetti B, Ryskeldi-Falcon B. TAF15 amyloid filaments in frontotemporal lobar degeneration. Nature 2024; 625:345-351. [PMID: 38057661 PMCID: PMC10781619 DOI: 10.1038/s41586-023-06801-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 10/30/2023] [Indexed: 12/08/2023]
Abstract
Frontotemporal lobar degeneration (FTLD) causes frontotemporal dementia (FTD), the most common form of dementia after Alzheimer's disease, and is often also associated with motor disorders1. The pathological hallmarks of FTLD are neuronal inclusions of specific, abnormally assembled proteins2. In the majority of cases the inclusions contain amyloid filament assemblies of TAR DNA-binding protein 43 (TDP-43) or tau, with distinct filament structures characterizing different FTLD subtypes3,4. The presence of amyloid filaments and their identities and structures in the remaining approximately 10% of FTLD cases are unknown but are widely believed to be composed of the protein fused in sarcoma (FUS, also known as translocated in liposarcoma). As such, these cases are commonly referred to as FTLD-FUS. Here we used cryogenic electron microscopy (cryo-EM) to determine the structures of amyloid filaments extracted from the prefrontal and temporal cortices of four individuals with FTLD-FUS. Surprisingly, we found abundant amyloid filaments of the FUS homologue TATA-binding protein-associated factor 15 (TAF15, also known as TATA-binding protein-associated factor 2N) rather than of FUS itself. The filament fold is formed from residues 7-99 in the low-complexity domain (LCD) of TAF15 and was identical between individuals. Furthermore, we found TAF15 filaments with the same fold in the motor cortex and brainstem of two of the individuals, both showing upper and lower motor neuron pathology. The formation of TAF15 amyloid filaments with a characteristic fold in FTLD establishes TAF15 proteinopathy in neurodegenerative disease. The structure of TAF15 amyloid filaments provides a basis for the development of model systems of neurodegenerative disease, as well as for the design of diagnostic and therapeutic tools targeting TAF15 proteinopathy.
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Affiliation(s)
| | - Diana Arseni
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | | | - Yazead Buhidma
- Department of Neurodegenerative Diseases, UCL Queen Square Institute of Neurology, London, UK
| | | | - Holly J Garringer
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Kathy L Newell
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Ruben Vidal
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Liana G Apostolova
- Department of Neurology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Tammaryn Lashley
- Department of Neurodegenerative Diseases, UCL Queen Square Institute of Neurology, London, UK
- The Queen Square Brain Bank for Neurological Disorders, Department of Clinical and Movement Neuroscience, UCL Queen Square Institute of Neurology, London, UK
| | - Bernardino Ghetti
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
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40
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Nagaraj PH. Determining Macromolecular Structures Using Cryo-Electron Microscopy. Methods Mol Biol 2024; 2787:315-332. [PMID: 38656500 DOI: 10.1007/978-1-0716-3778-4_22] [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] [Indexed: 04/26/2024]
Abstract
Structural insights into macromolecular and protein complexes provide key clues about the molecular basis of the function. Cryogenic electron microscopy (cryo-EM) has emerged as a powerful structural biology method for studying protein and macromolecular structures at high resolution in both native and near-native states. Despite the ability to get detailed structural insights into the processes underlying protein function using cryo-EM, there has been hesitancy amongst plant biologists to apply the method for biomolecular interaction studies. This is largely evident from the relatively fewer structural depositions of proteins and protein complexes from plant origin in electron microscopy databank. Even though the progress has been slow, cryo-EM has significantly contributed to our understanding of the molecular biology processes underlying photosynthesis, energy transfer in plants, besides viruses infecting plants. This chapter introduces sample preparation for both negative-staining electron microscopy (NSEM) and cryo-EM for plant proteins and macromolecular complexes and data analysis using single particle analysis for beginners.
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Affiliation(s)
- Pradeep Hiriyur Nagaraj
- Institute of Molecular Biotechnology, Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria.
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41
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Qi C, Verheijen BM, Kokubo Y, Shi Y, Tetter S, Murzin AG, Nakahara A, Morimoto S, Vermulst M, Sasaki R, Aronica E, Hirokawa Y, Oyanagi K, Kakita A, Ryskeldi-Falcon B, Yoshida M, Hasegawa M, Scheres SHW, Goedert M. Tau filaments from amyotrophic lateral sclerosis/parkinsonism-dementia complex adopt the CTE fold. Proc Natl Acad Sci U S A 2023; 120:e2306767120. [PMID: 38100415 PMCID: PMC10743375 DOI: 10.1073/pnas.2306767120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 10/31/2023] [Indexed: 12/17/2023] Open
Abstract
The amyotrophic lateral sclerosis/parkinsonism-dementia complex (ALS/PDC) of the island of Guam and the Kii peninsula of Japan is a fatal neurodegenerative disease of unknown cause that is characterized by the presence of abundant filamentous tau inclusions in brains and spinal cords. Here, we used electron cryo-microscopy to determine the structures of tau filaments from the cerebral cortex of three cases of ALS/PDC from Guam and eight cases from Kii, as well as from the spinal cord of two of the Guam cases. Tau filaments had the chronic traumatic encephalopathy (CTE) fold, with variable amounts of Type I and Type II filaments. Paired helical tau filaments were also found in three Kii cases and tau filaments with the corticobasal degeneration fold in one Kii case. We identified a new Type III CTE tau filament, where protofilaments pack against each other in an antiparallel fashion. ALS/PDC is the third known tauopathy with CTE-type filaments and abundant tau inclusions in cortical layers II/III, the others being CTE and subacute sclerosing panencephalitis. Because these tauopathies are believed to have environmental causes, our findings support the hypothesis that ALS/PDC is caused by exogenous factors.
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Affiliation(s)
- Chao Qi
- Medical Research Council, Laboratory of Molecular Biology, CambridgeCB2 0QH, United Kingdom
| | - Bert M. Verheijen
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA90089
| | - Yasumasa Kokubo
- Graduate School of Regional Innovation Studies, Mie University, Tsu514-8507, Japan
| | - Yang Shi
- Medical Research Council, Laboratory of Molecular Biology, CambridgeCB2 0QH, United Kingdom
| | - Stephan Tetter
- Medical Research Council, Laboratory of Molecular Biology, CambridgeCB2 0QH, United Kingdom
| | - Alexey G. Murzin
- Medical Research Council, Laboratory of Molecular Biology, CambridgeCB2 0QH, United Kingdom
| | - Asa Nakahara
- Department of Pathology, Brain Research Institute, Niigata University, Niigata951-8585, Japan
| | - Satoru Morimoto
- Department of Oncologic Pathology, Graduate School of Medicine, Mie University, Tsu514-8507, Japan
| | - Marc Vermulst
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA90089
| | - Ryogen Sasaki
- Department of Nursing, Suzuka University of Medical Science, Suzuka513-8670, Japan
| | - Eleonora Aronica
- Department of Neuropathology, Amsterdam University Medical Centers (UMC), University of Amsterdam, Amsterdam Neuroscience, Amsterdam1105 AZ, The Netherlands
| | - Yoshifumi Hirokawa
- Department of Oncologic Pathology, Graduate School of Medicine, Mie University, Tsu514-8507, Japan
| | - Kiyomitsu Oyanagi
- Department of Brain Disease Research, Shinshu University School of Medicine, Matsumoto390-8621, Japan
| | - Akiyoshi Kakita
- Department of Pathology, Brain Research Institute, Niigata University, Niigata951-8585, Japan
| | | | - Mari Yoshida
- Department of Neuropathology, Institute for Medical Science of Aging, Aichi Medical University, Nagakute480-1195, Japan
| | - Masato Hasegawa
- Department of Brain and Neuroscience, Tokyo Metropolitan Institute of Medical Science, Tokyo156-8506, Japan
| | - Sjors H. W. Scheres
- Medical Research Council, Laboratory of Molecular Biology, CambridgeCB2 0QH, United Kingdom
| | - Michel Goedert
- Medical Research Council, Laboratory of Molecular Biology, CambridgeCB2 0QH, United Kingdom
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42
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McMullan G, Naydenova K, Mihaylov D, Yamashita K, Peet MJ, Wilson H, Dickerson JL, Chen S, Cannone G, Lee Y, Hutchings KA, Gittins O, Sobhy MA, Wells T, El-Gomati MM, Dalby J, Meffert M, Schulze-Briese C, Henderson R, Russo CJ. Structure determination by cryoEM at 100 keV. Proc Natl Acad Sci U S A 2023; 120:e2312905120. [PMID: 38011573 PMCID: PMC10710074 DOI: 10.1073/pnas.2312905120] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 10/02/2023] [Indexed: 11/29/2023] Open
Abstract
Electron cryomicroscopy can, in principle, determine the structures of most biological molecules but is currently limited by access, specimen preparation difficulties, and cost. We describe a purpose-built instrument operating at 100 keV-including advances in electron optics, detection, and processing-that makes structure determination fast and simple at a fraction of current costs. The instrument attains its theoretical performance limits, allowing atomic resolution imaging of gold test specimens and biological molecular structure determination in hours. We demonstrate its capabilities by determining the structures of eleven different specimens, ranging in size from 140 kDa to 2 MDa, using a fraction of the data normally required. CryoEM with a microscope designed specifically for high-efficiency, on-the-spot imaging of biological molecules will expand structural biology to a wide range of previously intractable problems.
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Affiliation(s)
- Greg McMullan
- Medical Research Council (MRC) Laboratory of Molecular Biology, CambridgeCB2 0QH, United Kingdom
| | - Katerina Naydenova
- Medical Research Council (MRC) Laboratory of Molecular Biology, CambridgeCB2 0QH, United Kingdom
| | - Daniel Mihaylov
- Medical Research Council (MRC) Laboratory of Molecular Biology, CambridgeCB2 0QH, United Kingdom
| | - Keitaro Yamashita
- Medical Research Council (MRC) Laboratory of Molecular Biology, CambridgeCB2 0QH, United Kingdom
| | - Mathew J. Peet
- Medical Research Council (MRC) Laboratory of Molecular Biology, CambridgeCB2 0QH, United Kingdom
| | - Hugh Wilson
- Medical Research Council (MRC) Laboratory of Molecular Biology, CambridgeCB2 0QH, United Kingdom
| | - Joshua L. Dickerson
- Medical Research Council (MRC) Laboratory of Molecular Biology, CambridgeCB2 0QH, United Kingdom
| | - Shaoxia Chen
- Medical Research Council (MRC) Laboratory of Molecular Biology, CambridgeCB2 0QH, United Kingdom
| | - Giuseppe Cannone
- Medical Research Council (MRC) Laboratory of Molecular Biology, CambridgeCB2 0QH, United Kingdom
| | - Yang Lee
- Medical Research Council (MRC) Laboratory of Molecular Biology, CambridgeCB2 0QH, United Kingdom
| | - Katherine A. Hutchings
- Medical Research Council (MRC) Laboratory of Molecular Biology, CambridgeCB2 0QH, United Kingdom
| | - Olivia Gittins
- Newcastle University, Newcastle upon TyneNE2 4HH, United Kingdom
| | - Mohamed A. Sobhy
- King Abdullah University of Science and Technology, Thuwal23955, Saudi Arabia
| | - Torquil Wells
- York Probe Sources Ltd., YorkYO26 6QU, United Kingdom
| | | | - Jason Dalby
- JEOL U.K. Ltd., Welwyn Garden CityAL7 1LT, United Kingdom
| | | | | | - Richard Henderson
- Medical Research Council (MRC) Laboratory of Molecular Biology, CambridgeCB2 0QH, United Kingdom
| | - Christopher J. Russo
- Medical Research Council (MRC) Laboratory of Molecular Biology, CambridgeCB2 0QH, United Kingdom
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43
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Yang Y, Murzin AG, Peak-Chew S, Franco C, Garringer HJ, Newell KL, Ghetti B, Goedert M, Scheres SHW. Cryo-EM structures of Aβ40 filaments from the leptomeninges of individuals with Alzheimer's disease and cerebral amyloid angiopathy. Acta Neuropathol Commun 2023; 11:191. [PMID: 38049918 PMCID: PMC10694933 DOI: 10.1186/s40478-023-01694-8] [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: 10/05/2023] [Accepted: 11/13/2023] [Indexed: 12/06/2023] Open
Abstract
We used electron cryo-microscopy (cryo-EM) to determine the structures of Aβ40 filaments from the leptomeninges of individuals with Alzheimer's disease and cerebral amyloid angiopathy. In agreement with previously reported structures, which were solved to a resolution of 4.4 Å, we found three types of filaments. However, our new structures, solved to a resolution of 2.4 Å, revealed differences in the sequence assignment that redefine the fold of Aβ40 peptides and their interactions. Filaments are made of pairs of protofilaments, the ordered core of which comprises D1-G38. The different filament types comprise one, two or three protofilament pairs. In each pair, residues H14-G37 of both protofilaments adopt an extended conformation and pack against each other in an anti-parallel fashion, held together by hydrophobic interactions and hydrogen bonds between main chains and side chains. Residues D1-H13 fold back on the adjacent parts of their own chains through both polar and non-polar interactions. There are also several additional densities of unknown identity. Sarkosyl extraction and aqueous extraction gave the same structures. By cryo-EM, parenchymal deposits of Aβ42 and blood vessel deposits of Aβ40 have distinct structures, supporting the view that Alzheimer's disease and cerebral amyloid angiopathy are different Aβ proteinopathies.
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Affiliation(s)
- Yang Yang
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.
| | - Alexey G Murzin
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Sew Peak-Chew
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Catarina Franco
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Holly J Garringer
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Kathy L Newell
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Bernardino Ghetti
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Michel Goedert
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.
| | - Sjors H W Scheres
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.
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44
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Adamoski D, Dias MM, Quesñay JEN, Yang Z, Zagoriy I, Steyer AM, Rodrigues CT, da Silva Bastos AC, da Silva BN, Costa RKE, de Abreu FMO, Islam Z, Cassago A, van Heel MG, Consonni SR, Mattei S, Mahamid J, Portugal RV, Ambrosio ALB, Dias SMG. Molecular mechanism of glutaminase activation through filamentation and the role of filaments in mitophagy protection. Nat Struct Mol Biol 2023; 30:1902-1912. [PMID: 37857822 DOI: 10.1038/s41594-023-01118-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 09/06/2023] [Indexed: 10/21/2023]
Abstract
Glutaminase (GLS), which deaminates glutamine to form glutamate, is a mitochondrial tetrameric protein complex. Although inorganic phosphate (Pi) is known to promote GLS filamentation and activation, the molecular basis of this mechanism is unknown. Here we aimed to determine the molecular mechanism of Pi-induced mouse GLS filamentation and its impact on mitochondrial physiology. Single-particle cryogenic electron microscopy revealed an allosteric mechanism in which Pi binding at the tetramer interface and the activation loop is coupled to direct nucleophile activation at the active site. The active conformation is prone to enzyme filamentation. Notably, human GLS filaments form inside tubulated mitochondria following glutamine withdrawal, as shown by in situ cryo-electron tomography of cells thinned by cryo-focused ion beam milling. Mitochondria with GLS filaments exhibit increased protection from mitophagy. We reveal roles of filamentous GLS in mitochondrial morphology and recycling.
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Affiliation(s)
- Douglas Adamoski
- Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, Brazil
| | - Marilia Meira Dias
- Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, Brazil
- Cancer Research UK Beatson Institute, Glasgow, UK
| | - Jose Edwin Neciosup Quesñay
- Sao Carlos Institute of Physics, University of Sao Paulo, Sao Carlos, Brazil
- Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Zhengyi Yang
- EMBL Imaging Centre, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Ievgeniia Zagoriy
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Anna M Steyer
- EMBL Imaging Centre, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Camila Tanimoto Rodrigues
- Sao Carlos Institute of Physics, University of Sao Paulo, Sao Carlos, Brazil
- Biological Sciences Department, School of Science, Purdue University, Lafayette, IN, USA
| | - Alliny Cristiny da Silva Bastos
- Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, Brazil
- Division of Medical Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Bianca Novaes da Silva
- Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, Brazil
- Graduate Program in Genetics and Molecular Biology, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Renna Karoline Eloi Costa
- Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, Brazil
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | | | - Zeyaul Islam
- Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, Brazil
- Diabetes Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar
| | - Alexandre Cassago
- Brazilian Nanotechnology National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, Brazil
- SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA, USA
| | - Marin Gerard van Heel
- Brazilian Nanotechnology National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, Brazil
| | - Sílvio Roberto Consonni
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Simone Mattei
- EMBL Imaging Centre, European Molecular Biology Laboratory, Heidelberg, Germany
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Julia Mahamid
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Rodrigo Villares Portugal
- Brazilian Nanotechnology National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, Brazil
| | | | - Sandra Martha Gomes Dias
- Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, Brazil.
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45
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Catapano L, Long F, Yamashita K, Nicholls RA, Steiner RA, Murshudov GN. Neutron crystallographic refinement with REFMAC5 from the CCP4 suite. Acta Crystallogr D Struct Biol 2023; 79:1056-1070. [PMID: 37921806 PMCID: PMC7615533 DOI: 10.1107/s2059798323008793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 10/05/2023] [Indexed: 11/04/2023] Open
Abstract
Hydrogen (H) atoms are abundant in macromolecules and often play critical roles in enzyme catalysis, ligand-recognition processes and protein-protein interactions. However, their direct visualization by diffraction techniques is challenging. Macromolecular X-ray crystallography affords the localization of only the most ordered H atoms at (sub-)atomic resolution (around 1.2 Å or higher). However, many H atoms of biochemical significance remain undetectable by this method. In contrast, neutron diffraction methods enable the visualization of most H atoms, typically in the form of deuterium (2H) atoms, at much more common resolution values (better than 2.5 Å). Thus, neutron crystallography, although technically demanding, is often the method of choice when direct information on protonation states is sought. REFMAC5 from the Collaborative Computational Project No. 4 (CCP4) is a program for the refinement of macromolecular models against X-ray crystallographic and cryo-EM data. This contribution describes its extension to include the refinement of structural models obtained from neutron crystallographic data. Stereochemical restraints with accurate bond distances between H atoms and their parent atom nuclei are now part of the CCP4 Monomer Library, the source of prior chemical information used in the refinement. One new feature for neutron data analysis in REFMAC5 is refinement of the protium/deuterium (1H/2H) fraction. This parameter describes the relative 1H/2H contribution to neutron scattering for hydrogen isotopes. The newly developed REFMAC5 algorithms were tested by performing the (re-)refinement of several entries available in the PDB and of one novel structure (FutA) using either (i) neutron data only or (ii) neutron data supplemented by external restraints to a reference X-ray crystallographic structure. Re-refinement with REFMAC5 afforded models characterized by R-factor values that are consistent with, and in some cases better than, the originally deposited values. The use of external reference structure restraints during refinement has been observed to be a valuable strategy, especially for structures at medium-low resolution.
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Affiliation(s)
- Lucrezia Catapano
- Randall Centre for Cell and Molecular Biophysics, Faculty of Life Sciences and Medicine, King’s College London, London SE1 9RT, United Kingdom
- Structural Studies, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Fei Long
- Structural Studies, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Keitaro Yamashita
- Structural Studies, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Robert A. Nicholls
- Structural Studies, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Roberto A. Steiner
- Randall Centre for Cell and Molecular Biophysics, Faculty of Life Sciences and Medicine, King’s College London, London SE1 9RT, United Kingdom
- Department of Biomedical Sciences, University of Padova, Via Ugo Bassi 58/B, 35131 Padova, Italy
| | - Garib N. Murshudov
- Structural Studies, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
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46
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Im D, Kishikawa JI, Shiimura Y, Hisano H, Ito A, Fujita-Fujiharu Y, Sugita Y, Noda T, Kato T, Asada H, Iwata S. Structural insights into the agonists binding and receptor selectivity of human histamine H 4 receptor. Nat Commun 2023; 14:6538. [PMID: 37863901 PMCID: PMC10589313 DOI: 10.1038/s41467-023-42260-z] [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: 08/07/2022] [Accepted: 10/04/2023] [Indexed: 10/22/2023] Open
Abstract
Histamine is a biogenic amine that participates in allergic and inflammatory processes by stimulating histamine receptors. The histamine H4 receptor (H4R) is a potential therapeutic target for chronic inflammatory diseases such as asthma and atopic dermatitis. Here, we show the cryo-electron microscopy structures of the H4R-Gq complex bound with an endogenous agonist histamine or the selective agonist imetit bound in the orthosteric binding pocket. The structures demonstrate binding mode of histamine agonists and that the subtype-selective agonist binding causes conformational changes in Phe3447.39, which, in turn, form the "aromatic slot". The results provide insights into the molecular underpinnings of the agonism of H4R and subtype selectivity of histamine receptors, and show that the H4R structures may be valuable in rational drug design of drugs targeting the H4R.
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Affiliation(s)
- Dohyun Im
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Konoe-cho, Yoshida, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Jun-Ichi Kishikawa
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Yuki Shiimura
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Konoe-cho, Yoshida, Sakyo-ku, Kyoto, 606-8501, Japan
- Institute of Life Science, Kurume University, Kurume, Fukuoka, 830-0011, Japan
| | - Hiromi Hisano
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Konoe-cho, Yoshida, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Akane Ito
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Konoe-cho, Yoshida, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Yoko Fujita-Fujiharu
- Laboratory of Ultrastructural Virology, Institute for Life and Medical Sciences, Kyoto University, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto, 606-8507, Japan
- Laboratory of Ultrastructural Virology, Graduate School of Biostudies, Kyoto University, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto, 606-8507, Japan
- CREST, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan
| | - Yukihiko Sugita
- Laboratory of Ultrastructural Virology, Institute for Life and Medical Sciences, Kyoto University, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto, 606-8507, Japan
- Laboratory of Ultrastructural Virology, Graduate School of Biostudies, Kyoto University, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto, 606-8507, Japan
- Hakubi Center for Advanced Research, Kyoto University, Kyoto, 606-8501, Japan
| | - Takeshi Noda
- Laboratory of Ultrastructural Virology, Institute for Life and Medical Sciences, Kyoto University, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto, 606-8507, Japan
- Laboratory of Ultrastructural Virology, Graduate School of Biostudies, Kyoto University, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto, 606-8507, Japan
- CREST, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan
| | - Takayuki Kato
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan.
| | - Hidetsugu Asada
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Konoe-cho, Yoshida, Sakyo-ku, Kyoto, 606-8501, Japan.
| | - So Iwata
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Konoe-cho, Yoshida, Sakyo-ku, Kyoto, 606-8501, Japan.
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan.
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47
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Schweighauser M, Murzin AG, Macdonald J, Lavenir I, Crowther RA, Scheres SHW, Goedert M. Cryo-EM structures of tau filaments from the brains of mice transgenic for human mutant P301S Tau. Acta Neuropathol Commun 2023; 11:160. [PMID: 37798679 PMCID: PMC10552433 DOI: 10.1186/s40478-023-01658-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 09/24/2023] [Indexed: 10/07/2023] Open
Abstract
Mice transgenic for human mutant P301S tau are widely used as models for human tauopathies. They develop neurodegeneration and abundant filamentous inclusions made of human mutant four-repeat tau. Here we used electron cryo-microscopy (cryo-EM) to determine the structures of tau filaments from the brains of Tg2541 and PS19 mice. Both lines express human P301S tau (0N4R for Tg2541 and 1N4R for PS19) on mixed genetic backgrounds and downstream of different promoters (murine Thy1 for Tg2541 and murine Prnp for PS19). The structures of tau filaments from Tg2541 and PS19 mice differ from each other and those of wild-type tau filaments from human brains. The structures of tau filaments from the brains of humans with mutations P301L, P301S or P301T in MAPT are not known. Filaments from the brains of Tg2541 and PS19 mice share a substructure at the junction of repeats 2 and 3, which comprises residues I297-V312 of tau and includes the P301S mutation. The filament core from the brainstem of Tg2541 mice consists of residues K274-H329 of tau and two disconnected protein densities. Two non-proteinaceous densities are also in evidence. The filament core from the cerebral cortex of line PS19 extends from residues G271-P364 of tau. One strong non-proteinaceous density is also present. Unlike the tau filaments from human brains, the sequences following repeat 4 are missing from the cores of tau filaments from the brains of Tg2541 and PS19 mice.
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Affiliation(s)
| | - Alexey G Murzin
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | | | - Isabelle Lavenir
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | | | - Sjors H W Scheres
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.
| | - Michel Goedert
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.
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48
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Zhao C, Lu D, Zhao Q, Ren C, Zhang H, Zhai J, Gou J, Zhu S, Zhang Y, Gong X. Computational methods for in situ structural studies with cryogenic electron tomography. Front Cell Infect Microbiol 2023; 13:1135013. [PMID: 37868346 PMCID: PMC10586593 DOI: 10.3389/fcimb.2023.1135013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 08/29/2023] [Indexed: 10/24/2023] Open
Abstract
Cryo-electron tomography (cryo-ET) plays a critical role in imaging microorganisms in situ in terms of further analyzing the working mechanisms of viruses and drug exploitation, among others. A data processing workflow for cryo-ET has been developed to reconstruct three-dimensional density maps and further build atomic models from a tilt series of two-dimensional projections. Low signal-to-noise ratio (SNR) and missing wedge are two major factors that make the reconstruction procedure challenging. Because only few near-atomic resolution structures have been reconstructed in cryo-ET, there is still much room to design new approaches to improve universal reconstruction resolutions. This review summarizes classical mathematical models and deep learning methods among general reconstruction steps. Moreover, we also discuss current limitations and prospects. This review can provide software and methods for each step of the entire procedure from tilt series by cryo-ET to 3D atomic structures. In addition, it can also help more experts in various fields comprehend a recent research trend in cryo-ET. Furthermore, we hope that more researchers can collaborate in developing computational methods and mathematical models for high-resolution three-dimensional structures from cryo-ET datasets.
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Affiliation(s)
- Cuicui Zhao
- Mathematical Intelligence Application LAB, Institute for Mathematical Sciences, Renmin University of China, Beijing, China
| | - Da Lu
- Mathematical Intelligence Application LAB, Institute for Mathematical Sciences, Renmin University of China, Beijing, China
| | - Qian Zhao
- Mathematical Intelligence Application LAB, Institute for Mathematical Sciences, Renmin University of China, Beijing, China
| | - Chongjiao Ren
- Mathematical Intelligence Application LAB, Institute for Mathematical Sciences, Renmin University of China, Beijing, China
| | - Huangtao Zhang
- Mathematical Intelligence Application LAB, Institute for Mathematical Sciences, Renmin University of China, Beijing, China
| | - Jiaqi Zhai
- Mathematical Intelligence Application LAB, Institute for Mathematical Sciences, Renmin University of China, Beijing, China
| | - Jiaxin Gou
- Mathematical Intelligence Application LAB, Institute for Mathematical Sciences, Renmin University of China, Beijing, China
| | - Shilin Zhu
- Mathematical Intelligence Application LAB, Institute for Mathematical Sciences, Renmin University of China, Beijing, China
| | - Yaqi Zhang
- Mathematical Intelligence Application LAB, Institute for Mathematical Sciences, Renmin University of China, Beijing, China
| | - Xinqi Gong
- Mathematical Intelligence Application LAB, Institute for Mathematical Sciences, Renmin University of China, Beijing, China
- Beijing Academy of Intelligence, Beijing, China
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49
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Capper MJ, Yang S, Stone AC, Vatansever S, Zilberg G, Mathiharan YK, Habib R, Hutchinson K, Zhao Y, Schlessinger A, Mezei M, Osman R, Zhang B, Wacker D. Substrate binding and inhibition of the anion exchanger 1 transporter. Nat Struct Mol Biol 2023; 30:1495-1504. [PMID: 37679563 PMCID: PMC11008770 DOI: 10.1038/s41594-023-01085-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 07/28/2023] [Indexed: 09/09/2023]
Abstract
Anion exchanger 1 (AE1), a member of the solute carrier (SLC) family, is the primary bicarbonate transporter in erythrocytes, regulating pH levels and CO2 transport between lungs and tissues. Previous studies characterized its role in erythrocyte structure and provided insight into transport regulation. However, key questions remain regarding substrate binding and transport, mechanisms of drug inhibition and modulation by membrane components. Here we present seven cryo-EM structures in apo, bicarbonate-bound and inhibitor-bound states. These, combined with uptake and computational studies, reveal important molecular features of substrate recognition and transport, and illuminate sterol binding sites, to elucidate distinct inhibitory mechanisms of research chemicals and prescription drugs. We further probe the substrate binding site via structure-based ligand screening, identifying an AE1 inhibitor. Together, our findings provide insight into mechanisms of solute carrier transport and inhibition.
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Affiliation(s)
- Michael J Capper
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Shifan Yang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alexander C Stone
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sezen Vatansever
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Gregory Zilberg
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yamuna Kalyani Mathiharan
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Raul Habib
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Keino Hutchinson
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yihan Zhao
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Avner Schlessinger
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Artificial Intelligence and Human Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Mihaly Mezei
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Roman Osman
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Bin Zhang
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Artificial Intelligence and Human Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Daniel Wacker
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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50
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Tajima S, Kim YS, Fukuda M, Jo Y, Wang PY, Paggi JM, Inoue M, Byrne EFX, Kishi KE, Nakamura S, Ramakrishnan C, Takaramoto S, Nagata T, Konno M, Sugiura M, Katayama K, Matsui TE, Yamashita K, Kim S, Ikeda H, Kim J, Kandori H, Dror RO, Inoue K, Deisseroth K, Kato HE. Structural basis for ion selectivity in potassium-selective channelrhodopsins. Cell 2023; 186:4325-4344.e26. [PMID: 37652010 PMCID: PMC7615185 DOI: 10.1016/j.cell.2023.08.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 05/11/2023] [Accepted: 08/07/2023] [Indexed: 09/02/2023]
Abstract
KCR channelrhodopsins (K+-selective light-gated ion channels) have received attention as potential inhibitory optogenetic tools but more broadly pose a fundamental mystery regarding how their K+ selectivity is achieved. Here, we present 2.5-2.7 Å cryo-electron microscopy structures of HcKCR1 and HcKCR2 and of a structure-guided mutant with enhanced K+ selectivity. Structural, electrophysiological, computational, spectroscopic, and biochemical analyses reveal a distinctive mechanism for K+ selectivity; rather than forming the symmetrical filter of canonical K+ channels achieving both selectivity and dehydration, instead, three extracellular-vestibule residues within each monomer form a flexible asymmetric selectivity gate, while a distinct dehydration pathway extends intracellularly. Structural comparisons reveal a retinal-binding pocket that induces retinal rotation (accounting for HcKCR1/HcKCR2 spectral differences), and design of corresponding KCR variants with increased K+ selectivity (KALI-1/KALI-2) provides key advantages for optogenetic inhibition in vitro and in vivo. Thus, discovery of a mechanism for ion-channel K+ selectivity also provides a framework for next-generation optogenetics.
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Affiliation(s)
- Seiya Tajima
- Komaba Institute for Science, The University of Tokyo, Meguro, Tokyo, Japan
| | - Yoon Seok Kim
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Masahiro Fukuda
- Komaba Institute for Science, The University of Tokyo, Meguro, Tokyo, Japan
| | - YoungJu Jo
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Peter Y Wang
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Joseph M Paggi
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Masatoshi Inoue
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Eamon F X Byrne
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Koichiro E Kishi
- Komaba Institute for Science, The University of Tokyo, Meguro, Tokyo, Japan
| | - Seiwa Nakamura
- Komaba Institute for Science, The University of Tokyo, Meguro, Tokyo, Japan
| | | | - Shunki Takaramoto
- The Institute for Solid State Physics, The University of Tokyo, Kashiwa, Japan
| | - Takashi Nagata
- The Institute for Solid State Physics, The University of Tokyo, Kashiwa, Japan
| | - Masae Konno
- The Institute for Solid State Physics, The University of Tokyo, Kashiwa, Japan; PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan
| | - Masahiro Sugiura
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Japan
| | - Kota Katayama
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Japan
| | - Toshiki E Matsui
- Komaba Institute for Science, The University of Tokyo, Meguro, Tokyo, Japan
| | - Keitaro Yamashita
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | - Suhyang Kim
- Komaba Institute for Science, The University of Tokyo, Meguro, Tokyo, Japan
| | - Hisako Ikeda
- Komaba Institute for Science, The University of Tokyo, Meguro, Tokyo, Japan
| | - Jaeah Kim
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Japan; OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Japan
| | - Ron O Dror
- Department of Computer Science, Stanford University, Stanford, CA, USA; Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA
| | - Keiichi Inoue
- The Institute for Solid State Physics, The University of Tokyo, Kashiwa, Japan
| | - Karl Deisseroth
- Department of Bioengineering, Stanford University, Stanford, CA, USA; CNC Program, Stanford University, Stanford, CA, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA; Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA.
| | - Hideaki E Kato
- Komaba Institute for Science, The University of Tokyo, Meguro, Tokyo, Japan; Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, Japan; FOREST, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan.
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