1
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Moiseenko A, Zhang Y, Vorovitch MF, Ivanova AL, Liu Z, Osolodkin DI, Egorov AM, Ishmukhametov AA, Sokolova OS. Structural diversity of tick-borne encephalitis virus particles in the inactivated vaccine based on strain Sofjin. Emerg Microbes Infect 2024; 13:2290833. [PMID: 38073510 DOI: 10.1080/22221751.2023.2290833] [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: 10/16/2023] [Accepted: 11/29/2023] [Indexed: 03/12/2024]
Abstract
The main approach to preventing tick-borne encephalitis (TBE) is vaccination. Formaldehyde-inactivated TBE vaccines have a proven record of safety and efficiency but have never been characterized structurally with atomic resolution. We report a cryoelectron microscopy (cryo-EM) structure of the formaldehyde-inactivated TBE virus (TBEV) of Sofjin-Chumakov strain representing the Far-Eastern subtype. A 3.8 Å resolution reconstruction reveals the structural integrity of the envelope E proteins, specifically the E protein ectodomains. The comparative study shows a high structural similarity to the previously published structures of the TBEV European subtype strains Hypr and Kuutsalo-14. A fraction of inactivated virions exhibits asymmetric features including the deformations of the membrane profile. We propose that the heterogeneity is caused by inactivation and perform a local variability analysis on the small parts of the envelope protein shell to reveal membrane curvature features possibly induced by the inactivation. The results of this study will have implications for the design of novel vaccines against diseases caused by flaviviruses.
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Affiliation(s)
- Andrey Moiseenko
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Yichen Zhang
- Faculty of Biology, Shenzhen MSU-BIT University, Shenzhen, People's Republic of China
| | - Mikhail F Vorovitch
- FSASI "Chumakov FSC R&D IBP RAS" (Institute of Poliomyelitis), Moscow, Russia
- Sechenov First Moscow State Medical University, Moscow, Russia
| | - Alla L Ivanova
- FSASI "Chumakov FSC R&D IBP RAS" (Institute of Poliomyelitis), Moscow, Russia
| | - Zheng Liu
- Kobilka Institute of Innovative Drug Discovery, School of Medicine, Chinese University of Hong Kong, Shenzhen, People's Republic of China
| | - Dmitry I Osolodkin
- FSASI "Chumakov FSC R&D IBP RAS" (Institute of Poliomyelitis), Moscow, Russia
- Sechenov First Moscow State Medical University, Moscow, Russia
| | - Alexey M Egorov
- FSASI "Chumakov FSC R&D IBP RAS" (Institute of Poliomyelitis), Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Aydar A Ishmukhametov
- FSASI "Chumakov FSC R&D IBP RAS" (Institute of Poliomyelitis), Moscow, Russia
- Sechenov First Moscow State Medical University, Moscow, Russia
| | - Olga S Sokolova
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
- Faculty of Biology, Shenzhen MSU-BIT University, Shenzhen, People's Republic of China
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2
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Mark E, Ramos PC, Kayser F, Höckendorff J, Dohmen RJ, Wendler P. Structural roles of Ump1 and β-subunit propeptides in proteasome biogenesis. Life Sci Alliance 2024; 7:e202402865. [PMID: 39260885 DOI: 10.26508/lsa.202402865] [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: 06/04/2024] [Revised: 08/23/2024] [Accepted: 08/23/2024] [Indexed: 09/13/2024] Open
Abstract
The yeast pre1-1(β4-S142F) mutant accumulates late 20S proteasome core particle precursor complexes (late-PCs). We report a 2.1 Å cryo-EM structure of this intermediate with full-length Ump1 trapped inside, and Pba1-Pba2 attached to the α-ring surfaces. The structure discloses intimate interactions of Ump1 with β2- and β5-propeptides, which together fill most of the antechambers between the α- and β-rings. The β5-propeptide is unprocessed and separates Ump1 from β6 and β7. The β2-propeptide is disconnected from the subunit by autocatalytic processing and localizes between Ump1 and β3. A comparison of different proteasome maturation states reveals that maturation goes along with global conformational changes in the rings, initiated by structuring of the proteolytic sites and their autocatalytic activation. In the pre1-1 strain, β2 is activated first enabling processing of β1-, β6-, and β7-propeptides. Subsequent maturation of β5 and β1 precedes degradation of Ump1, tightening of the complex, and finally release of Pba1-Pba2.
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Affiliation(s)
- Eric Mark
- https://ror.org/03bnmw459 Institute of Biochemistry and Biology, Department of Biochemistry, University of Potsdam, Potsdam-Golm, Germany
| | - Paula C Ramos
- https://ror.org/00rcxh774 Institute for Genetics, Center of Molecular Biosciences, Department of Biology, Faculty of Mathematics and Natural Sciences, University of Cologne, Cologne, Germany
| | - Fleur Kayser
- https://ror.org/03bnmw459 Institute of Biochemistry and Biology, Department of Biochemistry, University of Potsdam, Potsdam-Golm, Germany
| | - Jörg Höckendorff
- https://ror.org/00rcxh774 Institute for Genetics, Center of Molecular Biosciences, Department of Biology, Faculty of Mathematics and Natural Sciences, University of Cologne, Cologne, Germany
| | - R Jürgen Dohmen
- https://ror.org/00rcxh774 Institute for Genetics, Center of Molecular Biosciences, Department of Biology, Faculty of Mathematics and Natural Sciences, University of Cologne, Cologne, Germany
| | - Petra Wendler
- https://ror.org/03bnmw459 Institute of Biochemistry and Biology, Department of Biochemistry, University of Potsdam, Potsdam-Golm, Germany
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3
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Bonilla SL, Jang K. Challenges, advances, and opportunities in RNA structural biology by Cryo-EM. Curr Opin Struct Biol 2024; 88:102894. [PMID: 39121532 DOI: 10.1016/j.sbi.2024.102894] [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: 03/26/2024] [Revised: 07/03/2024] [Accepted: 07/15/2024] [Indexed: 08/12/2024]
Abstract
RNAs are remarkably versatile molecules that can fold into intricate three-dimensional (3D) structures to perform diverse cellular and viral functions. Despite their biological importance, relatively few RNA 3D structures have been solved, and our understanding of RNA structure-function relationships remains in its infancy. This limitation partly arises from challenges posed by RNA's complex conformational landscape, characterized by structural flexibility, formation of multiple states, and a propensity to misfold. Recently, cryo-electron microscopy (cryo-EM) has emerged as a powerful tool for the visualization of conformationally dynamic RNA-only 3D structures. However, RNA's characteristics continue to pose challenges. We discuss experimental methods developed to overcome these hurdles, including the engineering of modular modifications that facilitate the visualization of small RNAs, improve particle alignment, and validate structural models.
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Affiliation(s)
- Steve L Bonilla
- Laboratory of RNA Structural Biology and Biophysics, The Rockefeller University, New York, NY, 10065, USA.
| | - Karen Jang
- Laboratory of RNA Structural Biology and Biophysics, The Rockefeller University, New York, NY, 10065, USA
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4
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Jia T, de Vries R, Kapelan Z, van Emmerik THM, Taormina R. Detecting floating litter in freshwater bodies with semi-supervised deep learning. WATER RESEARCH 2024; 266:122405. [PMID: 39265217 DOI: 10.1016/j.watres.2024.122405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Revised: 08/27/2024] [Accepted: 09/05/2024] [Indexed: 09/14/2024]
Abstract
Researchers and practitioners have extensively utilized supervised Deep Learning methods to quantify floating litter in rivers and canals. These methods require the availability of large amount of labeled data for training. The labeling work is expensive and laborious, resulting in small open datasets available in the field compared to the comprehensive datasets for computer vision, e.g., ImageNet. Fine-tuning models pre-trained on these larger datasets helps improve litter detection performances and reduces data requirements. Yet, the effectiveness of using features learned from generic datasets is limited in large-scale monitoring, where automated detection must adapt across different locations, environmental conditions, and sensor settings. To address this issue, we propose a two-stage semi-supervised learning method to detect floating litter based on the Swapping Assignments between multiple Views of the same image (SwAV). SwAV is a self-supervised learning approach that learns the underlying feature representation from unlabeled data. In the first stage, we used SwAV to pre-train a ResNet50 backbone architecture on about 100k unlabeled images. In the second stage, we added new layers to the pre-trained ResNet50 to create a Faster R-CNN architecture, and fine-tuned it with a limited number of labeled images (≈1.8k images with 2.6k annotated litter items). We developed and validated our semi-supervised floating litter detection methodology for images collected in canals and waterways of Delft (the Netherlands) and Jakarta (Indonesia). We tested for out-of-domain generalization performances in a zero-shot fashion using additional data from Ho Chi Minh City (Vietnam), Amsterdam and Groningen (the Netherlands). We benchmarked our results against the same Faster R-CNN architecture trained via supervised learning alone by fine-tuning ImageNet pre-trained weights. The findings indicate that the semi-supervised learning method matches or surpasses the supervised learning benchmark when tested on new images from the same training locations. We measured better performances when little data (≈200 images with about 300 annotated litter items) is available for fine-tuning and with respect to reducing false positive predictions. More importantly, the proposed approach demonstrates clear superiority for generalization on the unseen locations, with improvements in average precision of up to 12.7%. We attribute this superior performance to the more effective high-level feature extraction from SwAV pre-training from relevant unlabeled images. Our findings highlight a promising direction to leverage semi-supervised learning for developing foundational models, which have revolutionized artificial intelligence applications in most fields. By scaling our proposed approach with more data and compute, we can make significant strides in monitoring to address the global challenge of litter pollution in water bodies.
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Affiliation(s)
- Tianlong Jia
- Delft University of Technology, Faculty of Civil Engineering and Geosciences, Department of Water Management, Stevinweg 1, 2628 CN Delft, The Netherlands.
| | - Rinze de Vries
- Noria Sustainable Innovators, Schieweg 13, 2627 AN Delft, The Netherlands
| | - Zoran Kapelan
- Delft University of Technology, Faculty of Civil Engineering and Geosciences, Department of Water Management, Stevinweg 1, 2628 CN Delft, The Netherlands
| | - Tim H M van Emmerik
- Wageningen University and Research, Hydrology and Environmental Hydraulics Group, Wageningen, The Netherlands
| | - Riccardo Taormina
- Delft University of Technology, Faculty of Civil Engineering and Geosciences, Department of Water Management, Stevinweg 1, 2628 CN Delft, The Netherlands.
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5
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Brouwer PJM, Perrett HR, Beaumont T, Nijhuis H, Kruijer S, Burger JA, Bontjer I, Lee WH, Ferguson JA, Schauflinger M, Müller-Kräuter H, Sanders RW, Strecker T, van Gils MJ, Ward AB. Defining bottlenecks and opportunities for Lassa virus neutralization by structural profiling of vaccine-induced polyclonal antibody responses. Cell Rep 2024; 43:114708. [PMID: 39243373 DOI: 10.1016/j.celrep.2024.114708] [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: 01/03/2024] [Revised: 07/19/2024] [Accepted: 08/19/2024] [Indexed: 09/09/2024] Open
Abstract
Lassa fever continues to be a major public health burden in West Africa, yet effective therapies or vaccines are lacking. The isolation of protective neutralizing antibodies against the Lassa virus glycoprotein complex (GPC) justifies the development of vaccines that can elicit strong neutralizing antibody responses. However, Lassa vaccine candidates have generally been unsuccessful at doing so, and the associated antibody responses to these vaccines remain poorly characterized. Here, we establish an electron microscopy-based epitope mapping workflow that enables high-resolution structural characterization of polyclonal antibodies to the GPC. By applying this method to rabbits vaccinated with a recombinant GPC vaccine and a GPC-derived virus-like particle, we reveal determinants of neutralization that involve epitopes of the GPC-A competition cluster. Furthermore, by identifying undescribed immunogenic off-target epitopes, we expose the challenges that recombinant GPC vaccines face. By enabling detailed polyclonal antibody characterization, our work ushers in a next generation of more rational Lassa vaccine design.
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Affiliation(s)
- Philip J M Brouwer
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA 92037, USA
| | - Hailee R Perrett
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA 92037, USA
| | - Tim Beaumont
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Center, Location AMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Haye Nijhuis
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Center, Location AMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Sabine Kruijer
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Center, Location AMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Judith A Burger
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Center, Location AMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Ilja Bontjer
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Center, Location AMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Wen-Hsin Lee
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA 92037, USA
| | - James A Ferguson
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA 92037, USA
| | | | | | - Rogier W Sanders
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Center, Location AMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands; Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY 10021, USA
| | - Thomas Strecker
- Institute of Virology, Philipps University Marburg, 35043 Marburg, Germany
| | - Marit J van Gils
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Center, Location AMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, 1105 AZ Amsterdam, the Netherlands
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA 92037, USA.
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6
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Introini B, Cui W, Chu X, Zhang Y, Alves AC, Eckhardt-Strelau L, Golusik S, Tol M, Vogel H, Yuan S, Kudryashev M. Structure of tetrameric forms of the serotonin-gated 5-HT3 A receptor ion channel. EMBO J 2024:10.1038/s44318-024-00191-5. [PMID: 39232129 DOI: 10.1038/s44318-024-00191-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 06/16/2024] [Accepted: 07/15/2024] [Indexed: 09/06/2024] Open
Abstract
Multimeric membrane proteins are produced in the endoplasmic reticulum and transported to their target membranes which, for ion channels, is typically the plasma membrane. Despite the availability of many fully assembled channel structures, our understanding of assembly intermediates, multimer assembly mechanisms, and potential functions of non-standard assemblies is limited. We demonstrate that the pentameric ligand-gated serotonin 5-HT3A receptor (5-HT3AR) can assemble to tetrameric forms and report the structures of the tetramers in plasma membranes of cell-derived microvesicles and in membrane memetics using cryo-electron microscopy and tomography. The tetrameric structures have near-symmetric transmembrane domains, and asymmetric extracellular domains, and can bind serotonin molecules. Computer simulations, based on our cryo-EM structures, were used to decipher the assembly pathway of pentameric 5-HT3R and suggest a potential functional role for the tetrameric receptors.
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Affiliation(s)
- Bianca Introini
- Max Planck Institute of Biophysics, Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University of Frankfurt am Main, Frankfurt on Main, Germany
| | - Wenqiang Cui
- The Research Center for Computer-aided Drug Discovery, Institute of Biomedicine and Biotechnology, The Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaofeng Chu
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), In Situ Structural Biology, Robert-Rössle-Str. 10, 13125, Berlin, Germany
| | - Yingyi Zhang
- Max Planck Institute of Biophysics, Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University of Frankfurt am Main, Frankfurt on Main, Germany
| | - Ana Catarina Alves
- Institute of Chemical Sciences and Engineering (ISIC), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | | | - Sabrina Golusik
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), In Situ Structural Biology, Robert-Rössle-Str. 10, 13125, Berlin, Germany
| | - Menno Tol
- Institute of Chemical Sciences and Engineering (ISIC), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Horst Vogel
- The Research Center for Computer-aided Drug Discovery, Institute of Biomedicine and Biotechnology, The Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
- Institute of Chemical Sciences and Engineering (ISIC), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
- Faculty of Pharmaceutical Sciences, Shenzhen University of Advanced Technology (SUAT), Shenzhen, China.
| | - Shuguang Yuan
- The Research Center for Computer-aided Drug Discovery, Institute of Biomedicine and Biotechnology, The Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
- AlphaMol Science Ltd, Shenzhen, 518055, China.
| | - Mikhail Kudryashev
- Max Planck Institute of Biophysics, Frankfurt am Main, Germany.
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University of Frankfurt am Main, Frankfurt on Main, Germany.
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), In Situ Structural Biology, Robert-Rössle-Str. 10, 13125, Berlin, Germany.
- Institute of Medical Physics and Biophysics, Charité-Universitätsmedizin, Berlin, Germany.
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7
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Khan YA, White KI, Pfuetzner RA, Singal B, Esquivies L, Mckenzie G, Liu F, DeLong K, Choi UB, Montabana E, Mclaughlin T, Wickner WT, Brunger AT. Sec18 side-loading is essential for universal SNARE recycling across cellular contexts. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.30.610324. [PMID: 39257774 PMCID: PMC11384006 DOI: 10.1101/2024.08.30.610324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2024]
Abstract
SNARE proteins drive membrane fusion as their core domains zipper into a parallel four-helix bundle 1,2 . After fusion, these bundles are disassembled by the AAA+ protein Sec18/NSF and its adaptor Sec17/ α-SNAP 3,4 to make them available for subsequent rounds of membrane fusion. SNARE domains are often flanked by C-terminal transmembrane or N-terminal domains 5 . Previous structures of the NSF-α-SNAP-SNARE complex revealed SNARE domain threaded through the D1 ATPase ring 6 , posing a topological constraint as SNARE transmembrane domains would prevent complete substrate threading as suggested for other AAA+ systems 7 . Here, in vivo mass-spectrometry reveals N-terminal SNARE domain interactions with Sec18, exacerbating this topological issue. Cryo-EM structures of a yeast SNARE complex, Sec18, and Sec17 in a non-hydrolyzing condition shows SNARE Sso1 threaded through the D1 and D2 ATPase rings of Sec18, with its folded, N-terminal Habc domain interacting with the D2 ring. This domain does not unfold during Sec18/NSF activity. Cryo-EM structures under hydrolyzing conditions revealed substrate-released and substrate-free states of Sec18 with a coordinated opening in the side of the ATPase rings. Thus, Sec18/NSF operates by substrate side-loading and unloading topologically constrained SNARE substrates.
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8
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Kerfeld CA, Sutter M. Orange carotenoid proteins: structural understanding of evolution and function. Trends Biochem Sci 2024; 49:819-828. [PMID: 38789305 DOI: 10.1016/j.tibs.2024.04.010] [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: 01/26/2024] [Revised: 04/15/2024] [Accepted: 04/30/2024] [Indexed: 05/26/2024]
Abstract
Cyanobacteria uniquely contain a primitive water-soluble carotenoprotein, the orange carotenoid protein (OCP). Nearly all extant cyanobacterial genomes contain genes for the OCP or its homologs, implying an evolutionary constraint for cyanobacteria to conserve its function. Genes encoding the OCP and its two constituent structural domains, the N-terminal domain, helical carotenoid proteins (HCPs), and its C-terminal domain, are found in the most basal lineages of extant cyanobacteria. These three carotenoproteins exemplify the importance of the protein for carotenoid properties, including protein dynamics, in response to environmental changes in facilitating a photoresponse and energy quenching. Here, we review new structural insights for these carotenoproteins and situate the role of the protein in what is currently understood about their functions.
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Affiliation(s)
- 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.
| | - 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
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9
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Kochańczyk T, Hann ZS, Lux MC, Delos Reyes AMV, Ji C, Tan DS, Lima CD. Structural basis for transthiolation intermediates in the ubiquitin pathway. Nature 2024; 633:216-223. [PMID: 39143218 PMCID: PMC11374688 DOI: 10.1038/s41586-024-07828-9] [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: 03/26/2024] [Accepted: 07/12/2024] [Indexed: 08/16/2024]
Abstract
Transthiolation (also known as transthioesterification) reactions are used in the biosynthesis of acetyl coenzyme A, fatty acids and polyketides, and for post-translational modification by ubiquitin (Ub) and ubiquitin-like (Ubl) proteins1-3. For the Ub pathway, E1 enzymes catalyse transthiolation from an E1~Ub thioester to an E2~Ub thioester. Transthiolation is also required for transfer of Ub from an E2~Ub thioester to HECT (homologous to E6AP C terminus) and RBR (ring-between-ring) E3 ligases to form E3~Ub thioesters4-6. How isoenergetic transfer of thioester bonds is driven forward by enzymes in the Ub pathway remains unclear. Here we isolate mimics of transient transthiolation intermediates for E1-Ub(T)-E2 and E2-Ub(T)-E3HECT complexes (where T denotes Ub in a thioester or Ub undergoing transthiolation) using a chemical strategy with native enzymes and near-native Ub to capture and visualize a continuum of structures determined by single-particle cryo-electron microscopy. These structures and accompanying biochemical experiments illuminate conformational changes in Ub, E1, E2 and E3 that are coordinated with the chemical reactions to facilitate directional transfer of Ub from each enzyme to the next.
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Affiliation(s)
- Tomasz Kochańczyk
- Structural Biology Program, Sloan Kettering Institute, New York, NY, USA
- Howard Hughes Medical Institute, New York, NY, USA
| | - Zachary S Hann
- Structural Biology Program, Sloan Kettering Institute, New York, NY, USA
- Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michaelyn C Lux
- Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Chemical Biology Program, Sloan Kettering Institute, New York, NY, USA
| | - Avelyn Mae V Delos Reyes
- Chemical Biology Program, Sloan Kettering Institute, New York, NY, USA
- Pharmacology Graduate Program, Weill Cornell Graduate School of Medical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Cheng Ji
- Chemical Biology Program, Sloan Kettering Institute, New York, NY, USA
| | - Derek S Tan
- Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Chemical Biology Program, Sloan Kettering Institute, New York, NY, USA.
- Pharmacology Graduate Program, Weill Cornell Graduate School of Medical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Christopher D Lima
- Structural Biology Program, Sloan Kettering Institute, New York, NY, USA.
- Howard Hughes Medical Institute, New York, NY, USA.
- Tri-Institutional PhD Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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10
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Gusach A, Lee Y, Khoshgrudi AN, Mukhaleva E, Ma N, Koers EJ, Chen Q, Edwards PC, Huang F, Kim J, Mancia F, Veprintsev DB, Vaidehi N, Weyand SN, Tate CG. Molecular recognition of an odorant by the murine trace amine-associated receptor TAAR7f. Nat Commun 2024; 15:7555. [PMID: 39215004 PMCID: PMC11364543 DOI: 10.1038/s41467-024-51793-w] [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: 06/23/2023] [Accepted: 08/15/2024] [Indexed: 09/04/2024] Open
Abstract
There are two main families of G protein-coupled receptors that detect odours in humans, the odorant receptors (ORs) and the trace amine-associated receptors (TAARs). Their amino acid sequences are distinct, with the TAARs being most similar to the aminergic receptors such as those activated by adrenaline, serotonin, dopamine and histamine. To elucidate the structural determinants of ligand recognition by TAARs, we have determined the cryo-EM structure of a murine receptor, mTAAR7f, coupled to the heterotrimeric G protein Gs and bound to the odorant N,N-dimethylcyclohexylamine (DMCHA) to an overall resolution of 2.9 Å. DMCHA is bound in a hydrophobic orthosteric binding site primarily through van der Waals interactions and a strong charge-charge interaction between the tertiary amine of the ligand and an aspartic acid residue. This site is distinct and non-overlapping with the binding site for the odorant propionate in the odorant receptor OR51E2. The structure, in combination with mutagenesis data and molecular dynamics simulations suggests that the activation of the receptor follows a similar pathway to that of the β-adrenoceptors, with the significant difference that DMCHA interacts directly with one of the main activation microswitch residues, Trp6.48.
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Affiliation(s)
- Anastasiia Gusach
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Yang Lee
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Armin Nikpour Khoshgrudi
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, NG7 2RD, UK
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Elizaveta Mukhaleva
- Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, 1218 S 5th Ave, Monrovia, CA, 91016, USA
| | - Ning Ma
- Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, 1218 S 5th Ave, Monrovia, CA, 91016, USA
| | - Eline J Koers
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, NG7 2RD, UK
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Qingchao Chen
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Patricia C Edwards
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Fanglu Huang
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, UK
| | - Jonathan Kim
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Filippo Mancia
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Dmitry B Veprintsev
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, NG7 2RD, UK
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Nagarajan Vaidehi
- Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, 1218 S 5th Ave, Monrovia, CA, 91016, USA
| | - Simone N Weyand
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, UK.
- Department of Medicine, University of Cambridge, Victor Phillip Dahdaleh Building, Heart & Lung Research Institute, Papworth Road, Cambridge Biomedical Campus, Cambridge, CB2 0BB, UK.
- Cambridge Institute for Medical Research, Keith Peters Building, Biomedical Campus, Hills Rd, Cambridge, CB2 0XY, UK.
- EMBL's European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK.
| | - Christopher G Tate
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
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11
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Cooney I, Schubert HL, Cedeno K, Fisher ON, Carson R, Price JC, Hill CP, Shen PS. Visualization of the Cdc48 AAA+ ATPase protein unfolding pathway. Nat Commun 2024; 15:7505. [PMID: 39209885 PMCID: PMC11362554 DOI: 10.1038/s41467-024-51835-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 08/20/2024] [Indexed: 09/04/2024] Open
Abstract
The Cdc48 AAA+ ATPase is an abundant and essential enzyme that unfolds substrates in multiple protein quality control pathways. The enzyme includes two conserved AAA+ ATPase motor domains, D1 and D2, that assemble as hexameric rings with D1 stacked above D2. Here, we report an ensemble of native structures of Cdc48 affinity purified from budding yeast lysate in complex with the adaptor Shp1 in the act of unfolding substrate. Our analysis reveals a continuum of structural snapshots that spans the entire translocation cycle. These data uncover elements of Shp1-Cdc48 interactions and support a 'hand-over-hand' mechanism in which the sequential movement of individual subunits is closely coordinated. D1 hydrolyzes ATP and disengages from substrate prior to D2, while D2 rebinds ATP and re-engages with substrate prior to D1, thereby explaining the dominant role played by the D2 motor in substrate translocation/unfolding.
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Affiliation(s)
- Ian Cooney
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Heidi L Schubert
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Karina Cedeno
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Olivia N Fisher
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA
| | - Richard Carson
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
| | - John C Price
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
| | - Christopher P Hill
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA.
| | - Peter S Shen
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA.
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12
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Neumann B, McCarthy S, Gonen S. Structural basis of inhibition of human Na V1.8 by the tarantula venom peptide Protoxin-I. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.27.609828. [PMID: 39253517 PMCID: PMC11383277 DOI: 10.1101/2024.08.27.609828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/11/2024]
Abstract
Voltage-gated sodium channels (NaVs) selectively permit diffusion of sodium ions across the cell membrane and, in excitable cells, are responsible for propagating action potentials. One of the nine human NaV isoforms, NaV1.8, is a promising target for analgesics, and selective inhibitors are of interest as therapeutics. One such inhibitor, the gating-modifier peptide Protoxin-I derived from tarantula venom, blocks channel opening by shifting the activation voltage threshold to more depolarised potentials, but the structural basis for this inhibition has not previously been determined. Using monolayer graphene grids, we report the cryogenic electron microscopy structures of full-length human apo-NaV1.8 and the Protoxin-I-bound complex at 3.1 Å and 2.8 Å resolution, respectively. The apo structure shows an unexpected movement of the Domain I S4-S5 helix, and VSDI was unresolvable. We find that Protoxin-I binds to and displaces the VSDII S3-S4 linker, hindering translocation of the S4II helix during activation.
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Affiliation(s)
- Bryan Neumann
- Department of Molecular Biology and Biochemistry, University of California Irvine, CA 92617, USA
| | - Stephen McCarthy
- Department of Molecular Biology and Biochemistry, University of California Irvine, CA 92617, USA
| | - Shane Gonen
- Department of Molecular Biology and Biochemistry, University of California Irvine, CA 92617, USA
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13
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Parthasarathy D, Pothula KR, Ratnapriya S, Cervera Benet H, Parsons R, Huang X, Sammour S, Janowska K, Harris M, Sodroski J, Acharya P, Herschhorn A. Conformational flexibility of HIV-1 envelope glycoproteins modulates transmitted/founder sensitivity to broadly neutralizing antibodies. Nat Commun 2024; 15:7334. [PMID: 39187497 PMCID: PMC11347675 DOI: 10.1038/s41467-024-51656-4] [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: 07/07/2024] [Accepted: 08/09/2024] [Indexed: 08/28/2024] Open
Abstract
HIV-1 envelope glycoproteins (Envs) of most primary HIV-1 strains exist in closed conformation and infrequently sample open states, limiting access to internal epitopes. Thus, immunogen design aims to mimic the closed Env conformation as preferred target for eliciting broadly neutralizing antibodies (bnAbs). Here we identify incompletely closed Env conformations of 6 out of 13 transmitted/founder (T/F) strains that are sensitive to antibodies that recognize internal epitopes typically exposed on open Envs. A 3.6 Å cryo-electron microscopy structure of unliganded, incompletely closed T/F Envs (1059-SOSIP) reveals protomer motion that increased sampling of states with incompletely closed trimer apex. We reconstruct de novo the post-transmission evolutionary pathway of a second T/F. Evolved viruses exhibit increased Env resistance to cold, soluble CD4 and 19b, all of which correlate with closing of the adapted Env trimer. Lastly, we show that the ultra-broad N6 bnAb efficiently recognizes different Env conformations and exhibits improved antiviral breadth against VRC01-resistant Envs isolated during the first-in-humans antibody-mediated-prevention trial.
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Affiliation(s)
- Durgadevi Parthasarathy
- Division of Infectious Diseases and International Medicine, Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | | | - Sneha Ratnapriya
- Division of Infectious Diseases and International Medicine, Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Héctor Cervera Benet
- Division of Infectious Diseases and International Medicine, Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Ruth Parsons
- Duke Human Vaccine Institute, Duke University, Durham, NC, USA
- Department of Biochemistry, Duke University, Durham, NC, USA
| | - Xiao Huang
- Duke Human Vaccine Institute, Duke University, Durham, NC, USA
| | - Salam Sammour
- Duke Human Vaccine Institute, Duke University, Durham, NC, USA
| | | | - Miranda Harris
- Division of Infectious Diseases and International Medicine, Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Joseph Sodroski
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Priyamvada Acharya
- Duke Human Vaccine Institute, Duke University, Durham, NC, USA
- Department of Biochemistry, Duke University, Durham, NC, USA
- Department of Surgery, Duke University, Durham, NC, USA
| | - Alon Herschhorn
- Division of Infectious Diseases and International Medicine, Department of Medicine, University of Minnesota, Minneapolis, MN, USA.
- Institute for Molecular Virology, University of Minnesota, University of Minnesota, Minneapolis, MN, USA.
- Microbiology, Immunology, and Cancer Biology Graduate Program, University of Minnesota, Minneapolis, MN, USA.
- The College of Veterinary Medicine Graduate Program, University of Minnesota, Minneapolis, MN, USA.
- Molecular Pharmacology and Therapeutics Graduate Program, University of Minnesota, Minneapolis, MN, USA.
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14
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Shankar S, Pan J, Yang P, Bian Y, Oroszlán G, Yu Z, Mukherjee P, Filman DJ, Hogle JM, Shekhar M, Coen DM, Abraham J. Viral DNA polymerase structures reveal mechanisms of antiviral drug resistance. Cell 2024:S0092-8674(24)00842-0. [PMID: 39197451 DOI: 10.1016/j.cell.2024.07.048] [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: 12/22/2022] [Revised: 01/27/2024] [Accepted: 07/26/2024] [Indexed: 09/01/2024]
Abstract
DNA polymerases are important drug targets, and many structural studies have captured them in distinct conformations. However, a detailed understanding of the impact of polymerase conformational dynamics on drug resistance is lacking. We determined cryoelectron microscopy (cryo-EM) structures of DNA-bound herpes simplex virus polymerase holoenzyme in multiple conformations and interacting with antivirals in clinical use. These structures reveal how the catalytic subunit Pol and the processivity factor UL42 bind DNA to promote processive DNA synthesis. Unexpectedly, in the absence of an incoming nucleotide, we observed Pol in multiple conformations with the closed state sampled by the fingers domain. Drug-bound structures reveal how antivirals may selectively bind enzymes that more readily adopt the closed conformation. Molecular dynamics simulations and the cryo-EM structure of a drug-resistant mutant indicate that some resistance mutations modulate conformational dynamics rather than directly impacting drug binding, thus clarifying mechanisms that drive drug selectivity.
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Affiliation(s)
- Sundaresh Shankar
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Junhua Pan
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Biomedical Research Institute and School of Life and Health Sciences, Hubei University of Technology, Wuhan, Hubei, China
| | - Pan Yang
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Yuemin Bian
- School of Medicine, Shanghai University, Shanghai, China; Center for the Development of Therapeutics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Gábor Oroszlán
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Zishuo Yu
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Purba Mukherjee
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, UK
| | - David J Filman
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - James M Hogle
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Mrinal Shekhar
- Center for the Development of Therapeutics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Donald M Coen
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Jonathan Abraham
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA; Department of Medicine, Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA 02115, USA; Center for Integrated Solutions in Infectious Diseases, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
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15
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Hirano S, Altae-Tran H, Kannan S, Macrae RK, Zhang F. Structural determinants of DNA cleavage by a CRISPR HNH-Cascade system. Mol Cell 2024; 84:3154-3162.e5. [PMID: 39111310 DOI: 10.1016/j.molcel.2024.07.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 07/08/2024] [Accepted: 07/25/2024] [Indexed: 08/25/2024]
Abstract
Canonical prokaryotic type I CRISPR-Cas adaptive immune systems contain a multicomponent effector complex called Cascade, which degrades large stretches of DNA via Cas3 helicase-nuclease activity. Recently, a highly precise subtype I-F1 CRISPR-Cas system (HNH-Cascade) was found that lacks Cas3, the absence of which is compensated for by the insertion of an HNH endonuclease domain in the Cas8 Cascade component. Here, we describe the cryo-EM structure of Selenomonas sp. HNH-Cascade (SsCascade) in complex with target DNA and characterize its mechanism of action. The Cascade scaffold is complemented by the HNH domain, creating a ring-like structure in which the unwound target DNA is precisely cleaved. This structure visualizes a unique hybrid of two extensible biological systems-Cascade, an evolutionary platform for programmable DNA effectors, and an HNH nuclease, an adaptive domain with a spectrum of enzymatic activity.
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Affiliation(s)
- Seiichi Hirano
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA; Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Cambridge, MA 02139, USA
| | - Han Altae-Tran
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA; Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Cambridge, MA 02139, USA
| | - Soumya Kannan
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA; Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Cambridge, MA 02139, USA
| | - Rhiannon K Macrae
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA; Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Cambridge, MA 02139, USA
| | - Feng Zhang
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA; Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Cambridge, MA 02139, USA.
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16
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Träger TK, Kyrilis FL, Hamdi F, Tüting C, Alfes M, Hofmann T, Schmidt C, Kastritis PL. Disorder-to-order active site capping regulates the rate-limiting step of the inositol pathway. Proc Natl Acad Sci U S A 2024; 121:e2400912121. [PMID: 39145930 PMCID: PMC11348189 DOI: 10.1073/pnas.2400912121] [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: 01/23/2024] [Accepted: 07/16/2024] [Indexed: 08/16/2024] Open
Abstract
Myo-inositol-1-phosphate synthase (MIPS) catalyzes the NAD+-dependent isomerization of glucose-6-phosphate (G6P) into inositol-1-phosphate (IMP), controlling the rate-limiting step of the inositol pathway. Previous structural studies focused on the detailed molecular mechanism, neglecting large-scale conformational changes that drive the function of this 240 kDa homotetrameric complex. In this study, we identified the active, endogenous MIPS in cell extracts from the thermophilic fungus Thermochaetoides thermophila. By resolving the native structure at 2.48 Å (FSC = 0.143), we revealed a fully populated active site. Utilizing 3D variability analysis, we uncovered conformational states of MIPS, enabling us to directly visualize an order-to-disorder transition at its catalytic center. An acyclic intermediate of G6P occupied the active site in two out of the three conformational states, indicating a catalytic mechanism where electrostatic stabilization of high-energy intermediates plays a crucial role. Examination of all isomerases with known structures revealed similar fluctuations in secondary structure within their active sites. Based on these findings, we established a conformational selection model that governs substrate binding and eventually inositol availability. In particular, the ground state of MIPS demonstrates structural configurations regardless of substrate binding, a pattern observed across various isomerases. These findings contribute to the understanding of MIPS structure-based function, serving as a template for future studies targeting regulation and potential therapeutic applications.
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Affiliation(s)
- Toni K. Träger
- Faculty of Natural Sciences I, Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle/Saale06120, Germany
- Biozentrum, Martin Luther University Halle-Wittenberg, Halle/Saale06120, Germany
| | - Fotis L. Kyrilis
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens11635, Greece
| | - Farzad Hamdi
- Faculty of Natural Sciences I, Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle/Saale06120, Germany
- Biozentrum, Martin Luther University Halle-Wittenberg, Halle/Saale06120, Germany
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Halle/Saale06120, Germany
| | - Christian Tüting
- Faculty of Natural Sciences I, Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle/Saale06120, Germany
- Biozentrum, Martin Luther University Halle-Wittenberg, Halle/Saale06120, Germany
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Halle/Saale06120, Germany
| | - Marie Alfes
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Halle/Saale06120, Germany
- Biologics Analytical R&D, AbbVie Deutschland GmbH & Co. KG, Ludwigshafen67061, Germany
| | - Tommy Hofmann
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Halle/Saale06120, Germany
- Impfstoffwerk Dessau-Tornau Biologika, Dessau-Roßlau06861, Germany
| | - Carla Schmidt
- Faculty of Natural Sciences I, Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle/Saale06120, Germany
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Halle/Saale06120, Germany
- Department of Chemistry–Biochemistry, Johannes Gutenberg University Mainz, Mainz55128, Germany
| | - Panagiotis L. Kastritis
- Faculty of Natural Sciences I, Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Halle/Saale06120, Germany
- Biozentrum, Martin Luther University Halle-Wittenberg, Halle/Saale06120, Germany
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens11635, Greece
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Halle/Saale06120, Germany
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17
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Herbine K, Nayak AR, Temiakov D. Structural basis for substrate binding and selection by human mitochondrial RNA polymerase. Nat Commun 2024; 15:7134. [PMID: 39164235 PMCID: PMC11335763 DOI: 10.1038/s41467-024-50817-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Accepted: 07/22/2024] [Indexed: 08/22/2024] Open
Abstract
The mechanism by which RNAP selects cognate substrates and discriminates between deoxy and ribonucleotides is of fundamental importance to the fidelity of transcription. Here, we present cryo-EM structures of human mitochondrial transcription elongation complexes that reveal substrate ATP bound in Entry and Insertion Sites. In the Entry Site, the substrate binds along the O helix of the fingers domain of mtRNAP but does not interact with the templating DNA base. Interactions between RNAP and the triphosphate moiety of the NTP in the Entry Site ensure discrimination against nucleosides and their diphosphate and monophosphate derivatives but not against non-cognate rNTPs and dNTPs. Closing of the fingers domain over the catalytic site results in delivery of both the templating DNA base and the substrate into the Insertion Site and recruitment of the catalytic magnesium ions. The cryo-EM data also reveal a conformation adopted by mtRNAP to reject a non-cognate substrate from its active site. Our findings establish a structural basis for substrate binding and suggest a unified mechanism of NTP selection for single-subunit RNAPs.
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Affiliation(s)
- Karl Herbine
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust St, Philadelphia, PA, 19107, USA
| | - Ashok R Nayak
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust St, Philadelphia, PA, 19107, USA
| | - Dmitry Temiakov
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust St, Philadelphia, PA, 19107, USA.
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18
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Akasaka H, Sato D, Shihoya W, Nureki O, Kise Y. Cryo-EM structure of I domain-containing integrin αEβ7. Biochem Biophys Res Commun 2024; 721:150121. [PMID: 38781659 DOI: 10.1016/j.bbrc.2024.150121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Accepted: 05/13/2024] [Indexed: 05/25/2024]
Abstract
The integrin family is a transmembrane receptor that plays critical roles in the cell-cell and cell-extracellular matrix adhesion, signal transduction such as cell cycle regulation, organization of the intracellular cytoskeleton, and immune responses. Consequently, dysfunction of integrins is associated with a wide range of human diseases, including cancer and immune diseases, which makes integrins therapeutic targets for drug discovery. Here we report the cryo-EM structure of the human α-I domain-containing full-length integrin αEβ7, which is expressed in the leukocytes of the immune system and a drug target for inflammatory bowel disease (IBD). The structure reveals the half-bent conformation, an intermediate between the close and the open conformation, while the α-I domain responsible for the ligand binding covers the headpiece domain by a unique spatial arrangement. Our results provide the structural information for the drug design targeting IBD.
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Affiliation(s)
- Hiroaki Akasaka
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, 113-0033, Japan
| | - Dan Sato
- Curreio, Inc., Room 357, South Clinical Research Laboratory, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-8485, Japan
| | - Wataru Shihoya
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, 113-0033, Japan
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, 113-0033, Japan; Curreio, Inc., Room 357, South Clinical Research Laboratory, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-8485, Japan.
| | - Yoshiaki Kise
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, 113-0033, Japan; Curreio, Inc., Room 357, South Clinical Research Laboratory, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, 113-8485, Japan.
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19
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Carl AG, Reynolds MJ, Gurel PS, Phua DY, Sun X, Mei L, Hamilton K, Takagi Y, Noble AJ, Sellers JR, Alushin GM. Myosin forces elicit an F-actin structural landscape that mediates mechanosensitive protein recognition. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.15.608188. [PMID: 39185238 PMCID: PMC11343212 DOI: 10.1101/2024.08.15.608188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/27/2024]
Abstract
Cells mechanically interface with their surroundings through cytoskeleton-linked adhesions, allowing them to sense physical cues that instruct development and drive diseases such as cancer. Contractile forces generated by myosin motor proteins mediate these mechanical signal transduction processes through unclear protein structural mechanisms. Here, we show that myosin forces elicit structural changes in actin filaments (F-actin) that modulate binding by the mechanosensitive adhesion protein α-catenin. Using correlative cryo-fluorescence microscopy and cryo-electron tomography, we identify F-actin featuring domains of nanoscale oscillating curvature at cytoskeleton-adhesion interfaces enriched in zyxin, a marker of actin-myosin generated traction forces. We next introduce a reconstitution system for visualizing F-actin in the presence of myosin forces with cryo-electron microscopy, which reveals morphologically similar superhelical F-actin spirals. In simulations, transient forces mimicking tugging and release of filaments by motors produce spirals, supporting a mechanistic link to myosin's ATPase mechanochemical cycle. Three-dimensional reconstruction of spirals uncovers extensive asymmetric remodeling of F-actin's helical lattice. This is recognized by α-catenin, which cooperatively binds along individual strands, preferentially engaging interfaces featuring extended inter-subunit distances while simultaneously suppressing rotational deviations to regularize the lattice. Collectively, we find that myosin forces can deform F-actin, generating a conformational landscape that is detected and reciprocally modulated by a mechanosensitive protein, providing a direct structural glimpse at active force transduction through the cytoskeleton.
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Affiliation(s)
- Ayala G. Carl
- Laboratory of Structural Biophysics and Mechanobiology, The Rockefeller University, New York, NY, USA
- Tri-Institutional Program in Chemical Biology, The Rockefeller University, New York, NY, USA
| | - Matthew J. Reynolds
- Laboratory of Structural Biophysics and Mechanobiology, The Rockefeller University, New York, NY, USA
| | - Pinar S. Gurel
- Laboratory of Structural Biophysics and Mechanobiology, The Rockefeller University, New York, NY, USA
| | - Donovan Y.Z. Phua
- Laboratory of Structural Biophysics and Mechanobiology, The Rockefeller University, New York, NY, USA
| | - Xiaoyu Sun
- Laboratory of Structural Biophysics and Mechanobiology, The Rockefeller University, New York, NY, USA
| | - Lin Mei
- Laboratory of Structural Biophysics and Mechanobiology, The Rockefeller University, New York, NY, USA
- Tri-Institutional Program in Chemical Biology, The Rockefeller University, New York, NY, USA
| | - Keith Hamilton
- Laboratory of Structural Biophysics and Mechanobiology, The Rockefeller University, New York, NY, USA
| | - Yasuharu Takagi
- Laboratory of Molecular Physiology, Cell and Developmental Biology Center, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD, USA
| | - Alex J. Noble
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - James R. Sellers
- Laboratory of Molecular Physiology, Cell and Developmental Biology Center, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD, USA
| | - Gregory M. Alushin
- Laboratory of Structural Biophysics and Mechanobiology, The Rockefeller University, New York, NY, USA
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20
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Cai X, He Y, Yu I, Imani A, Scholl D, Miller JF, Zhou ZH. Atomic structures of a bacteriocin targeting Gram-positive bacteria. Nat Commun 2024; 15:7057. [PMID: 39152109 PMCID: PMC11329794 DOI: 10.1038/s41467-024-51038-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 07/29/2024] [Indexed: 08/19/2024] Open
Abstract
Due to envelope differences between Gram-positive and Gram-negative bacteria, engineering precision bactericidal contractile nanomachines requires atomic-level understanding of their structures; however, only those killing Gram-negative bacteria are currently known. Here, we report the atomic structures of an engineered diffocin, a contractile syringe-like molecular machine that kills the Gram-positive bacterium Clostridioides difficile. Captured in one pre-contraction and two post-contraction states, each structure fashions six proteins in the bacteria-targeting baseplate, two proteins in the energy-storing trunk, and a collar linking the sheath with the membrane-penetrating tube. Compared to contractile machines targeting Gram-negative bacteria, major differences reside in the baseplate and contraction magnitude, consistent with target envelope differences. The multifunctional hub-hydrolase protein connects the tube and baseplate and is positioned to degrade peptidoglycan during penetration. The full-length tape measure protein forms a coiled-coil helix bundle homotrimer spanning the entire diffocin. Our study offers mechanical insights and principles for designing potent protein-based precision antibiotics.
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Affiliation(s)
- Xiaoying Cai
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA, USA
- The California NanoSystems Institute (CNSI), University of California, Los Angeles (UCLA), Los Angeles, CA, USA
| | - Yao He
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA, USA
- The California NanoSystems Institute (CNSI), University of California, Los Angeles (UCLA), Los Angeles, CA, USA
| | - Iris Yu
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA, USA
- The California NanoSystems Institute (CNSI), University of California, Los Angeles (UCLA), Los Angeles, CA, USA
| | - Anthony Imani
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA, USA
- The California NanoSystems Institute (CNSI), University of California, Los Angeles (UCLA), Los Angeles, CA, USA
| | - Dean Scholl
- Pylum Biosciences, San Francisco, CA, 94080, USA
| | - Jeff F Miller
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA, USA.
- The California NanoSystems Institute (CNSI), University of California, Los Angeles (UCLA), Los Angeles, CA, USA.
| | - Z Hong Zhou
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA, USA.
- The California NanoSystems Institute (CNSI), University of California, Los Angeles (UCLA), Los Angeles, CA, USA.
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21
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Burgie ES, Basore K, Rau MJ, Summers B, Mickles AJ, Grigura V, Fitzpatrick JAJ, Vierstra RD. Signaling by a bacterial phytochrome histidine kinase involves a conformational cascade reorganizing the dimeric photoreceptor. Nat Commun 2024; 15:6853. [PMID: 39127720 DOI: 10.1038/s41467-024-50412-y] [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: 01/11/2024] [Accepted: 07/09/2024] [Indexed: 08/12/2024] Open
Abstract
Phytochromes (Phys) are a divergent cohort of bili-proteins that detect light through reversible interconversion between dark-adapted Pr and photoactivated Pfr states. While our understandings of downstream events are emerging, it remains unclear how Phys translate light into an interpretable conformational signal. Here, we present models of both states for a dimeric Phy with histidine kinase (HK) activity from the proteobacterium Pseudomonas syringae, which were built from high-resolution cryo-EM maps (2.8-3.4-Å) of the photosensory module (PSM) and its following signaling (S) helix together with lower resolution maps for the downstream output region augmented by RoseTTAFold and AlphaFold structural predictions. The head-to-head models reveal the PSM and its photointerconversion mechanism with strong clarity, while the HK region is interpretable but relatively mobile. Pr/Pfr comparisons show that bilin phototransformation alters PSM architecture culminating in a scissoring motion of the paired S-helices linking the PSMs to the HK bidomains that ends in reorientation of the paired catalytic ATPase modules relative to the phosphoacceptor histidines. This action apparently primes autophosphorylation enroute to phosphotransfer to the cognate DNA-binding response regulator AlgB which drives quorum-sensing behavior through transient association with the photoreceptor. Collectively, these models illustrate how light absorption conformationally translates into accelerated signaling by Phy-type kinases.
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Affiliation(s)
- E Sethe Burgie
- Department of Biology, Washington University in St. Louis, St. Louis, MO, 63130, USA
- Bayer Crop Sciences, Chesterfield, MO, USA
| | - Katherine Basore
- Washington University in St. Louis Center for Cellular Imaging, St. Louis, MO, 63130, USA
| | - Michael J Rau
- Washington University in St. Louis Center for Cellular Imaging, St. Louis, MO, 63130, USA
- Bayer Crop Sciences, Chesterfield, MO, USA
| | - Brock Summers
- Washington University in St. Louis Center for Cellular Imaging, St. Louis, MO, 63130, USA
| | - Alayna J Mickles
- Department of Biology, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Vadim Grigura
- Department of Biology, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - James A J Fitzpatrick
- Washington University in St. Louis Center for Cellular Imaging, St. Louis, MO, 63130, USA
- Roche Pharma Research and Early Development, F. Hoffmann-La Roche Ltd, Basel, Grenzacherstrasse, 124, 4070, Switzerland
| | - Richard D Vierstra
- Department of Biology, Washington University in St. Louis, St. Louis, MO, 63130, USA.
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22
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Chi G, Jaślan D, Kudrina V, Böck J, Li H, Pike ACW, Rautenberg S, Krogsaeter E, Bohstedt T, Wang D, McKinley G, Fernandez-Cid A, Mukhopadhyay SMM, Burgess-Brown NA, Keller M, Bracher F, Grimm C, Dürr KL. Structural basis for inhibition of the lysosomal two-pore channel TPC2 by a small molecule antagonist. Structure 2024; 32:1137-1149.e4. [PMID: 38815576 DOI: 10.1016/j.str.2024.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 10/22/2023] [Accepted: 05/03/2024] [Indexed: 06/01/2024]
Abstract
Two pore channels are lysosomal cation channels with crucial roles in tumor angiogenesis and viral release from endosomes. Inhibition of the two-pore channel 2 (TPC2) has emerged as potential therapeutic strategy for the treatment of cancers and viral infections, including Ebola and COVID-19. Here, we demonstrate that antagonist SG-094, a synthetic analog of the Chinese alkaloid medicine tetrandrine with increased potency and reduced toxicity, induces asymmetrical structural changes leading to a single binding pocket at only one intersubunit interface within the asymmetrical dimer. Supported by functional characterization of mutants by Ca2+ imaging and patch clamp experiments, we identify key residues in S1 and S4 involved in compound binding to the voltage sensing domain II. SG-094 arrests IIS4 in a downward shifted state which prevents pore opening via the IIS4/S5 linker, hence resembling gating modifiers of canonical VGICs. These findings may guide the rational development of new therapeutics antagonizing TPC2 activity.
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Affiliation(s)
- Gamma Chi
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Nuffield Department of Medicine Research Building, Oxford OX3 7FZ, UK; Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Nuffield Department of Medicine Research Building, Oxford OX3 7FZ, UK.
| | - Dawid Jaślan
- Walther-Straub-Institut für Pharmakologie und Toxikologie, Medizinische Fakultät, Ludwig-Maximilians-Universität, Nussbaumstrasse 26, 80336 Munich, Germany
| | - Veronika Kudrina
- Walther-Straub-Institut für Pharmakologie und Toxikologie, Medizinische Fakultät, Ludwig-Maximilians-Universität, Nussbaumstrasse 26, 80336 Munich, Germany
| | - Julia Böck
- Walther-Straub-Institut für Pharmakologie und Toxikologie, Medizinische Fakultät, Ludwig-Maximilians-Universität, Nussbaumstrasse 26, 80336 Munich, Germany
| | - Huanyu Li
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Nuffield Department of Medicine Research Building, Oxford OX3 7FZ, UK; Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Nuffield Department of Medicine Research Building, Oxford OX3 7FZ, UK
| | - Ashley C W Pike
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Nuffield Department of Medicine Research Building, Oxford OX3 7FZ, UK; Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Nuffield Department of Medicine Research Building, Oxford OX3 7FZ, UK
| | - Susanne Rautenberg
- Department of Pharmacy, Center for Drug Research, Ludwig-Maximilians-Universität, Butenandtstrasse 7, 81377 Munich, Germany
| | - Einar Krogsaeter
- Walther-Straub-Institut für Pharmakologie und Toxikologie, Medizinische Fakultät, Ludwig-Maximilians-Universität, Nussbaumstrasse 26, 80336 Munich, Germany
| | - Tina Bohstedt
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Nuffield Department of Medicine Research Building, Oxford OX3 7FZ, UK; Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Nuffield Department of Medicine Research Building, Oxford OX3 7FZ, UK
| | - Dong Wang
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Nuffield Department of Medicine Research Building, Oxford OX3 7FZ, UK; Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Nuffield Department of Medicine Research Building, Oxford OX3 7FZ, UK
| | - Gavin McKinley
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Nuffield Department of Medicine Research Building, Oxford OX3 7FZ, UK; Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Nuffield Department of Medicine Research Building, Oxford OX3 7FZ, UK
| | - Alejandra Fernandez-Cid
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Nuffield Department of Medicine Research Building, Oxford OX3 7FZ, UK; Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Nuffield Department of Medicine Research Building, Oxford OX3 7FZ, UK
| | - Shubhashish M M Mukhopadhyay
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Nuffield Department of Medicine Research Building, Oxford OX3 7FZ, UK; Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Nuffield Department of Medicine Research Building, Oxford OX3 7FZ, UK
| | - Nicola A Burgess-Brown
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Nuffield Department of Medicine Research Building, Oxford OX3 7FZ, UK; Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Nuffield Department of Medicine Research Building, Oxford OX3 7FZ, UK
| | - Marco Keller
- Department of Pharmacy, Center for Drug Research, Ludwig-Maximilians-Universität, Butenandtstrasse 7, 81377 Munich, Germany
| | - Franz Bracher
- Department of Pharmacy, Center for Drug Research, Ludwig-Maximilians-Universität, Butenandtstrasse 7, 81377 Munich, Germany
| | - Christian Grimm
- Walther-Straub-Institut für Pharmakologie und Toxikologie, Medizinische Fakultät, Ludwig-Maximilians-Universität, Nussbaumstrasse 26, 80336 Munich, Germany; Immunology, Infection and Pandemic Research IIP, Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Munich/Frankfurt, Germany
| | - Katharina L Dürr
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Nuffield Department of Medicine Research Building, Oxford OX3 7FZ, UK; Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Nuffield Department of Medicine Research Building, Oxford OX3 7FZ, UK
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23
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Powell BM, Davis JH. Learning structural heterogeneity from cryo-electron sub-tomograms with tomoDRGN. Nat Methods 2024; 21:1525-1536. [PMID: 38459385 DOI: 10.1038/s41592-024-02210-z] [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: 05/31/2023] [Accepted: 02/13/2024] [Indexed: 03/10/2024]
Abstract
Cryo-electron tomography (cryo-ET) enables observation of macromolecular complexes in their native, spatially contextualized cellular environment. Cryo-ET processing software to visualize such complexes at nanometer resolution via iterative alignment and averaging are well developed but rely upon assumptions of structural homogeneity among the complexes of interest. Recently developed tools allow for some assessment of structural diversity but have limited capacity to represent highly heterogeneous structures, including those undergoing continuous conformational changes. Here we extend the highly expressive cryoDRGN (Deep Reconstructing Generative Networks) deep learning architecture, originally created for single-particle cryo-electron microscopy analysis, to cryo-ET. Our new tool, tomoDRGN, learns a continuous low-dimensional representation of structural heterogeneity in cryo-ET datasets while also learning to reconstruct heterogeneous structural ensembles supported by the underlying data. Using simulated and experimental data, we describe and benchmark architectural choices within tomoDRGN that are uniquely necessitated and enabled by cryo-ET. We additionally illustrate tomoDRGN's efficacy in analyzing diverse datasets, using it to reveal high-level organization of human immunodeficiency virus (HIV) capsid complexes assembled in virus-like particles and to resolve extensive structural heterogeneity among ribosomes imaged in situ.
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Affiliation(s)
- Barrett M Powell
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Joseph H Davis
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Program in Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
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24
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Strauss A, Gonzalez-Hernandez AJ, Lee J, Abreu N, Selvakumar P, Salas-Estrada L, Kristt M, Arefin A, Huynh K, Marx DC, Gilliland K, Melancon BJ, Filizola M, Meyerson J, Levitz J. Structural basis of positive allosteric modulation of metabotropic glutamate receptor activation and internalization. Nat Commun 2024; 15:6498. [PMID: 39090128 PMCID: PMC11294631 DOI: 10.1038/s41467-024-50548-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: 03/21/2024] [Accepted: 07/12/2024] [Indexed: 08/04/2024] Open
Abstract
The metabotropic glutamate receptors (mGluRs) are neuromodulatory family C G protein coupled receptors which assemble as dimers and allosterically couple extracellular ligand binding domains (LBDs) to transmembrane domains (TMDs) to drive intracellular signaling. Pharmacologically, mGluRs can be targeted at the LBDs by glutamate and synthetic orthosteric compounds or at the TMDs by allosteric modulators. Despite the potential of allosteric compounds as therapeutics, an understanding of the functional and structural basis of their effects is limited. Here we use multiple approaches to dissect the functional and structural effects of orthosteric versus allosteric ligands. We find, using electrophysiological and live cell imaging assays, that both agonists and positive allosteric modulators (PAMs) can drive activation and internalization of group II and III mGluRs. The effects of PAMs are pleiotropic, boosting the maximal response to orthosteric agonists and serving independently as internalization-biased agonists across mGluR subtypes. Motivated by this and intersubunit FRET analyses, we determine cryo-electron microscopy structures of mGluR3 in the presence of either an agonist or antagonist alone or in combination with a PAM. These structures reveal PAM-driven re-shaping of intra- and inter-subunit conformations and provide evidence for a rolling TMD dimer interface activation pathway that controls G protein and beta-arrestin coupling.
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Affiliation(s)
- Alexa Strauss
- Department of Biochemistry, Weill Cornell Medicine, New York, NY, 10065, USA
- Tri-Institutional Program in Chemical Biology, New York, NY, 10065, USA
| | | | - Joon Lee
- Department of Biochemistry, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Nohely Abreu
- Department of Biochemistry, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Purushotham Selvakumar
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Leslie Salas-Estrada
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Melanie Kristt
- Department of Biochemistry, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Anisul Arefin
- Department of Biochemistry, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Kevin Huynh
- Department of Biochemistry, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Dagan C Marx
- Department of Biochemistry, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Kristen Gilliland
- Warren Center for Neuroscience Drug Discovery at Vanderbilt University, Vanderbilt University, Nashville, TN, 37232, USA
| | - Bruce J Melancon
- Warren Center for Neuroscience Drug Discovery at Vanderbilt University, Vanderbilt University, Nashville, TN, 37232, USA
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
| | - Marta Filizola
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Joel Meyerson
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Joshua Levitz
- Department of Biochemistry, Weill Cornell Medicine, New York, NY, 10065, USA.
- Tri-Institutional Program in Chemical Biology, New York, NY, 10065, USA.
- Department of Psychiatry, Weill Cornell Medicine, New York, NY, 10065, USA.
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25
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Kefauver JM, Hakala M, Zou L, Alba J, Espadas J, Tettamanti MG, Gajić J, Gabus C, Campomanes P, Estrozi LF, Sen NE, Vanni S, Roux A, Desfosses A, Loewith R. Cryo-EM architecture of a near-native stretch-sensitive membrane microdomain. Nature 2024; 632:664-671. [PMID: 39048819 PMCID: PMC11324527 DOI: 10.1038/s41586-024-07720-6] [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: 08/25/2023] [Accepted: 06/14/2024] [Indexed: 07/27/2024]
Abstract
Biological membranes are partitioned into functional zones termed membrane microdomains, which contain specific lipids and proteins1-3. The composition and organization of membrane microdomains remain controversial because few techniques are available that allow the visualization of lipids in situ without disrupting their native behaviour3,4. The yeast eisosome, composed of the BAR-domain proteins Pil1 and Lsp1 (hereafter, Pil1/Lsp1), scaffolds a membrane compartment that senses and responds to mechanical stress by flattening and releasing sequestered factors5-9. Here we isolated near-native eisosomes as helical tubules made up of a lattice of Pil1/Lsp1 bound to plasma membrane lipids, and solved their structures by helical reconstruction. Our structures reveal a striking organization of membrane lipids, and, using in vitro reconstitutions and molecular dynamics simulations, we confirmed the positioning of individual PI(4,5)P2, phosphatidylserine and sterol molecules sequestered beneath the Pil1/Lsp1 coat. Three-dimensional variability analysis of the native-source eisosomes revealed a dynamic stretching of the Pil1/Lsp1 lattice that affects the sequestration of these lipids. Collectively, our results support a mechanism in which stretching of the Pil1/Lsp1 lattice liberates lipids that would otherwise be anchored by the Pil1/Lsp1 coat, and thus provide mechanistic insight into how eisosome BAR-domain proteins create a mechanosensitive membrane microdomain.
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Affiliation(s)
- Jennifer M Kefauver
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland
- Nanomaterials and Nanotechnology Research Center (CINN), Spanish National Research Council (CSIC), El Entrego, Spain
| | - Markku Hakala
- Department of Biochemistry, University of Geneva, Geneva, Switzerland
| | - Luoming Zou
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland
| | - Josephine Alba
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Javier Espadas
- Department of Biochemistry, University of Geneva, Geneva, Switzerland
| | - Maria G Tettamanti
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland
- Department of Biochemistry, University of Geneva, Geneva, Switzerland
| | - Jelena Gajić
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland
- Department of Organic Chemistry, University of Geneva, Geneva, Switzerland
| | - Caroline Gabus
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland
| | - Pablo Campomanes
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Leandro F Estrozi
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
| | - Nesli E Sen
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland
| | - Stefano Vanni
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- Swiss National Center for Competence in Research (NCCR) Bio-inspired Materials, University of Fribourg, Fribourg, Switzerland
| | - Aurélien Roux
- Department of Biochemistry, University of Geneva, Geneva, Switzerland
| | - Ambroise Desfosses
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France
| | - Robbie Loewith
- Department of Molecular and Cellular Biology, University of Geneva, Geneva, Switzerland.
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26
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Zhang L, Einsle O. Architecture of the RNF1 complex that drives biological nitrogen fixation. Nat Chem Biol 2024; 20:1078-1085. [PMID: 38890433 DOI: 10.1038/s41589-024-01641-1] [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: 07/13/2022] [Accepted: 05/10/2024] [Indexed: 06/20/2024]
Abstract
Biological nitrogen fixation requires substantial metabolic energy in form of ATP as well as low-potential electrons that must derive from central metabolism. During aerobic growth, the free-living soil diazotroph Azotobacter vinelandii transfers electrons from the key metabolite NADH to the low-potential ferredoxin FdxA that serves as a direct electron donor to the dinitrogenase reductases. This process is mediated by the RNF complex that exploits the proton motive force over the cytoplasmic membrane to lower the midpoint potential of the transferred electron. Here we report the cryogenic electron microscopy structure of the nitrogenase-associated RNF complex of A. vinelandii, a seven-subunit membrane protein assembly that contains four flavin cofactors and six iron-sulfur centers. Its function requires the strict coupling of electron and proton transfer but also involves major conformational changes within the assembly that can be traced with a combination of electron microscopy and modeling.
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Affiliation(s)
- Lin Zhang
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Oliver Einsle
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany.
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27
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Li YD, Ma MW, Hassan MM, Hunkeler M, Teng M, Puvar K, Rutter JC, Lumpkin RJ, Sandoval B, Jin CY, Schmoker AM, Ficarro SB, Cheong H, Metivier RJ, Wang MY, Xu S, Byun WS, Groendyke BJ, You I, Sigua LH, Tavares I, Zou C, Tsai JM, Park PMC, Yoon H, Majewski FC, Sperling HT, Marto JA, Qi J, Nowak RP, Donovan KA, Słabicki M, Gray NS, Fischer ES, Ebert BL. Template-assisted covalent modification underlies activity of covalent molecular glues. Nat Chem Biol 2024:10.1038/s41589-024-01668-4. [PMID: 39075252 DOI: 10.1038/s41589-024-01668-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 06/05/2024] [Indexed: 07/31/2024]
Abstract
Molecular glues are proximity-inducing small molecules that have emerged as an attractive therapeutic approach. However, developing molecular glues remains challenging, requiring innovative mechanistic strategies to stabilize neoprotein interfaces and expedite discovery. Here we unveil a trans-labeling covalent molecular glue mechanism, termed 'template-assisted covalent modification'. We identified a new series of BRD4 molecular glue degraders that recruit CUL4DCAF16 ligase to the second bromodomain of BRD4 (BRD4BD2). Through comprehensive biochemical, structural and mutagenesis analyses, we elucidated how pre-existing structural complementarity between DCAF16 and BRD4BD2 serves as a template to optimally orient the degrader for covalent modification of DCAF16Cys58. This process stabilizes the formation of BRD4-degrader-DCAF16 ternary complex and facilitates BRD4 degradation. Supporting generalizability, we found that a subset of degraders also induces GAK-BRD4BD2 interaction through trans-labeling of GAK. Together, our work establishes 'template-assisted covalent modification' as a mechanism for covalent molecular glues, which opens a new path to proximity-driven pharmacology.
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Affiliation(s)
- Yen-Der Li
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Michelle W Ma
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Muhammad Murtaza Hassan
- Department of Chemical and Systems Biology, Chem-H and Stanford Cancer Institute, Stanford School of Medicine, Stanford University, Stanford, CA, USA
| | - Moritz Hunkeler
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Mingxing Teng
- Center for Drug Discovery, Department of Pathology & Immunology, and Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA
| | - Kedar Puvar
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Justine C Rutter
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ryan J Lumpkin
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Brittany Sandoval
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Cyrus Y Jin
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Anna M Schmoker
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Scott B Ficarro
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Blais Proteomics Center and Center for Emergent Drug Targets, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Hakyung Cheong
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Rebecca J Metivier
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Michelle Y Wang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Shawn Xu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Woong Sub Byun
- Department of Chemical and Systems Biology, Chem-H and Stanford Cancer Institute, Stanford School of Medicine, Stanford University, Stanford, CA, USA
| | - Brian J Groendyke
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Inchul You
- Department of Chemical and Systems Biology, Chem-H and Stanford Cancer Institute, Stanford School of Medicine, Stanford University, Stanford, CA, USA
| | - Logan H Sigua
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Isidoro Tavares
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Blais Proteomics Center and Center for Emergent Drug Targets, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Charles Zou
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jonathan M Tsai
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Paul M C Park
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Hojong Yoon
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Felix C Majewski
- Department of Chemical and Systems Biology, Chem-H and Stanford Cancer Institute, Stanford School of Medicine, Stanford University, Stanford, CA, USA
| | - Haniya T Sperling
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jarrod A Marto
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Blais Proteomics Center and Center for Emergent Drug Targets, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Jun Qi
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Radosław P Nowak
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Katherine A Donovan
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Mikołaj Słabicki
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nathanael S Gray
- Department of Chemical and Systems Biology, Chem-H and Stanford Cancer Institute, Stanford School of Medicine, Stanford University, Stanford, CA, USA.
| | - Eric S Fischer
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
| | - Benjamin L Ebert
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Boston, MA, USA.
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28
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Yi G, Ye M, Carrique L, El-Sagheer A, Brown T, Norbury CJ, Zhang P, Gilbert RJC. Structural basis for activity switching in polymerases determining the fate of let-7 pre-miRNAs. Nat Struct Mol Biol 2024:10.1038/s41594-024-01357-9. [PMID: 39054354 DOI: 10.1038/s41594-024-01357-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 06/17/2024] [Indexed: 07/27/2024]
Abstract
Tumor-suppressor let-7 pre-microRNAs (miRNAs) are regulated by terminal uridylyltransferases TUT7 and TUT4 that either promote let-7 maturation by adding a single uridine nucleotide to the pre-miRNA 3' end or mark them for degradation by the addition of multiple uridines. Oligo-uridylation is increased in cells by enhanced TUT7/4 expression and especially by the RNA-binding pluripotency factor LIN28A. Using cryogenic electron microscopy, we captured high-resolution structures of active forms of TUT7 alone, of TUT7 plus pre-miRNA and of both TUT7 and TUT4 bound with pre-miRNA and LIN28A. Our structures reveal that pre-miRNAs engage the enzymes in fundamentally different ways depending on the presence of LIN28A, which clamps them onto the TUTs to enable processive 3' oligo-uridylation. This study reveals the molecular basis for mono- versus oligo-uridylation by TUT7/4, as determined by the presence of LIN28A, and thus their mechanism of action in the regulation of cell fate and in cancer.
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Affiliation(s)
- Gangshun Yi
- Division of Structural Biology, Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Calleva Centre for Evolution and Human Science, Magdalen College, Oxford, UK
| | - Mingda Ye
- Centre for Medicines Discovery, University of Oxford, Oxford, UK
| | - Loic Carrique
- Division of Structural Biology, Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Afaf El-Sagheer
- Chemistry Research Laboratory, University of Oxford, Oxford, UK
- Institute for Life Sciences, University of Southampton Highfield Campus, Southampton, UK
| | - Tom Brown
- Chemistry Research Laboratory, University of Oxford, Oxford, UK
| | - Chris J Norbury
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Peijun Zhang
- Division of Structural Biology, Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
- Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, UK
| | - Robert J C Gilbert
- Division of Structural Biology, Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
- Calleva Centre for Evolution and Human Science, Magdalen College, Oxford, UK.
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29
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Lynch EM, Lu Y, Park JH, Shao L, Kollman J, Rego EH. Evolutionarily divergent Mycobacterium tuberculosis CTP synthase filaments are under selective pressure. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.25.605180. [PMID: 39091829 PMCID: PMC11291164 DOI: 10.1101/2024.07.25.605180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
The final and rate-limiting enzyme in pyrimidine biosynthesis, CTP synthase (CTPS), is essential for the viability of Mycobacterium tuberculosis and other mycobacteria. Its product, CTP, is critical for RNA, DNA, lipid and cell wall synthesis, and is involved in chromosome segregation. In various organisms across the tree of life, CTPS assembles into higher-order filaments, leading us to hypothesize that M. tuberculosis CTPS (mtCTPS) also forms higher-order structures. Here, we show that mtCTPS does assemble into filaments but with an unusual architecture not seen in other organisms. Through a combination of structural, biochemical, and cellular techniques, we show that polymerization stabilizes the active conformation of the enzyme and resists product inhibition, potentially allowing for the highly localized production of CTP within the cell. Indeed, CTPS filaments localize near the CTP-dependent complex needed for chromosome segregation, and cells expressing mutant enzymes unable to polymerize are altered in their ability to robustly form this complex. Intriguingly, mutants that alter filament formation are under positive selection in clinical isolates of M. tuberculosis , pointing to a critical role needed to withstand pressures imposed by the host and/or antibiotics. Taken together, our data reveal an unexpected mechanism for the spatially organized production of a critical nucleotide in M. tuberculosis , which may represent a vulnerability of the pathogen that can be exploited with chemotherapy.
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30
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Drulyte I, Ghai R, Ow SY, Kapp EA, Quek AJ, Panousis C, Wilson MJ, Nash AD, Pelzing M. Structural basis for the inhibition of βFXIIa by garadacimab. Structure 2024:S0969-2126(24)00239-9. [PMID: 39059382 DOI: 10.1016/j.str.2024.07.001] [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: 04/04/2024] [Revised: 05/24/2024] [Accepted: 07/01/2024] [Indexed: 07/28/2024]
Abstract
Activated FXII (FXIIa) is the principal initiator of the plasma contact system and can activate both procoagulant and proinflammatory pathways. Its activity is important in the pathophysiology of hereditary angioedema (HAE). Here, we describe a high-resolution cryoelectron microscopy (cryo-EM) structure of the beta-chain from FXIIa (βFXIIa) complexed with the Fab fragment of garadacimab. Garadacimab binds to βFXIIa through an unusually long CDR-H3 that inserts into the S1 pocket in a non-canonical way. This structural mechanism is likely the primary contributor to the inhibition of activated FXIIa proteolytic activity in HAE. Garadacimab Fab-βFXIIa structure also reveals critical determinants of high-affinity binding of garadacimab to activated FXIIa. Structural analysis with other bona fide FXIIa inhibitors, such as benzamidine and C1-INH, reveals a surprisingly similar mechanism of βFXIIa inhibition by garadacimab. In summary, the garadacimab Fab-βFXIIa structure provides crucial insights into its mechanism of action and delineates primary and auxiliary paratopes/epitopes.
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Affiliation(s)
- Ieva Drulyte
- Materials and Structural Analysis, Thermo Fisher Scientific, Eindhoven, the Netherlands
| | - Rajesh Ghai
- Research and Development, CSL Limited, Bio21 Molecular Science and Biotechnology Institute, Parkville, Victoria, Australia
| | - Saw Yen Ow
- Research and Development, CSL Limited, Bio21 Molecular Science and Biotechnology Institute, Parkville, Victoria, Australia
| | - Eugene A Kapp
- Research and Development, CSL Limited, Bio21 Molecular Science and Biotechnology Institute, Parkville, Victoria, Australia
| | - Adam J Quek
- Research and Development, CSL Limited, Bio21 Molecular Science and Biotechnology Institute, Parkville, Victoria, Australia
| | - Con Panousis
- Research and Development, CSL Limited, Bio21 Molecular Science and Biotechnology Institute, Parkville, Victoria, Australia
| | - Michael J Wilson
- Research and Development, CSL Limited, Bio21 Molecular Science and Biotechnology Institute, Parkville, Victoria, Australia
| | - Andrew D Nash
- Research and Development, CSL Limited, Bio21 Molecular Science and Biotechnology Institute, Parkville, Victoria, Australia
| | - Matthias Pelzing
- Research and Development, CSL Limited, Bio21 Molecular Science and Biotechnology Institute, Parkville, Victoria, Australia.
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31
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Schneider S, Kühlbrandt W, Yildiz Ö. Complementary structures of the yeast phosphate transporter Pho90 provide insights into its transport mechanism. Structure 2024; 32:979-988.e4. [PMID: 38688287 DOI: 10.1016/j.str.2024.04.005] [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: 11/17/2023] [Revised: 03/01/2024] [Accepted: 04/03/2024] [Indexed: 05/02/2024]
Abstract
Phosphate homeostasis is essential for all living organisms. Low-affinity phosphate transporters are involved in phosphate import and regulation in a range of eukaryotic organisms. We have determined the structures of the Saccharomyces cerevisiae phosphate importer Pho90 by electron cryomicroscopy in two complementary states at 2.3 and 3.1 Å resolution. The symmetrical, outward-open structure in the presence of phosphate indicates bound substrate ions in the binding pocket. In the absence of phosphate, Pho90 assumes an asymmetric structure with one monomer facing inward and one monomer facing outward, providing insights into the transport mechanism. The Pho90 transport domain binds phosphate ions on one side of the membrane, then flips to the other side where the substrate is released. Together with functional experiments, these complementary structures illustrate the transport mechanism of eukaryotic low-affinity phosphate transporters.
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Affiliation(s)
- Simon Schneider
- Department of Structural Biology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Werner Kühlbrandt
- Department of Structural Biology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Özkan Yildiz
- Department of Structural Biology, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany; Structural Biology Unit, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany.
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32
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Dong Y, Bonin JP, Devant P, Liang Z, Sever AIM, Mintseris J, Aramini JM, Du G, Gygi SP, Kagan JC, Kay LE, Wu H. Structural transitions enable interleukin-18 maturation and signaling. Immunity 2024; 57:1533-1548.e10. [PMID: 38733997 PMCID: PMC11236505 DOI: 10.1016/j.immuni.2024.04.015] [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: 10/26/2023] [Revised: 02/28/2024] [Accepted: 04/17/2024] [Indexed: 05/13/2024]
Abstract
Several interleukin-1 (IL-1) family members, including IL-1β and IL-18, require processing by inflammasome-associated caspases to unleash their activities. Here, we unveil, by cryoelectron microscopy (cryo-EM), two major conformations of the complex between caspase-1 and pro-IL-18. One conformation is similar to the complex of caspase-4 and pro-IL-18, with interactions at both the active site and an exosite (closed conformation), and the other only contains interactions at the active site (open conformation). Thus, pro-IL-18 recruitment and processing by caspase-1 is less dependent on the exosite than the active site, unlike caspase-4. Structure determination by nuclear magnetic resonance uncovers a compact fold of apo pro-IL-18, which is similar to caspase-1-bound pro-IL-18 but distinct from cleaved IL-18. Binding sites for IL-18 receptor and IL-18 binding protein are only formed upon conformational changes after pro-IL-18 cleavage. These studies show how pro-IL-18 is selected as a caspase-1 substrate, and why cleavage is necessary for its inflammatory activity.
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Affiliation(s)
- Ying Dong
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Jeffrey P Bonin
- Departments of Molecular Genetics and Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada; Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON M5G 0A4, Canada
| | - Pascal Devant
- Division of Gastroenterology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Zhuoyi Liang
- Bioscience and Biomedical Engineering Thrust, Brain and Intelligence Research Institute, The Hong Kong University of Science and Technology (Guangzhou), Guangzhou, China
| | - Alexander I M Sever
- Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada; Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON M5G 0A4, Canada
| | - Julian Mintseris
- Department of Cell Biology, Harvard Medical School, Harvard University, Boston, MA, USA
| | - James M Aramini
- Departments of Molecular Genetics and Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada; Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON M5G 0A4, Canada
| | - Gang Du
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Stephen P Gygi
- Department of Cell Biology, Harvard Medical School, Harvard University, Boston, MA, USA
| | - Jonathan C Kagan
- Division of Gastroenterology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
| | - Lewis E Kay
- Departments of Molecular Genetics and Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada; Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON M5G 0A4, Canada.
| | - Hao Wu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA.
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33
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Karuppan S, Schrag LG, Pastrano CM, Jara-Oseguera A, Zubcevic L. Structural dynamics at cytosolic interprotomer interfaces control gating of a mammalian TRPM5 channel. Proc Natl Acad Sci U S A 2024; 121:e2403333121. [PMID: 38923985 PMCID: PMC11228501 DOI: 10.1073/pnas.2403333121] [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: 02/20/2024] [Accepted: 05/15/2024] [Indexed: 06/28/2024] Open
Abstract
The transient receptor potential melastatin (TRPM) tetrameric cation channels are involved in a wide range of biological functions, from temperature sensing and taste transduction to regulation of cardiac function, inflammatory pain, and insulin secretion. The structurally conserved TRPM cytoplasmic domains make up >70 % of the total protein. To investigate the mechanism by which the TRPM cytoplasmic domains contribute to gating, we employed electrophysiology and cryo-EM to study TRPM5-a channel that primarily relies on activation via intracellular Ca2+. Here, we show that activation of mammalian TRPM5 channels is strongly altered by Ca2+-dependent desensitization. Structures of rat TRPM5 identify a series of conformational transitions triggered by Ca2+ binding, whereby formation and dissolution of cytoplasmic interprotomer interfaces appear to control activation and desensitization of the channel. This study shows the importance of the cytoplasmic assembly in TRPM5 channel function and sets the stage for future investigations of other members of the TRPM family.
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Affiliation(s)
- Sebastian Karuppan
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, KS66160
| | - Lynn Goss Schrag
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, KS66160
| | - Caroline M. Pastrano
- Department of Molecular Biosciences, College of Natural Sciences, The University of Texas at Austin, Austin, TX78712
| | - Andrés Jara-Oseguera
- Department of Molecular Biosciences, College of Natural Sciences, The University of Texas at Austin, Austin, TX78712
| | - Lejla Zubcevic
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, KS66160
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34
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Harikumar KG, Zhao P, Cary BP, Xu X, Desai AJ, Dong M, Mobbs JI, Toufaily C, Furness SGB, Christopoulos A, Belousoff MJ, Wootten D, Sexton PM, Miller LJ. Cholesterol-dependent dynamic changes in the conformation of the type 1 cholecystokinin receptor affect ligand binding and G protein coupling. PLoS Biol 2024; 22:e3002673. [PMID: 39083706 PMCID: PMC11290853 DOI: 10.1371/journal.pbio.3002673] [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: 02/26/2024] [Accepted: 05/13/2024] [Indexed: 08/02/2024] Open
Abstract
Development of optimal therapeutics for disease states that can be associated with increased membrane cholesterol requires better molecular understanding of lipid modulation of the drug target. Type 1 cholecystokinin receptor (CCK1R) agonist actions are affected by increased membrane cholesterol, enhancing ligand binding and reducing calcium signaling, while agonist actions of the closely related CCK2R are not. In this work, we identified a set of chimeric human CCK1R/CCK2R mutations that exchange the cholesterol sensitivity of these 2 receptors, providing powerful tools when expressed in CHO and HEK-293 model cell lines to explore mechanisms. Static, low energy, high-resolution structures of the mutant CCK1R constructs, stabilized in complex with G protein, were not substantially different, suggesting that alterations to receptor dynamics were key to altered function. We reveal that cholesterol-dependent dynamic changes in the conformation of the helical bundle of CCK receptors affects both ligand binding at the extracellular surface and G protein coupling at the cytosolic surface, as well as their interrelationships involved in stimulus-response coupling. This provides an ideal setting for potential allosteric modulators to correct the negative impact of membrane cholesterol on CCK1R.
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Affiliation(s)
- Kaleeckal G. Harikumar
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Scottsdale, Arizona, United States of America
| | - Peishen Zhao
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Brian P. Cary
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Xiaomeng Xu
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Aditya J. Desai
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Scottsdale, Arizona, United States of America
| | - Maoqing Dong
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Scottsdale, Arizona, United States of America
| | - Jesse I. Mobbs
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Chirine Toufaily
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Scottsdale, Arizona, United States of America
| | - Sebastian G. B. Furness
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
- School of Biomedical Sciences, University Queensland, Queensland, Australia
| | - Arthur Christopoulos
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Matthew J. Belousoff
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Denise Wootten
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Patrick M. Sexton
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Laurence J. Miller
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Scottsdale, Arizona, United States of America
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35
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Wankowicz SA, Fraser JS. Comprehensive encoding of conformational and compositional protein structural ensembles through the mmCIF data structure. IUCRJ 2024; 11:494-501. [PMID: 38958015 PMCID: PMC11220883 DOI: 10.1107/s2052252524005098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 05/29/2024] [Indexed: 07/04/2024]
Abstract
In the folded state, biomolecules exchange between multiple conformational states crucial for their function. However, most structural models derived from experiments and computational predictions only encode a single state. To represent biomolecules accurately, we must move towards modeling and predicting structural ensembles. Information about structural ensembles exists within experimental data from X-ray crystallography and cryo-electron microscopy. Although new tools are available to detect conformational and compositional heterogeneity within these ensembles, the legacy PDB data structure does not robustly encapsulate this complexity. We propose modifications to the macromolecular crystallographic information file (mmCIF) to improve the representation and interrelation of conformational and compositional heterogeneity. These modifications will enable the capture of macromolecular ensembles in a human and machine-interpretable way, potentially catalyzing breakthroughs for ensemble-function predictions, analogous to the achievements of AlphaFold with single-structure prediction.
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Affiliation(s)
- Stephanie A. Wankowicz
- Department of Bioengineering and Therapeutic ScienceUniversity of CaliforniaSan FranciscoCA94117USA
| | - James S. Fraser
- Department of Bioengineering and Therapeutic ScienceUniversity of CaliforniaSan FranciscoCA94117USA
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36
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Saecker RM, Mueller AU, Malone B, Chen J, Budell WC, Dandey VP, Maruthi K, Mendez JH, Molina N, Eng ET, Yen LY, Potter CS, Carragher B, Darst SA. Early intermediates in bacterial RNA polymerase promoter melting visualized by time-resolved cryo-electron microscopy. Nat Struct Mol Biol 2024:10.1038/s41594-024-01349-9. [PMID: 38951624 DOI: 10.1038/s41594-024-01349-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 06/06/2024] [Indexed: 07/03/2024]
Abstract
During formation of the transcription-competent open complex (RPo) by bacterial RNA polymerases (RNAPs), transient intermediates pile up before overcoming a rate-limiting step. Structural descriptions of these interconversions in real time are unavailable. To address this gap, here we use time-resolved cryogenic electron microscopy (cryo-EM) to capture four intermediates populated 120 ms or 500 ms after mixing Escherichia coli σ70-RNAP and the λPR promoter. Cryo-EM snapshots revealed that the upstream edge of the transcription bubble unpairs rapidly, followed by stepwise insertion of two conserved nontemplate strand (nt-strand) bases into RNAP pockets. As the nt-strand 'read-out' extends, the RNAP clamp closes, expelling an inhibitory σ70 domain from the active-site cleft. The template strand is fully unpaired by 120 ms but remains dynamic, indicating that yet unknown conformational changes complete RPo formation in subsequent steps. Given that these events likely describe DNA opening at many bacterial promoters, this study provides insights into how DNA sequence regulates steps of RPo formation.
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Affiliation(s)
- Ruth M Saecker
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY, USA
| | - Andreas U Mueller
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY, USA
| | - Brandon Malone
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY, USA
- Memorial Sloan Kettering Cancer Center, Sloan Kettering Institute, New York, NY, USA
| | - James Chen
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY, USA
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY, USA
| | - William C Budell
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Venkata P Dandey
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
- National Institute of Environmental Health Sciences, Durham, NC, USA
| | - Kashyap Maruthi
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Joshua H Mendez
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Nina Molina
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY, USA
| | - Edward T Eng
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Laura Y Yen
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Clinton S Potter
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
- Chan Zuckerberg Imaging Institute, San Francisco, CA, USA
| | - Bridget Carragher
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
- Chan Zuckerberg Imaging Institute, San Francisco, CA, USA
| | - Seth A Darst
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY, USA.
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37
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Ennist NM, Wang S, Kennedy MA, Curti M, Sutherland GA, Vasilev C, Redler RL, Maffeis V, Shareef S, Sica AV, Hua AS, Deshmukh AP, Moyer AP, Hicks DR, Swartz AZ, Cacho RA, Novy N, Bera AK, Kang A, Sankaran B, Johnson MP, Phadkule A, Reppert M, Ekiert D, Bhabha G, Stewart L, Caram JR, Stoddard BL, Romero E, Hunter CN, Baker D. De novo design of proteins housing excitonically coupled chlorophyll special pairs. Nat Chem Biol 2024; 20:906-915. [PMID: 38831036 PMCID: PMC11213709 DOI: 10.1038/s41589-024-01626-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 04/15/2024] [Indexed: 06/05/2024]
Abstract
Natural photosystems couple light harvesting to charge separation using a 'special pair' of chlorophyll molecules that accepts excitation energy from the antenna and initiates an electron-transfer cascade. To investigate the photophysics of special pairs independently of the complexities of native photosynthetic proteins, and as a first step toward creating synthetic photosystems for new energy conversion technologies, we designed C2-symmetric proteins that hold two chlorophyll molecules in closely juxtaposed arrangements. X-ray crystallography confirmed that one designed protein binds two chlorophylls in the same orientation as native special pairs, whereas a second designed protein positions them in a previously unseen geometry. Spectroscopy revealed that the chlorophylls are excitonically coupled, and fluorescence lifetime imaging demonstrated energy transfer. The cryo-electron microscopy structure of a designed 24-chlorophyll octahedral nanocage with a special pair on each edge closely matched the design model. The results suggest that the de novo design of artificial photosynthetic systems is within reach of current computational methods.
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Affiliation(s)
- Nathan M Ennist
- Institute for Protein Design, University of Washington, Seattle, WA, USA.
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
| | - Shunzhi Wang
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Madison A Kennedy
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Mariano Curti
- Institute of Chemical Research of Catalonia (ICIQ-CERCA), Barcelona Institute of Science and Technology (BIST), Tarragona, Spain
| | | | | | - Rachel L Redler
- Department of Cell Biology and Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY, USA
| | - Valentin Maffeis
- Institute of Chemical Research of Catalonia (ICIQ-CERCA), Barcelona Institute of Science and Technology (BIST), Tarragona, Spain
| | - Saeed Shareef
- Institute of Chemical Research of Catalonia (ICIQ-CERCA), Barcelona Institute of Science and Technology (BIST), Tarragona, Spain
- Departament de Química Física i Inorgànica, Universitat Rovira i Virgili, Tarragona, Spain
| | - Anthony V Sica
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Ash Sueh Hua
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Arundhati P Deshmukh
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Adam P Moyer
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Derrick R Hicks
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Avi Z Swartz
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Ralph A Cacho
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Nathan Novy
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Asim K Bera
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Alex Kang
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Banumathi Sankaran
- Molecular Biophysics and Integrated Bioimaging, Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - Amala Phadkule
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | - Mike Reppert
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | - Damian Ekiert
- Department of Cell Biology and Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY, USA
- Department of Microbiology, New York University School of Medicine, New York, NY, USA
| | - Gira Bhabha
- Department of Cell Biology and Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY, USA
| | - Lance Stewart
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Justin R Caram
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Barry L Stoddard
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Elisabet Romero
- Institute of Chemical Research of Catalonia (ICIQ-CERCA), Barcelona Institute of Science and Technology (BIST), Tarragona, Spain
| | - C Neil Hunter
- School of Biosciences, University of Sheffield, Sheffield, UK
| | - David Baker
- Institute for Protein Design, University of Washington, Seattle, WA, USA.
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
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Kukimoto-Niino M, Katsura K, Ishizuka-Katsura Y, Mishima-Tsumagari C, Yonemochi M, Inoue M, Nakagawa R, Kaushik R, Zhang KYJ, Shirouzu M. RhoG facilitates a conformational transition in the guanine nucleotide exchange factor complex DOCK5/ELMO1 to an open state. J Biol Chem 2024; 300:107459. [PMID: 38857861 PMCID: PMC11267001 DOI: 10.1016/j.jbc.2024.107459] [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: 12/28/2023] [Revised: 05/19/2024] [Accepted: 06/03/2024] [Indexed: 06/12/2024] Open
Abstract
The dedicator of cytokinesis (DOCK)/engulfment and cell motility (ELMO) complex serves as a guanine nucleotide exchange factor (GEF) for the GTPase Rac. RhoG, another GTPase, activates the ELMO-DOCK-Rac pathway during engulfment and migration. Recent cryo-EM structures of the DOCK2/ELMO1 and DOCK2/ELMO1/Rac1 complexes have identified closed and open conformations that are key to understanding the autoinhibition mechanism. Nevertheless, the structural details of RhoG-mediated activation of the DOCK/ELMO complex remain elusive. Herein, we present cryo-EM structures of DOCK5/ELMO1 alone and in complex with RhoG and Rac1. The DOCK5/ELMO1 structure exhibits a closed conformation similar to that of DOCK2/ELMO1, suggesting a shared regulatory mechanism of the autoinhibitory state across DOCK-A/B subfamilies (DOCK1-5). Conversely, the RhoG/DOCK5/ELMO1/Rac1 complex adopts an open conformation that differs from that of the DOCK2/ELMO1/Rac1 complex, with RhoG binding to both ELMO1 and DOCK5. The alignment of the DOCK5 phosphatidylinositol (3,4,5)-trisphosphate binding site with the RhoG C-terminal lipidation site suggests simultaneous binding of RhoG and DOCK5/ELMO1 to the plasma membrane. Structural comparison of the apo and RhoG-bound states revealed that RhoG facilitates a closed-to-open state conformational change of DOCK5/ELMO1. Biochemical and surface plasmon resonance (SPR) assays confirm that RhoG enhances the Rac GEF activity of DOCK5/ELMO1 and increases its binding affinity for Rac1. Further analysis of structural variability underscored the conformational flexibility of the DOCK5/ELMO1/Rac1 complex core, potentially facilitating the proximity of the DOCK5 GEF domain to the plasma membrane. These findings elucidate the structural mechanism underlying the RhoG-induced allosteric activation and membrane binding of the DOCK/ELMO complex.
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Affiliation(s)
- Mutsuko Kukimoto-Niino
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, Kanagawa, Japan.
| | - Kazushige Katsura
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, Kanagawa, Japan
| | - Yoshiko Ishizuka-Katsura
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, Kanagawa, Japan
| | - Chiemi Mishima-Tsumagari
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, Kanagawa, Japan
| | - Mayumi Yonemochi
- Drug Discovery Structural Biology Platform Unit, RIKEN Center for Biosystems Dynamics Research, Yokohama, Kanagawa, Japan
| | - Mio Inoue
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, Kanagawa, Japan
| | - Reiko Nakagawa
- Laboratory for Cell-Free Protein Synthesis, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, Japan
| | - Rahul Kaushik
- Laboratory for Structural Bioinformatics, RIKEN Center for Biosystems Dynamics Research, Yokohama, Kanagawa, Japan
| | - Kam Y J Zhang
- Laboratory for Structural Bioinformatics, RIKEN Center for Biosystems Dynamics Research, Yokohama, Kanagawa, Japan
| | - Mikako Shirouzu
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, Yokohama, Kanagawa, Japan; Drug Discovery Structural Biology Platform Unit, RIKEN Center for Biosystems Dynamics Research, Yokohama, Kanagawa, Japan.
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39
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Tenjo-Castaño F, Sofos N, Stutzke LS, Temperini P, Fuglsang A, Pape T, Mesa P, Montoya G. Conformational landscape of the type V-K CRISPR-associated transposon integration assembly. Mol Cell 2024; 84:2353-2367.e5. [PMID: 38834066 DOI: 10.1016/j.molcel.2024.05.005] [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: 12/08/2023] [Revised: 03/11/2024] [Accepted: 05/07/2024] [Indexed: 06/06/2024]
Abstract
CRISPR-associated transposons (CASTs) are mobile genetic elements that co-opt CRISPR-Cas systems for RNA-guided DNA transposition. CASTs integrate large DNA cargos into the attachment (att) site independently of homology-directed repair and thus hold promise for eukaryotic genome engineering. However, the functional diversity and complexity of CASTs hinder an understanding of their mechanisms. Here, we present the high-resolution cryoelectron microscopy (cryo-EM) structure of the reconstituted ∼1 MDa post-transposition complex of the type V-K CAST, together with different assembly intermediates and diverse TnsC filament lengths, thus enabling the recapitulation of the integration complex formation. The results of mutagenesis experiments probing the roles of specific residues and TnsB-binding sites show that transposition activity can be enhanced and suggest that the distance between the PAM and att sites is determined by the lengths of the TnsB C terminus and the TnsC filament. This singular model of RNA-guided transposition provides a foundation for repurposing the system for genome-editing applications.
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Affiliation(s)
- Francisco Tenjo-Castaño
- Structural Molecular Biology Group, Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Nicholas Sofos
- Structural Molecular Biology Group, Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Luisa S Stutzke
- Structural Molecular Biology Group, Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Piero Temperini
- Structural Molecular Biology Group, Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Anders Fuglsang
- Structural Molecular Biology Group, Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Tillmann Pape
- Structural Molecular Biology Group, Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark; Core Facility for Integrated Microscopy (CFIM), Faculty of Health and Medical Sciences University of Copenhagen; Blegdamsvej 3B, DK-2200 Copenhagen, Denmark
| | - Pablo Mesa
- Structural Molecular Biology Group, Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Guillermo Montoya
- Structural Molecular Biology Group, Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark.
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40
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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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41
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Lin HH, Wang CH, Huang SH, Lin SY, Kato T, Namba K, Hosogi N, Song C, Murata K, Yen CH, Hsu TL, Wong CH, Wu YM, Tu IP, Chang WH. Use of phase plate cryo-EM reveals conformation diversity of therapeutic IgG with 50 kDa Fab fragment resolved below 6 Å. Sci Rep 2024; 14:14079. [PMID: 38890341 PMCID: PMC11189423 DOI: 10.1038/s41598-024-62045-8] [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: 06/28/2023] [Accepted: 05/13/2024] [Indexed: 06/20/2024] Open
Abstract
While cryogenic electron microscopy (cryo-EM) is fruitfully used for harvesting high-resolution structures of sizable macromolecules, its application to small or flexible proteins composed of small domains like immunoglobulin (IgG) remain challenging. Here, we applied single particle cryo-EM to Rituximab, a therapeutic IgG mediating anti-tumor toxicity, to explore its solution conformations. We found Rituximab molecules exhibited aggregates in cryo-EM specimens contrary to its solution behavior, and utilized a non-ionic detergent to successfully disperse them as isolated particles amenable to single particle analysis. As the detergent adversely reduced the protein-to-solvent contrast, we employed phase plate contrast to mitigate the impaired protein visibility. Assisted by phase plate imaging, we obtained a canonical three-arm IgG structure with other structures displaying variable arm densities co-existing in solution, affirming high flexibility of arm-connecting linkers. Furthermore, we showed phase plate imaging enables reliable structure determination of Fab to sub-nanometer resolution from ab initio, yielding a characteristic two-lobe structure that could be unambiguously docked with crystal structure. Our findings revealed conformation diversity of IgG and demonstrated phase plate was viable for cryo-EM analysis of small proteins without symmetry. This work helps extend cryo-EM boundaries, providing a valuable imaging and structural analysis framework for macromolecules with similar challenging features.
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Affiliation(s)
- Hsin-Hung Lin
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
- Institute of Statistical Science, Academia Sinica, Taipei, Taiwan
| | - Chun-Hsiung Wang
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
- Academia Sinica Cryo-EM Facility, Academia Sinica, Taipei, Taiwan
| | - Shih-Hsin Huang
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
- Institute of Preventive Medicine, National Defense Medical Center, New Taipei City, Taiwan
| | - Sung-Yao Lin
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
| | - Takayuki Kato
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka, Japan
- Institute of Protein Research, Osaka University, Suita, Osaka, Japan
| | - Keiichi Namba
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka, Japan
| | - Naoki Hosogi
- JEOL Ltd., 1-2 Musashino 3-chome, Akishima, Tokyo, Japan
| | - Chihong Song
- Exploratory Research Center on Life and Living Systems (ExCELLS) and National Institute for Physiological Sciences (NIPS), National Institutes of Natural Sciences, 38 Nishigonaka Myodaiji, Okazaki, Aichi, Japan
| | - Kazuyoshi Murata
- Exploratory Research Center on Life and Living Systems (ExCELLS) and National Institute for Physiological Sciences (NIPS), National Institutes of Natural Sciences, 38 Nishigonaka Myodaiji, Okazaki, Aichi, Japan
| | | | - Tsui-Ling Hsu
- Genomic Research Center, Academia Sinica, Taipei, Taiwan
| | - Chi-Huey Wong
- Genomic Research Center, Academia Sinica, Taipei, Taiwan
| | - Yi-Min Wu
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
- Cryo-EM Facility, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - I-Ping Tu
- Institute of Statistical Science, Academia Sinica, Taipei, Taiwan
| | - Wei-Hau Chang
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan.
- Genomic Research Center, Academia Sinica, Taipei, Taiwan.
- Institute of Physics, Academia Sinica, Taipei, Taiwan.
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42
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Grba DN, Wright JJ, Yin Z, Fisher W, Hirst J. Molecular mechanism of the ischemia-induced regulatory switch in mammalian complex I. Science 2024; 384:1247-1253. [PMID: 38870289 DOI: 10.1126/science.ado2075] [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: 01/22/2024] [Accepted: 05/01/2024] [Indexed: 06/15/2024]
Abstract
Respiratory complex I is an efficient driver for oxidative phosphorylation in mammalian mitochondria, but its uncontrolled catalysis under challenging conditions leads to oxidative stress and cellular damage. Ischemic conditions switch complex I from rapid, reversible catalysis into a dormant state that protects upon reoxygenation, but the molecular basis for the switch is unknown. We combined precise biochemical definition of complex I catalysis with high-resolution cryo-electron microscopy structures in the phospholipid bilayer of coupled vesicles to reveal the mechanism of the transition into the dormant state, modulated by membrane interactions. By implementing a versatile membrane system to unite structure and function, attributing catalytic and regulatory properties to specific structural states, we define how a conformational switch in complex I controls its physiological roles.
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Affiliation(s)
| | | | | | | | - Judy Hirst
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge CB2 0XY, UK
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43
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Wang F, He Q, Yao NY, O'Donnell ME, Li H. The human ATAD5 has evolved unique structural elements to function exclusively as a PCNA unloader. Nat Struct Mol Biol 2024:10.1038/s41594-024-01332-4. [PMID: 38871854 DOI: 10.1038/s41594-024-01332-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 05/13/2024] [Indexed: 06/15/2024]
Abstract
Humans have three different proliferating cell nuclear antigen (PCNA) clamp-loading complexes: RFC and CTF18-RFC load PCNA onto DNA, but ATAD5-RFC can only unload PCNA from DNA. The underlying structural basis of ATAD5-RFC unloading is unknown. We show here that ATAD5 has two unique locking loops that appear to tie the complex into a rigid structure, and together with a domain that plugs the DNA-binding chamber, prevent conformation changes required for DNA binding, likely explaining why ATAD5-RFC is exclusively a PCNA unloader. These features are conserved in the yeast PCNA unloader Elg1-RFC. We observe intermediates in which PCNA bound to ATAD5-RFC exists as a closed planar ring, a cracked spiral or a gapped spiral. Surprisingly, ATAD5-RFC can open a PCNA gap between PCNA protomers 2 and 3, different from the PCNA protomers 1 and 3 gap observed in all previously characterized clamp loaders.
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Affiliation(s)
- Feng Wang
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA
| | - Qing He
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA
| | - Nina Y Yao
- DNA Replication Laboratory and Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA
| | - Michael E O'Donnell
- DNA Replication Laboratory and Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA.
| | - Huilin Li
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA.
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44
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Arkinson C, Dong KC, Gee CL, Costello SM, Marqusee S, Martin A. Nub1 traps unfolded FAT10 for ubiquitin-independent degradation by the 26S proteasome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.12.598715. [PMID: 38915702 PMCID: PMC11195292 DOI: 10.1101/2024.06.12.598715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
The ubiquitin-like modifier FAT10 targets hundreds of proteins in the mammalian immune system to the 26S proteasome for degradation. This degradation pathway requires the cofactor Nub1, yet the underlying mechanisms remain unknown. Here, we reconstituted a minimal in vitro system and revealed that Nub1 utilizes FAT10's intrinsic instability to trap its N-terminal ubiquitin-like domain in an unfolded state and deliver it to the 26S proteasome for engagement, allowing the degradation of FAT10-ylated substrates in a ubiquitin- and p97-independent manner. Through hydrogen-deuterium exchange, structural modeling, and site-directed mutagenesis, we identified the formation of a peculiar complex with FAT10 that activates Nub1 for docking to the 26S proteasome, and our cryo-EM studies visualized the highly dynamic Nub1 complex bound to the proteasomal Rpn1 subunit during FAT10 delivery and the early stages of ATP-dependent degradation. These studies thus identified a novel mode of cofactor-mediated, ubiquitin-independent substrate delivery to the 26S proteasome that relies on trapping partially unfolded states for engagement by the proteasomal ATPase motor.
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Affiliation(s)
- Connor Arkinson
- California Institute for Quantitative Biosciences, University of California at Berkeley, Berkeley, CA94720, USA
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA94720, USA
- Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA94720, USA
| | - Ken C. Dong
- Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA94720, USA
| | - Christine L. Gee
- California Institute for Quantitative Biosciences, University of California at Berkeley, Berkeley, CA94720, USA
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA94720, USA
- Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA94720, USA
| | - Shawn M. Costello
- Biophysics Graduate Program, University of California, Berkeley, CA, USA
| | - Susan Marqusee
- California Institute for Quantitative Biosciences, University of California at Berkeley, Berkeley, CA94720, USA
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA94720, USA
- Department of Chemistry, University of California, Berkeley, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Andreas Martin
- California Institute for Quantitative Biosciences, University of California at Berkeley, Berkeley, CA94720, USA
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA94720, USA
- Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA94720, USA
- Lead contact
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45
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Anderson TK, Hoferle PJ, Chojnacki KJ, Lee K, Coon J, Kirchdoerfer R. An alphacoronavirus polymerase structure reveals conserved replication factor functions. Nucleic Acids Res 2024; 52:5975-5986. [PMID: 38442273 PMCID: PMC11162792 DOI: 10.1093/nar/gkae153] [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: 08/23/2023] [Revised: 01/18/2024] [Accepted: 02/19/2024] [Indexed: 03/07/2024] Open
Abstract
Coronaviruses are a diverse subfamily of viruses containing pathogens of humans and animals. This subfamily of viruses replicates their RNA genomes using a core polymerase complex composed of viral non-structural proteins: nsp7, nsp8 and nsp12. Most of our understanding of coronavirus molecular biology comes from betacoronaviruses like SARS-CoV and SARS-CoV-2, the latter of which is the causative agent of COVID-19. In contrast, members of the alphacoronavirus genus are relatively understudied despite their importance in human and animal health. Here we have used cryo-electron microscopy to determine structures of the alphacoronavirus porcine epidemic diarrhea virus (PEDV) core polymerase complex bound to RNA. One structure shows an unexpected nsp8 stoichiometry despite remaining bound to RNA. Biochemical analysis shows that the N-terminal extension of one nsp8 is not required for in vitro RNA synthesis for alpha- and betacoronaviruses. Our work demonstrates the importance of studying diverse coronaviruses in revealing aspects of coronavirus replication and identifying areas of conservation to be targeted by antiviral drugs.
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Affiliation(s)
- Thomas K Anderson
- Biochemistry Department, University of Wisconsin-Madison, Madison, WI 53706, USA
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI 53706, USA
- Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Peter J Hoferle
- Biochemistry Department, University of Wisconsin-Madison, Madison, WI 53706, USA
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI 53706, USA
- Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Kennan J Chojnacki
- Biochemistry Department, University of Wisconsin-Madison, Madison, WI 53706, USA
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI 53706, USA
- Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Kenneth W Lee
- Biomolecular Chemistry Department, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Joshua J Coon
- Biomolecular Chemistry Department, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53715, USA
- Morgridge Institute for Research, Madison, WI 53715, USA
| | - Robert N Kirchdoerfer
- Biochemistry Department, University of Wisconsin-Madison, Madison, WI 53706, USA
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI 53706, USA
- Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, WI 53706, USA
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Niedzialkowska E, Runyan LA, Kudryashova E, Egelman EH, Kudryashov DS. Stabilization of F-actin by Salmonella effector SipA resembles the structural effects of inorganic phosphate and phalloidin. Structure 2024; 32:725-738.e8. [PMID: 38518780 PMCID: PMC11162321 DOI: 10.1016/j.str.2024.02.022] [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: 01/02/2024] [Revised: 02/08/2024] [Accepted: 02/26/2024] [Indexed: 03/24/2024]
Abstract
Entry of Salmonella into host enterocytes relies on its pathogenicity island 1 effector SipA. We found that SipA binds to F-actin in a 1:2 stoichiometry with sub-nanomolar affinity. A cryo-EM reconstruction revealed that SipA's globular core binds at the groove between actin strands, whereas the extended C-terminal arm penetrates deeply into the inter-strand space, stabilizing F-actin from within. The unusually strong binding of SipA is achieved by a combination of fast association via the core and very slow dissociation dictated by the arm. Similar to Pi, BeF3, and phalloidin, SipA potently inhibited actin depolymerization by actin depolymerizing factor (ADF)/cofilin, which correlated with increased filament stiffness, supporting the hypothesis that F-actin's mechanical properties contribute to the recognition of its nucleotide state by protein partners. The remarkably strong binding to F-actin maximizes the toxin's effects at the injection site while minimizing global influence on the cytoskeleton and preventing pathogen detection by the host cell.
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Affiliation(s)
- Ewa Niedzialkowska
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22903, USA
| | - Lucas A Runyan
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Elena Kudryashova
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Edward H Egelman
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22903, USA.
| | - Dmitri S Kudryashov
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA.
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47
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Liao Z, Gopalasingam CC, Kameya M, Gerle C, Shigematsu H, Ishii M, Arakawa T, Fushinobu S. Structural insights into thermophilic chaperonin complexes. Structure 2024; 32:679-689.e4. [PMID: 38492570 DOI: 10.1016/j.str.2024.02.012] [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: 11/02/2023] [Revised: 02/07/2024] [Accepted: 02/20/2024] [Indexed: 03/18/2024]
Abstract
Group I chaperonins are dual heptamer protein complexes that play significant roles in protein homeostasis. The structure and function of the Escherichia coli chaperonin are well characterized. However, the dynamic properties of chaperonins, such as large ATPase-dependent conformational changes by binding of lid-like co-chaperonin GroES, have made structural analyses challenging, and our understanding of these changes during the turnover of chaperonin complex formation is limited. In this study, we used single-particle cryogenic electron microscopy to investigate the structures of GroES-bound chaperonin complexes from the thermophilic hydrogen-oxidizing bacteria Hydrogenophilus thermoluteolus and Hydrogenobacter thermophilus in the presence of ATP and AMP-PNP. We captured the structure of an intermediate state chaperonin complex, designated as an asymmetric football-shaped complex, and performed analyses to decipher the dynamic structural variations. Our structural analyses of inter- and intra-subunit communications revealed a unique mechanism of complex formation through the binding of a second GroES to a bullet-shaped complex.
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Affiliation(s)
- Zengwei Liao
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo City, Tokyo 113-8654, Japan
| | - Chai C Gopalasingam
- Life Science Research Infrastructure Group, RIKEN SPring-8 Center, Kouto, Sayo, Hyogo 1-1-1, Japan
| | - Masafumi Kameya
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo City, Tokyo 113-8654, Japan; Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo City, Tokyo 113-8654, Japan
| | - Christoph Gerle
- Life Science Research Infrastructure Group, RIKEN SPring-8 Center, Kouto, Sayo, Hyogo 1-1-1, Japan
| | - Hideki Shigematsu
- Structural Biology Division, Japan Synchrotron Radiation Research Institute, SPring-8, Sayo, Hyogo, Japan
| | - Masaharu Ishii
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo City, Tokyo 113-8654, Japan; Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo City, Tokyo 113-8654, Japan
| | - Takatoshi Arakawa
- Faculty of Pharmaceutical Sciences, Tokyo University of Science, Noda, Chiba 278-8510, Japan.
| | - Shinya Fushinobu
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo City, Tokyo 113-8654, Japan; Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo City, Tokyo 113-8654, Japan.
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48
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Lin TY, Chung SC. CLEAPA: a framework for exploring the conformational landscape of cryo-EM using energy-aware pathfinding algorithm. Bioinformatics 2024; 40:btae345. [PMID: 38837333 PMCID: PMC11167209 DOI: 10.1093/bioinformatics/btae345] [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: 01/15/2024] [Revised: 04/02/2024] [Accepted: 05/27/2024] [Indexed: 06/07/2024] Open
Abstract
MOTIVATION Cryo-electron microscopy (cryo-EM) is a powerful technique for studying macromolecules and holds the potential for identifying kinetically preferred transition sequences between conformational states. Typically, these sequences are explored within two-dimensional energy landscapes. However, due to the complexity of biomolecules, representing conformational changes in two dimensions can be challenging. Recent advancements in reconstruction models have successfully extracted structural heterogeneity from cryo-EM images using higher-dimension latent space. Nonetheless, creating high-dimensional conformational landscapes in the latent space and then searching for preferred paths continues to be a formidable task. RESULTS This study introduces an innovative framework for identifying preferred trajectories within high-dimensional conformational landscapes. Our method encompasses the search for the minimum energy path in the graph, where edge weights are determined based on the energy estimation at each node using local density. The effectiveness of this approach is demonstrated by identifying accurate transition states in both synthetic and real-world datasets featuring continuous conformational changes. AVAILABILITY AND IMPLEMENTATION The CLEAPA package is available at https://github.com/tengyulin/energy_aware_pathfinding/.
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Affiliation(s)
- Teng-Yu Lin
- Department of Applied Mathematics, National Sun Yat-sen University, Kaohsiung 804, Taiwan
| | - Szu-Chi Chung
- Department of Applied Mathematics, National Sun Yat-sen University, Kaohsiung 804, Taiwan
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49
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Cao S, Shi H, Garcia SF, Kito Y, Shi H, Goldberg HV, Ponce J, Ueberheide B, Lignitto L, Pagano M, Zheng N. Distinct Perception Mechanisms of BACH1 Quaternary Structure Degrons by Two F-box Proteins under Oxidative Stress. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.03.594717. [PMID: 38895309 PMCID: PMC11185555 DOI: 10.1101/2024.06.03.594717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
The transcription factor BACH1 regulates heme homeostasis and oxidative stress responses and promotes cancer metastasis upon aberrant accumulation. Its stability is controlled by two F-box protein ubiquitin ligases, FBXO22 and FBXL17. Here we show that the homodimeric BTB domain of BACH1 functions as a previously undescribed quaternary structure degron, which is deciphered by the two F-box proteins via distinct mechanisms. After BACH1 is released from chromatin by heme, FBXO22 asymmetrically recognizes a cross-protomer interface of the intact BACH1 BTB dimer, which is otherwise masked by the co-repressor NCOR1. If the BACH1 BTB dimer escapes the surveillance by FBXO22 due to oxidative modifications, its quaternary structure integrity is probed by a pair of FBXL17, which simultaneously engage and remodel the two BTB protomers into E3-bound monomers for ubiquitination. By unveiling the multifaceted regulatory mechanisms of BACH1 stability, our studies highlight the abilities of ubiquitin ligases to decode high-order protein assemblies and reveal therapeutic opportunities to block cancer invasion via compound-induced BACH1 destabilization.
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Affiliation(s)
- Shiyun Cao
- Department of Pharmacology, Box 357280, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Huigang Shi
- Department of Pharmacology, Box 357280, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Sheena Faye Garcia
- Department of Biochemistry and Molecular Pharmacology
- Laura and Isaac Perlmutter Cancer Center, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Yuki Kito
- Department of Biochemistry and Molecular Pharmacology
- Laura and Isaac Perlmutter Cancer Center, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Hui Shi
- Department of Pharmacology, Box 357280, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Hailey V. Goldberg
- Department of Biochemistry and Molecular Pharmacology
- Laura and Isaac Perlmutter Cancer Center, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Jackeline Ponce
- Department of Biochemistry and Molecular Pharmacology
- Laura and Isaac Perlmutter Cancer Center, New York University Grossman School of Medicine, New York, NY 10016, USA
- Proteomics Laboratory, Division of Advanced Research Technologies, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Beatrix Ueberheide
- Department of Biochemistry and Molecular Pharmacology
- Laura and Isaac Perlmutter Cancer Center, New York University Grossman School of Medicine, New York, NY 10016, USA
- Proteomics Laboratory, Division of Advanced Research Technologies, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Luca Lignitto
- Department of Biochemistry and Molecular Pharmacology
- Laura and Isaac Perlmutter Cancer Center, New York University Grossman School of Medicine, New York, NY 10016, USA
- Cancer Research Center of Marseille (CRCM), CNRS, Aix Marseille Univ, INSERM, Institut Paoli-Calmettes, Marseille, France
| | - Michele Pagano
- Department of Biochemistry and Molecular Pharmacology
- Laura and Isaac Perlmutter Cancer Center, New York University Grossman School of Medicine, New York, NY 10016, USA
- Howard Hughes Medical Institute, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Ning Zheng
- Department of Pharmacology, Box 357280, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
- Lead contact
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50
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Shi B, Zhang K, Fleet DJ, McLeod RA, Dwayne Miller RJ, Howe JY. Deep generative priors for biomolecular 3D heterogeneous reconstruction from cryo-EM projections. J Struct Biol 2024; 216:108073. [PMID: 38432598 DOI: 10.1016/j.jsb.2024.108073] [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: 11/08/2023] [Revised: 02/25/2024] [Accepted: 02/25/2024] [Indexed: 03/05/2024]
Abstract
Cryo-electron microscopy has become a powerful tool to determine three-dimensional (3D) structures of rigid biological macromolecules from noisy micrographs with single-particle reconstruction. Recently, deep neural networks, e.g., CryoDRGN, have demonstrated conformational and compositional heterogeneity of complexes. However, the lack of ground-truth conformations poses a challenge to assess the performance of heterogeneity analysis methods. In this work, variational autoencoders (VAE) with three types of deep generative priors were learned for latent variable inference and heterogeneous 3D reconstruction via Bayesian inference. More specifically, VAEs with "Variational Mixture of Posteriors" priors (VampPrior-SPR), non-parametric exemplar-based priors (ExemplarPrior-SPR) and priors from latent score-based generative models (LSGM-SPR) were quantitatively compared with CryoDRGN. We built four simulated datasets composed of hypothetical continuous conformation or discrete states of the hERG K + channel. Empirical and quantitative comparisons of inferred latent representations were performed with affine-transformation-based metrics. These models with more informative priors gave better regularized, interpretable factorized latent representations with better conserved pairwise distances, less deformed latent distributions and lower within-cluster variances. They were also tested on experimental datasets to resolve compositional and conformational heterogeneity (50S ribosome assembly, cowpea chlorotic mottle virus, and pre-catalytic spliceosome) with comparable high resolution. Codes and data are available: https://github.com/benjamin3344/DGP-SPR.
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Affiliation(s)
- Bin Shi
- Department of Materials Science and Engineering, University of Toronto, ON M5S 3H5, Canada
| | - Kevin Zhang
- Department of Materials Science and Engineering, University of Toronto, ON M5S 3H5, Canada
| | - David J Fleet
- Department of Computer Science, University of Toronto, ON M5S 3H5, Canada
| | - Robert A McLeod
- Hitachi High-Technologies Canada, Inc. Based out of Victoria, BC, Canada, British Columbia, Canada
| | - R J Dwayne Miller
- Departments of Chemistry and Physics, University of Toronto, ON M5S 3H6, Canada.
| | - Jane Y Howe
- Department of Materials Science and Engineering, University of Toronto, ON M5S 3H5, Canada; Department of Chemical Engineering and Applied Chemistry, University of Toronto, ON M5S 3E5, Canada
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