101
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Fortea E, Lee S, Chadda R, Argyros Y, Sandal P, Mahoney-Kruszka R, Ciftci HD, Falzone ME, Huysmans G, Robertson JL, Boudker O, Accardi A. Structural basis of pH-dependent activation in a CLC transporter. Nat Struct Mol Biol 2024; 31:644-656. [PMID: 38279055 DOI: 10.1038/s41594-023-01210-5] [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: 08/16/2023] [Accepted: 12/22/2023] [Indexed: 01/28/2024]
Abstract
CLCs are dimeric chloride channels and anion/proton exchangers that regulate processes such as muscle contraction and endo-lysosome acidification. Common gating controls their activity; its closure simultaneously silences both protomers, and its opening allows them to independently transport ions. Mutations affecting common gating in human CLCs cause dominant genetic disorders. The structural rearrangements underlying common gating are unknown. Here, using single-particle cryo-electron microscopy, we show that the prototypical Escherichia coli CLC-ec1 undergoes large-scale rearrangements in activating conditions. The slow, pH-dependent remodeling of the dimer interface leads to the concerted opening of the intracellular H+ pathways and is required for transport. The more frequent formation of short water wires in the open H+ pathway enables Cl- pore openings. Mutations at disease-causing sites favor CLC-ec1 activation and accelerate common gate opening in the human CLC-7 exchanger. We suggest that the pH activation mechanism of CLC-ec1 is related to the common gating of CLC-7.
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Affiliation(s)
- Eva Fortea
- Department of Physiology and Biophysics, Weill Cornell Medical School, New York, NY, USA
- Department of Anesthesiology, Weill Cornell Medical School, New York, NY, USA
| | - Sangyun Lee
- Department of Anesthesiology, Weill Cornell Medical School, New York, NY, USA
| | - Rahul Chadda
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
| | - Yiorgos Argyros
- Department of Anesthesiology, Weill Cornell Medical School, New York, NY, USA
- Department of Biochemistry, Weill Cornell Medical School, New York, NY, USA
| | - Priyanka Sandal
- Department of Molecular Physiology and Biophysics, The University of Iowa, Iowa City, IA, USA
| | - Robyn Mahoney-Kruszka
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
| | - Hatice Didar Ciftci
- Department of Physiology and Biophysics, Weill Cornell Medical School, New York, NY, USA
- Tri-Institutional Training Program in Chemical Biology, New York, NY, USA
| | - Maria E Falzone
- Department of Anesthesiology, Weill Cornell Medical School, New York, NY, USA
- Department of Biochemistry, Weill Cornell Medical School, New York, NY, USA
| | - Gerard Huysmans
- Department of Physiology and Biophysics, Weill Cornell Medical School, New York, NY, USA
- Erasmus University, Jette, Belgium
| | - Janice L Robertson
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
| | - Olga Boudker
- Department of Physiology and Biophysics, Weill Cornell Medical School, New York, NY, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
| | - Alessio Accardi
- Department of Physiology and Biophysics, Weill Cornell Medical School, New York, NY, USA.
- Department of Anesthesiology, Weill Cornell Medical School, New York, NY, USA.
- Department of Biochemistry, Weill Cornell Medical School, New York, NY, USA.
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102
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Bloch Y, Felix J, Merceron R, Provost M, Symakani RA, De Backer R, Lambert E, Mehdipour AR, Savvides SN. Structures of complete extracellular receptor assemblies mediated by IL-12 and IL-23. Nat Struct Mol Biol 2024; 31:591-597. [PMID: 38287195 DOI: 10.1038/s41594-023-01190-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 11/22/2023] [Indexed: 01/31/2024]
Abstract
Cell-surface receptor complexes mediated by pro-inflammatory interleukin (IL)-12 and IL-23, both validated therapeutic targets, are incompletely understood due to the lack of structural insights into their complete extracellular assemblies. Furthermore, there is a paucity of structural details describing the IL-12-receptor interaction interfaces, in contrast to IL-23-receptor complexes. Here we report structures of fully assembled mouse IL-12/human IL-23-receptor complexes comprising the complete extracellular segments of the cognate receptors determined by electron cryo-microscopy. The structures reveal key commonalities but also surprisingly diverse features. Most notably, whereas IL-12 and IL-23 both utilize a conspicuously presented aromatic residue on their α-subunit as a hotspot to interact with the N-terminal Ig domain of their high-affinity receptors, only IL-12 juxtaposes receptor domains proximal to the cell membrane. Collectively, our findings will help to complete our understanding of cytokine-mediated assemblies of tall cytokine receptors and will enable a cytokine-specific interrogation of IL-12/IL-23 signaling in physiology and disease.
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Affiliation(s)
- Yehudi Bloch
- Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
- Unit for Structural Biology, VIB-UGent Center for Inflammation Research, Ghent, Belgium
- European Molecular Biology Laboratory, Hamburg Unit c/o DESY, Hamburg, Germany
| | - Jan Felix
- Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium.
- Unit for Structural Biology, VIB-UGent Center for Inflammation Research, Ghent, Belgium.
| | - Romain Merceron
- Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
- Unit for Structural Biology, VIB-UGent Center for Inflammation Research, Ghent, Belgium
- Eurofins DiscoverX Products France, Celle-Lévescault, France
| | - Mathias Provost
- Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
- Unit for Structural Biology, VIB-UGent Center for Inflammation Research, Ghent, Belgium
- Argenx, Ghent, Belgium
| | - Royan Alipour Symakani
- Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
- Unit for Structural Biology, VIB-UGent Center for Inflammation Research, Ghent, Belgium
- VIB Center for Medical Biotechnology, Ghent, Belgium
| | - Robin De Backer
- Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
- Unit for Structural Biology, VIB-UGent Center for Inflammation Research, Ghent, Belgium
| | - Elisabeth Lambert
- Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
- Unit for Structural Biology, VIB-UGent Center for Inflammation Research, Ghent, Belgium
- Solvias, Basel, Switzerland
| | | | - Savvas N Savvides
- Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium.
- Unit for Structural Biology, VIB-UGent Center for Inflammation Research, Ghent, Belgium.
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103
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Kahne SC, Yoo JH, Chen J, Nakedi K, Iyer LM, Putzel G, Samhadaneh NM, Pironti A, Aravind L, Ekiert DC, Bhabha G, Rhee KY, Darwin KH. Identification of a proteolysis regulator for an essential enzyme in Mycobacterium tuberculosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.29.587195. [PMID: 38585835 PMCID: PMC10996600 DOI: 10.1101/2024.03.29.587195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
In Mycobacterium tuberculosis proteins that are post-translationally modified with Pup, a prokaryotic ubiquitin-like protein, can be degraded by proteasomes. While pupylation is reversible, mechanisms regulating substrate specificity have not been identified. Here, we identify the first depupylation regulators: CoaX, a pseudokinase, and pantothenate, an essential, central metabolite. In a Δ coaX mutant, pantothenate synthesis enzymes were more abundant, including PanB, a substrate of the Pup-proteasome system. Media supplementation with pantothenate decreased PanB levels in a coaX and Pup-proteasome-dependent manner. In vitro , CoaX accelerated depupylation of Pup∼PanB, while addition of pantothenate inhibited this reaction. Collectively, we propose CoaX contributes to proteasomal degradation of PanB by modulating depupylation of Pup∼PanB in response to pantothenate levels. One Sentence Summary A pseudo-pantothenate kinase regulates proteasomal degradation of a pantothenate synthesis enzyme in M. tuberculosis .
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104
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Zhou D, Supasa P, Liu C, Dijokaite-Guraliuc A, Duyvesteyn HME, Selvaraj M, Mentzer AJ, Das R, Dejnirattisai W, Temperton N, Klenerman P, Dunachie SJ, Fry EE, Mongkolsapaya J, Ren J, Stuart DI, Screaton GR. The SARS-CoV-2 neutralizing antibody response to SD1 and its evasion by BA.2.86. Nat Commun 2024; 15:2734. [PMID: 38548763 PMCID: PMC10978878 DOI: 10.1038/s41467-024-46982-6] [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: 12/22/2023] [Accepted: 03/15/2024] [Indexed: 04/01/2024] Open
Abstract
Under pressure from neutralising antibodies induced by vaccination or infection the SARS-CoV-2 spike gene has become a hotspot for evolutionary change, leading to the failure of all mAbs developed for clinical use. Most potent antibodies bind to the receptor binding domain which has become heavily mutated. Here we study responses to a conserved epitope in sub-domain-1 (SD1) of spike which have become more prominent because of mutational escape from antibodies directed to the receptor binding domain. Some SD1 reactive mAbs show potent and broad neutralization of SARS-CoV-2 variants. We structurally map the dominant SD1 epitope and provide a mechanism of action by blocking interaction with ACE2. Mutations in SD1 have not been sustained to date, but one, E554K, leads to escape from mAbs. This mutation has now emerged in several sublineages including BA.2.86, reflecting selection pressure on the virus exerted by the increasing prominence of the anti-SD1 response.
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Affiliation(s)
- Daming Zhou
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, Centre for Human Genetics, Oxford, UK
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Piyada Supasa
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
- Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Chang Liu
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
- Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Helen M E Duyvesteyn
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, Centre for Human Genetics, Oxford, UK
| | - Muneeswaran Selvaraj
- Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Alexander J Mentzer
- Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Raksha Das
- Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Wanwisa Dejnirattisai
- Division of Emerging Infectious Disease, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok-Noi, Bangkok, 10700, Thailand
| | - Nigel Temperton
- Viral Pseudotype Unit, Medway School of Pharmacy, University of Kent and Greenwich Chatham Maritime, Kent, ME4 4TB, UK
| | - Paul Klenerman
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Susanna J Dunachie
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
- NDM Centre For Global Health Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand
| | - Elizabeth E Fry
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, Centre for Human Genetics, Oxford, UK.
| | - Juthathip Mongkolsapaya
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK.
- Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
- Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand.
| | - Jingshan Ren
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, Centre for Human Genetics, Oxford, UK.
| | - David I Stuart
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK.
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, Centre for Human Genetics, Oxford, UK.
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK.
| | - Gavin R Screaton
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK.
- Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
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105
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Zhou M, Gamage ST, Tran KA, Bartee D, Wei X, Yin B, Berger S, Meier JL, Marmorstein R. Molecular Basis for RNA Cytidine Acetylation by NAT10. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.27.587050. [PMID: 38585770 PMCID: PMC10996708 DOI: 10.1101/2024.03.27.587050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Human NAT10 acetylates the N4 position of cytidine in RNA, predominantly on rRNA and tRNA, to facilitate ribosome biogenesis and protein translation. NAT10 has been proposed as a therapeutic target in cancers as well as aging-associated pathologies such as Hutchinson-Gilford Progeria Syndrome (HGPS). The ∼120 kDa NAT10 protein uses its acetyl-CoA-dependent acetyltransferase, ATP-dependent helicase, and RNA binding domains in concert to mediate RNA-specific N4-cytidine acetylation. While the biochemical activity of NAT10 is well known, the molecular basis for catalysis of eukaryotic RNA acetylation remains relatively undefined. To provide molecular insights into the RNA-specific acetylation by NAT10, we determined the single particle cryo-EM structures of Chaetomium thermophilum NAT10 ( Ct NAT10) bound to a bisubstrate cytidine-CoA probe with and without ADP. The structures reveal that NAT10 forms a symmetrical heart-shaped dimer with conserved functional domains surrounding the acetyltransferase active sites harboring the cytidine-CoA probe. Structure-based mutagenesis with analysis of mutants in vitro supports the catalytic role of two conserved active site residues (His548 and Tyr549 in Ct NAT10), and two basic patches, both proximal and distal to the active site for RNA-specific acetylation. Yeast complementation analyses and senescence assays in human cells also implicates NAT10 catalytic activity in yeast thermoadaptation and cellular senescence. Comparison of the NAT10 structure to protein lysine and N-terminal acetyltransferase enzymes reveals an unusually open active site suggesting that these enzymes have been evolutionarily tailored for RNA recognition and cytidine-specific acetylation.
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106
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Abstract
The vesicular monoamine transporter 2 (VMAT2) is a proton-dependent antiporter responsible for loading monoamine neurotransmitters into synaptic vesicles. Dysregulation of VMAT2 can lead to several neuropsychiatric disorders including Parkinson's disease and schizophrenia. Furthermore, drugs such as amphetamine and MDMA are known to act on VMAT2, exemplifying its role in the mechanisms of actions for drugs of abuse. Despite VMAT2's importance, there remains a critical lack of mechanistic understanding, largely driven by a lack of structural information. Here, we report a 3.1 Å resolution cryo-electron microscopy (cryo-EM) structure of VMAT2 complexed with tetrabenazine (TBZ), a non-competitive inhibitor used in the treatment of Huntington's chorea. We find TBZ interacts with residues in a central binding site, locking VMAT2 in an occluded conformation and providing a mechanistic basis for non-competitive inhibition. We further identify residues critical for cytosolic and lumenal gating, including a cluster of hydrophobic residues which are involved in a lumenal gating strategy. Our structure also highlights three distinct polar networks that may determine VMAT2 conformational dynamics and play a role in proton transduction. The structure elucidates mechanisms of VMAT2 inhibition and transport, providing insights into VMAT2 architecture, function, and the design of small-molecule therapeutics.
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Affiliation(s)
- Michael P Dalton
- Department of Structural Biology, University of PittsburghPittsburghUnited States
| | - Mary Hongying Cheng
- Laufer Center for Physical and Quantitative Biology, and Department of Biochemistry and Cell Biology, School of Medicine, Stony Brook UniversityStony BrookUnited States
| | - Ivet Bahar
- Laufer Center for Physical and Quantitative Biology, and Department of Biochemistry and Cell Biology, School of Medicine, Stony Brook UniversityStony BrookUnited States
| | - Jonathan A Coleman
- Department of Structural Biology, University of PittsburghPittsburghUnited States
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107
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Driggers CM, Kuo YY, Zhu P, ElSheikh A, Shyng SL. Structure of an open K ATP channel reveals tandem PIP 2 binding sites mediating the Kir6.2 and SUR1 regulatory interface. Nat Commun 2024; 15:2502. [PMID: 38509107 PMCID: PMC10954709 DOI: 10.1038/s41467-024-46751-5] [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: 01/18/2024] [Accepted: 03/08/2024] [Indexed: 03/22/2024] Open
Abstract
ATP-sensitive potassium (KATP) channels, composed of four pore-lining Kir6.2 subunits and four regulatory sulfonylurea receptor 1 (SUR1) subunits, control insulin secretion in pancreatic β-cells. KATP channel opening is stimulated by PIP2 and inhibited by ATP. Mutations that increase channel opening by PIP2 reduce ATP inhibition and cause neonatal diabetes. Although considerable evidence has implicated a role for PIP2 in KATP channel function, previously solved open-channel structures have lacked bound PIP2, and mechanisms by which PIP2 regulates KATP channels remain unresolved. Here, we report the cryoEM structure of a KATP channel harboring the neonatal diabetes mutation Kir6.2-Q52R, in the open conformation, bound to amphipathic molecules consistent with natural C18:0/C20:4 long-chain PI(4,5)P2 at two adjacent binding sites between SUR1 and Kir6.2. The canonical PIP2 binding site is conserved among PIP2-gated Kir channels. The non-canonical PIP2 binding site forms at the interface of Kir6.2 and SUR1. Functional studies demonstrate both binding sites determine channel activity. Kir6.2 pore opening is associated with a twist of the Kir6.2 cytoplasmic domain and a rotation of the N-terminal transmembrane domain of SUR1, which widens the inhibitory ATP binding pocket to disfavor ATP binding. The open conformation is particularly stabilized by the Kir6.2-Q52R residue through cation-π bonding with SUR1-W51. Together, these results uncover the cooperation between SUR1 and Kir6.2 in PIP2 binding and gating, explain the antagonistic regulation of KATP channels by PIP2 and ATP, and provide a putative mechanism by which Kir6.2-Q52R stabilizes an open channel to cause neonatal diabetes.
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Affiliation(s)
- Camden M Driggers
- Department of Chemical Physiology and Biochemistry, School of Medicine, Oregon Health & Science University, Portland, OR, 97239, USA.
| | - Yi-Ying Kuo
- Department of Chemical Physiology and Biochemistry, School of Medicine, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Phillip Zhu
- Department of Chemical Physiology and Biochemistry, School of Medicine, Oregon Health & Science University, Portland, OR, 97239, USA
| | - Assmaa ElSheikh
- Department of Chemical Physiology and Biochemistry, School of Medicine, Oregon Health & Science University, Portland, OR, 97239, USA
- Department of Medical Biochemistry, Tanta University, Tanta, Egypt
| | - Show-Ling Shyng
- Department of Chemical Physiology and Biochemistry, School of Medicine, Oregon Health & Science University, Portland, OR, 97239, USA.
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108
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Watanabe S, Kise Y, Yonezawa K, Inoue M, Shimizu N, Nureki O, Inaba K. Structure of full-length ERGIC-53 in complex with MCFD2 for cargo transport. Nat Commun 2024; 15:2404. [PMID: 38493152 PMCID: PMC10944485 DOI: 10.1038/s41467-024-46747-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 03/07/2024] [Indexed: 03/18/2024] Open
Abstract
ERGIC-53 transports certain subsets of newly synthesized secretory proteins and membrane proteins from the endoplasmic reticulum to the Golgi apparatus. Despite numerous structural and functional studies since its identification, the overall architecture and mechanism of action of ERGIC-53 remain unclear. Here we present cryo-EM structures of full-length ERGIC-53 in complex with its functional partner MCFD2. These structures reveal that ERGIC-53 exists as a homotetramer, not a homohexamer as previously suggested, and comprises a four-leaf clover-like head and a long stalk composed of three sets of four-helix coiled-coil followed by a transmembrane domain. 3D variability analysis visualizes the flexible motion of the long stalk and local plasticity of the head region. Notably, MCFD2 is shown to possess a Zn2+-binding site in its N-terminal lid, which appears to modulate cargo binding. Altogether, distinct mechanisms of cargo capture and release by ERGIC- 53 via the stalk bending and metal binding are proposed.
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Affiliation(s)
- Satoshi Watanabe
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, Miyagi, 980-8577, Japan.
- Department of Molecular and Chemical Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, 980-8577, Japan.
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, Miyagi, 980-8578, Japan.
| | - Yoshiaki Kise
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Kento Yonezawa
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki, 305-0801, Japan
- Center for Digital Green-innovation, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
| | - Mariko Inoue
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, Miyagi, 980-8577, Japan
| | - Nobutaka Shimizu
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki, 305-0801, Japan
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Kenji Inaba
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, Miyagi, 980-8577, Japan.
- Department of Molecular and Chemical Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, 980-8577, Japan.
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, Miyagi, 980-8578, Japan.
- Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan.
- Core Research for Evolutional Science and Technology (CREST), Japan Agency for Medical Research and Development (AMED), Tokyo, Japan.
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109
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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. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.13.584744. [PMID: 38559232 PMCID: PMC10979975 DOI: 10.1101/2024.03.13.584744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
During formation of the transcription-competent open complex (RPo) by bacterial RNA polymerases (RNAP), transient intermediates pile up before overcoming a rate-limiting step. Structural descriptions of these interconversions in real time are unavailable. To address this gap, time-resolved cryo-electron microscopy (cryo-EM) was used to capture four intermediates populated 120 or 500 milliseconds (ms) after mixing Escherichia coli σ70-RNAP and the λPR promoter. Cryo-EM snapshots revealed 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 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 yet unknown conformational changes load it in subsequent steps. Because these events likely describe DNA opening at many bacterial promoters, this study provides needed 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 10065 USA
| | - Andreas U. Mueller
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065 USA
| | - Brandon Malone
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065 USA
| | - James Chen
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065 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
| | - 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 10065 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
| | - 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
| | - Seth A. Darst
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY 10065 USA
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110
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Nishio S, Emori C, Wiseman B, Fahrenkamp D, Dioguardi E, Zamora-Caballero S, Bokhove M, Han L, Stsiapanava A, Algarra B, Lu Y, Kodani M, Bainbridge RE, Komondor KM, Carlson AE, Landreh M, de Sanctis D, Yasumasu S, Ikawa M, Jovine L. ZP2 cleavage blocks polyspermy by modulating the architecture of the egg coat. Cell 2024; 187:1440-1459.e24. [PMID: 38490181 DOI: 10.1016/j.cell.2024.02.013] [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: 05/29/2023] [Revised: 11/07/2023] [Accepted: 02/09/2024] [Indexed: 03/17/2024]
Abstract
Following the fertilization of an egg by a single sperm, the egg coat or zona pellucida (ZP) hardens and polyspermy is irreversibly blocked. These events are associated with the cleavage of the N-terminal region (NTR) of glycoprotein ZP2, a major subunit of ZP filaments. ZP2 processing is thought to inactivate sperm binding to the ZP, but its molecular consequences and connection with ZP hardening are unknown. Biochemical and structural studies show that cleavage of ZP2 triggers its oligomerization. Moreover, the structure of a native vertebrate egg coat filament, combined with AlphaFold predictions of human ZP polymers, reveals that two protofilaments consisting of type I (ZP3) and type II (ZP1/ZP2/ZP4) components interlock into a left-handed double helix from which the NTRs of type II subunits protrude. Together, these data suggest that oligomerization of cleaved ZP2 NTRs extensively cross-links ZP filaments, rigidifying the egg coat and making it physically impenetrable to sperm.
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Affiliation(s)
- Shunsuke Nishio
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Chihiro Emori
- Department of Experimental Genome Research, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan; Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan
| | - Benjamin Wiseman
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Dirk Fahrenkamp
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Elisa Dioguardi
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | | | - Marcel Bokhove
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Ling Han
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Alena Stsiapanava
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Blanca Algarra
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Yonggang Lu
- Department of Experimental Genome Research, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan; Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan
| | - Mayo Kodani
- Department of Experimental Genome Research, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan; Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan
| | - Rachel E Bainbridge
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Kayla M Komondor
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Anne E Carlson
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Michael Landreh
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden; Department of Cell and Molecular Biology, Uppsala University, 75124 Uppsala, Sweden
| | | | - Shigeki Yasumasu
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, Tokyo, Japan
| | - Masahito Ikawa
- Department of Experimental Genome Research, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan; Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan; Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan; Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Osaka, Japan
| | - Luca Jovine
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden.
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111
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Roisné-Hamelin F, Liu HW, Taschner M, Li Y, Gruber S. Structural basis for plasmid restriction by SMC JET nuclease. Mol Cell 2024; 84:883-896.e7. [PMID: 38309275 DOI: 10.1016/j.molcel.2024.01.009] [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: 10/03/2023] [Revised: 12/06/2023] [Accepted: 01/09/2024] [Indexed: 02/05/2024]
Abstract
DNA loop-extruding SMC complexes play crucial roles in chromosome folding and DNA immunity. Prokaryotic SMC Wadjet (JET) complexes limit the spread of plasmids through DNA cleavage, yet the mechanisms for plasmid recognition are unresolved. We show that artificial DNA circularization renders linear DNA susceptible to JET nuclease cleavage. Unlike free DNA, JET cleaves immobilized plasmid DNA at a specific site, the plasmid-anchoring point, showing that the anchor hinders DNA extrusion but not DNA cleavage. Structures of plasmid-bound JetABC reveal two presumably stalled SMC motor units that are drastically rearranged from the resting state, together entrapping a U-shaped DNA segment, which is further converted to kinked V-shaped cleavage substrate by JetD nuclease binding. Our findings uncover mechanical bending of residual unextruded DNA as molecular signature for plasmid recognition and non-self DNA elimination. We moreover elucidate key elements of SMC loop extrusion, including the motor direction and the structure of a DNA-holding state.
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Affiliation(s)
- Florian Roisné-Hamelin
- Department of Fundamental Microbiology (DMF), Faculty of Biology and Medicine (FBM), University of Lausanne (UNIL), 1015 Lausanne, Switzerland
| | - Hon Wing Liu
- Department of Fundamental Microbiology (DMF), Faculty of Biology and Medicine (FBM), University of Lausanne (UNIL), 1015 Lausanne, Switzerland
| | - Michael Taschner
- Department of Fundamental Microbiology (DMF), Faculty of Biology and Medicine (FBM), University of Lausanne (UNIL), 1015 Lausanne, Switzerland
| | - Yan Li
- Department of Fundamental Microbiology (DMF), Faculty of Biology and Medicine (FBM), University of Lausanne (UNIL), 1015 Lausanne, Switzerland
| | - Stephan Gruber
- Department of Fundamental Microbiology (DMF), Faculty of Biology and Medicine (FBM), University of Lausanne (UNIL), 1015 Lausanne, Switzerland.
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112
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Gardner S, Jin Y, Fyfe PK, Voisin TB, Bellón JS, Pohler E, Piehler J, Moraga I, Bubeck D. Structural insights into IL-11-mediated signalling and human IL6ST variant-associated immunodeficiency. Nat Commun 2024; 15:2071. [PMID: 38453915 PMCID: PMC10920896 DOI: 10.1038/s41467-024-46235-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 02/16/2024] [Indexed: 03/09/2024] Open
Abstract
IL-11 and IL-6 activate signalling via assembly of the cell surface receptor gp130; however, it is unclear how signals are transmitted across the membrane to instruct cellular responses. Here we solve the cryoEM structure of the IL-11 receptor recognition complex to discover how differences in gp130-binding interfaces may drive signalling outcomes. We explore how mutations in the IL6ST gene encoding for gp130, which cause severe immune deficiencies in humans, impair signalling without blocking cytokine binding. We use cryoEM to solve structures of both IL-11 and IL-6 complexes with a mutant form of gp130 associated with human disease. Together with molecular dynamics simulations, we show that the disease-associated variant led to an increase in flexibility including motion within the cytokine-binding core and increased distance between extracellular domains. However, these distances are minimized as the transmembrane helix exits the membrane, suggesting a stringency in geometry for signalling and dimmer switch mode of action.
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Affiliation(s)
- Scott Gardner
- Department of Life Sciences, Sir Ernst Chain Building, Imperial College London, London, SW7 2AZ, UK
| | - Yibo Jin
- Department of Life Sciences, Sir Ernst Chain Building, Imperial College London, London, SW7 2AZ, UK
| | - Paul K Fyfe
- Division of Cell Signalling and Immunology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Tomas B Voisin
- Department of Life Sciences, Sir Ernst Chain Building, Imperial College London, London, SW7 2AZ, UK
| | - Junel Sotolongo Bellón
- Department of Biology/Chemistry and Centre for Cellular Nanoanalytics, Osnabrück University, Osnabrück, Germany
| | - Elizabeth Pohler
- Division of Cell Signalling and Immunology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Jacob Piehler
- Department of Biology/Chemistry and Centre for Cellular Nanoanalytics, Osnabrück University, Osnabrück, Germany
| | - Ignacio Moraga
- Division of Cell Signalling and Immunology, School of Life Sciences, University of Dundee, Dundee, UK.
| | - Doryen Bubeck
- Department of Life Sciences, Sir Ernst Chain Building, Imperial College London, London, SW7 2AZ, UK.
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113
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Mazza T, Roumeliotis TI, Garitta E, Drew D, Rashid ST, Indiveri C, Choudhary JS, Linton KJ, Beis K. Structural basis for the modulation of MRP2 activity by phosphorylation and drugs. Nat Commun 2024; 15:1983. [PMID: 38438394 PMCID: PMC10912322 DOI: 10.1038/s41467-024-46392-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 02/26/2024] [Indexed: 03/06/2024] Open
Abstract
Multidrug resistance-associated protein 2 (MRP2/ABCC2) is a polyspecific efflux transporter of organic anions expressed in hepatocyte canalicular membranes. MRP2 dysfunction, in Dubin-Johnson syndrome or by off-target inhibition, for example by the uricosuric drug probenecid, elevates circulating bilirubin glucuronide and is a cause of jaundice. Here, we determine the cryo-EM structure of rat Mrp2 (rMrp2) in an autoinhibited state and in complex with probenecid. The autoinhibited state exhibits an unusual conformation for this class of transporter in which the regulatory domain is folded within the transmembrane domain cavity. In vitro phosphorylation, mass spectrometry and transport assays show that phosphorylation of the regulatory domain relieves this autoinhibition and enhances rMrp2 transport activity. The in vitro data is confirmed in human hepatocyte-like cells, in which inhibition of endogenous kinases also reduces human MRP2 transport activity. The drug-bound state reveals two probenecid binding sites that suggest a dynamic interplay with autoinhibition. Mapping of the Dubin-Johnson mutations onto the rodent structure indicates that many may interfere with the transition between conformational states.
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Affiliation(s)
- Tiziano Mazza
- Department of Life Sciences, Imperial College London, SW7 2AZ, London, UK
- Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot, Oxfordshire, OX11 0FA, UK
- Department DiBEST (Biologia, Ecologia, Scienze Della Terra) Unit of Biochemistry and Molecular Biotechnology, University of Calabria, 87036, Arcavacata di Rende, Italy
| | - Theodoros I Roumeliotis
- Functional Proteomics group, Chester Beatty Laboratories, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Elena Garitta
- Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, E1 2A, London, UK
| | - David Drew
- Department of Biochemistry and Biophysics, Stockholm University, 10691, Stockholm, Sweden
| | - S Tamir Rashid
- Department of Metabolism, Digestion & Reproduction, Imperial College London, W12 0NN, London, UK
| | - Cesare Indiveri
- Department DiBEST (Biologia, Ecologia, Scienze Della Terra) Unit of Biochemistry and Molecular Biotechnology, University of Calabria, 87036, Arcavacata di Rende, Italy
- CNR Institute of Biomembranes, Bioenergetics and Molecular Biotechnology (IBIOM), 70126, Bari, Italy
| | - Jyoti S Choudhary
- Functional Proteomics group, Chester Beatty Laboratories, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Kenneth J Linton
- Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, E1 2A, London, UK
| | - Konstantinos Beis
- Department of Life Sciences, Imperial College London, SW7 2AZ, London, UK.
- Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot, Oxfordshire, OX11 0FA, UK.
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114
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Majumdar S, Chiu YT, Pickett JE, Roth BL. Illuminating the understudied GPCR-ome. Drug Discov Today 2024; 29:103848. [PMID: 38052317 DOI: 10.1016/j.drudis.2023.103848] [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: 10/03/2023] [Revised: 11/17/2023] [Accepted: 11/28/2023] [Indexed: 12/07/2023]
Abstract
G-protein-coupled receptors (GPCRs) are the target of >30% of approved drugs. Despite their popularity, many of the >800 human GPCRs remain understudied. The Illuminating the Druggable Genome (IDG) project has generated many tools leading to important insights into the function and druggability of these so-called 'dark' receptors. These tools include assays, such as PRESTO-TANGO and TRUPATH, billions of small molecules made available via the ZINC virtual library, solved orphan GPCR structures, GPCR knock-in mice, and more. Together, these tools are illuminating the remaining 'dark' GPCRs.
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Affiliation(s)
- Sreeparna Majumdar
- Department of Pharmacology, UNC Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Yi-Ting Chiu
- Department of Pharmacology, UNC Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Julie E Pickett
- Department of Pharmacology, UNC Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Bryan L Roth
- Department of Pharmacology, UNC Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA.
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115
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Sakuragi T, Kanai R, Otani M, Kikkawa M, Toyoshima C, Nagata S. The role of the C-terminal tail region as a plug to regulate XKR8 lipid scramblase. J Biol Chem 2024; 300:105755. [PMID: 38364890 PMCID: PMC10938166 DOI: 10.1016/j.jbc.2024.105755] [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: 12/19/2023] [Revised: 01/27/2024] [Accepted: 02/10/2024] [Indexed: 02/18/2024] Open
Abstract
XK-related 8 (XKR8), in complex with the transmembrane glycoprotein basigin, functions as a phospholipid scramblase activated by the caspase-mediated cleavage or phosphorylation of its C-terminal tail. It carries a putative phospholipid translocation path of multiple hydrophobic and charged residues in the transmembrane region. It also has a crucial tryptophan at the exoplasmic end of the path that regulates its scrambling activity. We herein investigated the tertiary structure of the human XKR8-basigin complex embedded in lipid nanodiscs at an overall resolution of 3.66 Å. We found that the C-terminal tail engaged in intricate polar and van der Waals interactions with a groove at the cytoplasmic surface of XKR8. These interactions maintained the inactive state of XKR8. Point mutations to disrupt these interactions strongly enhanced the scrambling activity of XKR8, suggesting that the activation of XKR8 is mediated by releasing the C-terminal tail from the cytoplasmic groove. We speculate that the cytoplasmic tail region of XKR8 functions as a plug to prevent the scrambling of phospholipids.
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Affiliation(s)
- Takaharu Sakuragi
- Laboratory of Biochemistry and Immunology, World Premier International Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan
| | - Ryuta Kanai
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
| | - Mayumi Otani
- Laboratory of Biochemistry and Immunology, World Premier International Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan
| | - Masahide Kikkawa
- Department of Cell Biology and Anatomy, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Chikashi Toyoshima
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
| | - Shigekazu Nagata
- Laboratory of Biochemistry and Immunology, World Premier International Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan.
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116
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Dai Z, Liang L, Wang W, Zuo P, Yu S, Liu Y, Zhao X, Lu Y, Jin Y, Zhang F, Ding D, Deng W, Yin Y. Structural insights into the ubiquitylation strategy of the oligomeric CRL2 FEM1B E3 ubiquitin ligase. EMBO J 2024; 43:1089-1109. [PMID: 38360992 PMCID: PMC10943247 DOI: 10.1038/s44318-024-00047-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 01/26/2024] [Accepted: 01/29/2024] [Indexed: 02/17/2024] Open
Abstract
Cullin-RING E3 ubiquitin ligase (CRL) family members play critical roles in numerous biological processes and diseases including cancer and Alzheimer's disease. Oligomerization of CRLs has been reported to be crucial for the regulation of their activities. However, the structural basis for its regulation and mechanism of its oligomerization are not fully known. Here, we present cryo-EM structures of oligomeric CRL2FEM1B in its unneddylated state, neddylated state in complex with BEX2 as well as neddylated state in complex with FNIP1/FLCN. These structures reveal that asymmetric dimerization of N8-CRL2FEM1B is critical for the ubiquitylation of BEX2 while FNIP1/FLCN is ubiquitylated by monomeric CRL2FEM1B. Our data present an example of the asymmetric homo-dimerization of CRL. Taken together, this study sheds light on the ubiquitylation strategy of oligomeric CRL2FEM1B according to substrates with different scales.
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Affiliation(s)
- Zonglin Dai
- Institute of Systems Biomedicine, Beijing Key Laboratory of Tumor Systems Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
- Department of Pathology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Ling Liang
- Institute of Systems Biomedicine, Beijing Key Laboratory of Tumor Systems Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
- Department of Biophysics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Weize Wang
- Institute of Systems Biomedicine, Beijing Key Laboratory of Tumor Systems Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Peng Zuo
- Institute of Systems Biomedicine, Beijing Key Laboratory of Tumor Systems Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
- Department of Pathology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Shang Yu
- Department of Biophysics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Yaqi Liu
- Department of Physiology and Cellular Biophysics, Clyde and Helen Wu Center for Molecular Cardiology, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, 10032, USA
| | - Xuyang Zhao
- Institute of Systems Biomedicine, Beijing Key Laboratory of Tumor Systems Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Yishuo Lu
- Institute of Systems Biomedicine, Beijing Key Laboratory of Tumor Systems Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Yan Jin
- Institute of Systems Biomedicine, Beijing Key Laboratory of Tumor Systems Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Fangting Zhang
- Institute of Precision Medicine, Peking University Shenzhen Hospital, Shenzhen, 518036, China
| | - Dian Ding
- Institute of Systems Biomedicine, Beijing Key Laboratory of Tumor Systems Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Weiwei Deng
- Department of Mechanics and Aerospace Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Yuxin Yin
- Institute of Systems Biomedicine, Beijing Key Laboratory of Tumor Systems Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China.
- Department of Pathology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China.
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China.
- Institute of Precision Medicine, Peking University Shenzhen Hospital, Shenzhen, 518036, China.
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Yang A, Liu S, Zhang Y, Chen J, Fan Y, Wang F, Zou Y, Feng S, Wu J, Hu Q. Regulation of RAS palmitoyltransferases by accessory proteins and palmitoylation. Nat Struct Mol Biol 2024; 31:436-446. [PMID: 38182928 DOI: 10.1038/s41594-023-01183-5] [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: 03/02/2023] [Accepted: 11/17/2023] [Indexed: 01/07/2024]
Abstract
Palmitoylation of cysteine residues at the C-terminal hypervariable regions in human HRAS and NRAS, which is necessary for RAS signaling, is catalyzed by the acyltransferase DHHC9 in complex with its accessory protein GCP16. The molecular basis for the acyltransferase activity and the regulation of DHHC9 by GCP16 is not clear. Here we report the cryo-electron microscopy structures of the human DHHC9-GCP16 complex and its yeast counterpart-the Erf2-Erf4 complex, demonstrating that GCP16 and Erf4 are not directly involved in the catalytic process but stabilize the architecture of DHHC9 and Erf2, respectively. We found that a phospholipid binding to an arginine-rich region of DHHC9 and palmitoylation on three residues (C24, C25 and C288) were essential for the catalytic activity of the DHHC9-GCP16 complex. Moreover, we showed that GCP16 also formed complexes with DHHC14 and DHHC18 to catalyze RAS palmitoylation. These findings provide insights into the regulatory mechanism of RAS palmitoyltransferases.
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Affiliation(s)
- Anlan Yang
- College of Life Sciences, Zhejiang University, Hangzhou, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
| | - Shengjie Liu
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
- Fudan University, Shanghai, China
| | - Yuqi Zhang
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
| | - Jia Chen
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
- Mass Spectrometry & Metabolomics Core Facility, Westlake University, Hangzhou, China
| | - Yujing Fan
- Westlake Four-Dimensional Dynamic Metabolomics (Meta4D) Laboratory, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
| | - Fengxiang Wang
- Westlake Four-Dimensional Dynamic Metabolomics (Meta4D) Laboratory, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
- School of Life Sciences, Westlake University, Hangzhou, China
| | - Yilong Zou
- Westlake Four-Dimensional Dynamic Metabolomics (Meta4D) Laboratory, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
- School of Life Sciences, Westlake University, Hangzhou, China
| | - Shan Feng
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
- Mass Spectrometry & Metabolomics Core Facility, Westlake University, Hangzhou, China
| | - Jianping Wu
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China.
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China.
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China.
| | - Qi Hu
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China.
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China.
- Westlake AI Therapeutics Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China.
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118
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Mohammed BM, Basore K, Summers B, Pelc LA, Di Cera E. Structural architecture of the acidic region of the B domain of coagulation factor V. J Thromb Haemost 2024; 22:709-714. [PMID: 38007061 PMCID: PMC10922652 DOI: 10.1016/j.jtha.2023.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 11/03/2023] [Accepted: 11/06/2023] [Indexed: 11/27/2023]
Abstract
BACKGROUND Coagulation factor (F)V features an A1-A2-B-A3-C1-C2 domain organization and functions as the inactive precursor of FVa, a component of the prothrombinase complex required for rapid thrombin generation in the penultimate step of the coagulation cascade. An intramolecular interaction within the large B domain (residues 710-1545) involves the basic region (BR, residues 963-1008) and acidic region (AR, residues 1493-1537) and locks FV in its inactive state. However, structural information on this important regulatory interaction or on the separate architecture of the AR and BR remains elusive due to conformational disorder of the B domain. OBJECTIVES To reveal the structure of the BR-AR interaction or of its separate components. METHODS The structure of FV is solved by cryogenic electron microscopy. RESULTS A new 3.05 Å resolution cryogenic electron microscopy structure of FV confirms the overall organization of the A and C domains but resolves the segment 1507 to 1545 within a largely disordered B domain. The segment contains most of the AR and is organized as recently reported in FV short, a spliced variant of FV with a significantly shorter and less disordered B domain. CONCLUSION The similar architecture of the AR in FV and FV short provides structural context for physiologically important interactions of this region with the BR in FV and with the basic C-terminal end of tissue factor pathway inhibitor α in FV short.
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Affiliation(s)
- Bassem M Mohammed
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri, USA
| | - Katherine Basore
- Washington University Center for Cellular Imaging, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - Brock Summers
- Washington University Center for Cellular Imaging, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - Leslie A Pelc
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri, USA
| | - Enrico Di Cera
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri, USA.
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Tuck OT, Adler BA, Armbruster EG, Lahiri A, Hu JJ, Zhou J, Pogliano J, Doudna JA. Hachiman is a genome integrity sensor. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.29.582594. [PMID: 38464307 PMCID: PMC10925250 DOI: 10.1101/2024.02.29.582594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Hachiman is a broad-spectrum antiphage defense system of unknown function. We show here that Hachiman comprises a heterodimeric nuclease-helicase complex, HamAB. HamA, previously a protein of unknown function, is the effector nuclease. HamB is the sensor helicase. HamB constrains HamA activity during surveillance of intact dsDNA. When the HamAB complex detects DNA damage, HamB helicase activity liberates HamA, unleashing nuclease activity. Hachiman activation degrades all DNA in the cell, creating 'phantom' cells devoid of both phage and host DNA. We demonstrate Hachiman activation in the absence of phage by treatment with DNA-damaging agents, suggesting that Hachiman responds to aberrant DNA states. Phylogenetic similarities between the Hachiman helicase and eukaryotic enzymes suggest this bacterial immune system has been repurposed for diverse functions across all domains of life.
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Affiliation(s)
- Owen T. Tuck
- Department of Chemistry, University of California, Berkeley, Berkeley, CA USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA USA
| | - Benjamin A. Adler
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA USA
| | - Emily G. Armbruster
- School of Biological Sciences, University of California San Diego, La Jolla, CA USA
| | - Arushi Lahiri
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California USA
| | - Jason J. Hu
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California USA
| | - Julia Zhou
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California USA
| | - Joe Pogliano
- School of Biological Sciences, University of California San Diego, La Jolla, CA USA
| | - Jennifer A. Doudna
- Department of Chemistry, University of California, Berkeley, Berkeley, CA USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California USA
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA USA
- MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA USA
- Gladstone Institutes, University of California, San Francisco, San Francisco, CA USA
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA USA
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Burke SM, Avstrikova M, Noviello CM, Mukhtasimova N, Changeux JP, Thakur GA, Sine SM, Cecchini M, Hibbs RE. Structural mechanisms of α7 nicotinic receptor allosteric modulation and activation. Cell 2024; 187:1160-1176.e21. [PMID: 38382524 PMCID: PMC10950261 DOI: 10.1016/j.cell.2024.01.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 12/05/2023] [Accepted: 01/22/2024] [Indexed: 02/23/2024]
Abstract
The α7 nicotinic acetylcholine receptor is a pentameric ligand-gated ion channel that plays an important role in cholinergic signaling throughout the nervous system. Its unique physiological characteristics and implications in neurological disorders and inflammation make it a promising but challenging therapeutic target. Positive allosteric modulators overcome limitations of traditional α7 agonists, but their potentiation mechanisms remain unclear. Here, we present high-resolution structures of α7-modulator complexes, revealing partially overlapping binding sites but varying conformational states. Structure-guided functional and computational tests suggest that differences in modulator activity arise from the stable rotation of a channel gating residue out of the pore. We extend the study using a time-resolved cryoelectron microscopy (cryo-EM) approach to reveal asymmetric state transitions for this homomeric channel and also find that a modulator with allosteric agonist activity exploits a distinct channel-gating mechanism. These results define mechanisms of α7 allosteric modulation and activation with implications across the pentameric receptor superfamily.
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Affiliation(s)
- Sean M Burke
- Molecular Biophysics Graduate Program, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Neurobiology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Mariia Avstrikova
- Institut de Chimie de Strasbourg, UMR7177, CNRS, Université de Strasbourg, 67081 Strasbourg Cedex, France
| | - Colleen M Noviello
- Department of Neurobiology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Nuriya Mukhtasimova
- Receptor Biology Laboratory, Department of Physiology and Biomedical Engineering, Mayo Clinic College of Medicine, Rochester, MN 55902, USA; Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic College of Medicine, Rochester, MN 55902, USA
| | - Jean-Pierre Changeux
- Neuroscience Department, Institut Pasteur, Collège de France, 75015 Paris, France
| | - Ganesh A Thakur
- Department of Pharmaceutical Sciences, Northeastern University, Boston, MA 02115, USA
| | - Steven M Sine
- Receptor Biology Laboratory, Department of Physiology and Biomedical Engineering, Mayo Clinic College of Medicine, Rochester, MN 55902, USA; Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic College of Medicine, Rochester, MN 55902, USA; Department of Neurology, Mayo Clinic College of Medicine, Rochester, MN 55902, USA.
| | - Marco Cecchini
- Institut de Chimie de Strasbourg, UMR7177, CNRS, Université de Strasbourg, 67081 Strasbourg Cedex, France.
| | - Ryan E Hibbs
- Department of Neurobiology, University of California, San Diego, La Jolla, CA 92093, USA; Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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121
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Qi CH, Wang GL, Wang FF, Wang J, Wang XP, Zou MJ, Ma F, Madigan MT, Kimura Y, Wang-Otomo ZY, Yu LJ. Structural insights into the unusual core photocomplex from a triply extremophilic purple bacterium, Halorhodospira halochloris. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024. [PMID: 38411333 DOI: 10.1111/jipb.13628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 01/17/2024] [Accepted: 02/03/2024] [Indexed: 02/28/2024]
Abstract
Halorhodospira (Hlr.) halochloris is a triply extremophilic phototrophic purple sulfur bacterium, as it is thermophilic, alkaliphilic, and extremely halophilic. The light-harvesting-reaction center (LH1-RC) core complex of this bacterium displays an LH1-Qy transition at 1,016 nm, which is the lowest-energy wavelength absorption among all known phototrophs. Here we report the cryo-EM structure of the LH1-RC at 2.42 Å resolution. The LH1 complex forms a tricyclic ring structure composed of 16 αβγ-polypeptides and one αβ-heterodimer around the RC. From the cryo-EM density map, two previously unrecognized integral membrane proteins, referred to as protein G and protein Q, were identified. Both of these proteins are single transmembrane-spanning helices located between the LH1 ring and the RC L-subunit and are absent from the LH1-RC complexes of all other purple bacteria of which the structures have been determined so far. Besides bacteriochlorophyll b molecules (B1020) located on the periplasmic side of the Hlr. halochloris membrane, there are also two arrays of bacteriochlorophyll b molecules (B800 and B820) located on the cytoplasmic side. Only a single copy of a carotenoid (lycopene) was resolved in the Hlr. halochloris LH1-α3β3 and this was positioned within the complex. The potential quinone channel should be the space between the LH1-α3β3 that accommodates the single lycopene but does not contain a γ-polypeptide, B800 and B820. Our results provide a structural explanation for the unusual Qy red shift and carotenoid absorption in the Hlr. halochloris spectrum and reveal new insights into photosynthetic mechanisms employed by a species that thrives under the harshest conditions of any phototrophic microorganism known.
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Affiliation(s)
- Chen-Hui Qi
- Key Laboratory of Photobiology, Photosynthesis Research Center, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Guang-Lei Wang
- Key Laboratory of Photobiology, Photosynthesis Research Center, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fang-Fang Wang
- Zhangjiang Lab, National Facility for Protein Science in Shanghai, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China
| | - Jie Wang
- Key Laboratory of Photobiology, Photosynthesis Research Center, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiang-Ping Wang
- Key Laboratory of Photobiology, Photosynthesis Research Center, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Mei-Juan Zou
- Key Laboratory of Photobiology, Photosynthesis Research Center, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Fei Ma
- Key Laboratory of Photobiology, Photosynthesis Research Center, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Michael T Madigan
- Department of Microbiology, School of Biological Sciences, Southern Illinois University, Carbondale, IL, 62901, USA
| | - Yukihiro Kimura
- Department of Agrobioscience, Graduate School of Agricultural Science, Kobe University, Nada, Kobe, 657-8501, Japan
| | | | - Long-Jiang Yu
- Key Laboratory of Photobiology, Photosynthesis Research Center, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
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122
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Kinsolving J, Bous J, Kozielewicz P, Košenina S, Shekhani R, Grätz L, Masuyer G, Wang Y, Stenmark P, Dong M, Schulte G. Structural and functional insight into the interaction of Clostridioides difficile toxin B and FZD 7. Cell Rep 2024; 43:113727. [PMID: 38308843 DOI: 10.1016/j.celrep.2024.113727] [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: 09/25/2023] [Revised: 01/12/2024] [Accepted: 01/15/2024] [Indexed: 02/05/2024] Open
Abstract
The G protein-coupled receptors of the Frizzled (FZD) family, in particular FZD1,2,7, are receptors that are exploited by Clostridioides difficile toxin B (TcdB), the major virulence factor responsible for pathogenesis associated with Clostridioides difficile infection. We employ a live-cell assay examining the affinity between full-length FZDs and TcdB. Moreover, we present cryoelectron microscopy structures of TcdB alone and in complex with full-length FZD7, which reveal that large structural rearrangements of the combined repetitive polypeptide domain are required for interaction with FZDs and other TcdB receptors, constituting a first step for receptor recognition. Furthermore, we show that bezlotoxumab, an FDA-approved monoclonal antibody to treat Clostridioides difficile infection, favors the apo-TcdB structure and thus disrupts binding with FZD7. The dynamic transition between the two conformations of TcdB also governs the stability of the pore-forming region. Thus, our work provides structural and functional insight into how conformational dynamics of TcdB determine receptor binding.
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Affiliation(s)
- Julia Kinsolving
- Karolinska Institutet, Department Physiology & Pharmacology, Sec. Receptor Biology & Signaling, Biomedicum, 17165 Stockholm, Sweden
| | - Julien Bous
- Karolinska Institutet, Department Physiology & Pharmacology, Sec. Receptor Biology & Signaling, Biomedicum, 17165 Stockholm, Sweden
| | - Pawel Kozielewicz
- Karolinska Institutet, Department Physiology & Pharmacology, Sec. Receptor Biology & Signaling, Biomedicum, 17165 Stockholm, Sweden
| | - Sara Košenina
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Rawan Shekhani
- Karolinska Institutet, Department Physiology & Pharmacology, Sec. Receptor Biology & Signaling, Biomedicum, 17165 Stockholm, Sweden
| | - Lukas Grätz
- Karolinska Institutet, Department Physiology & Pharmacology, Sec. Receptor Biology & Signaling, Biomedicum, 17165 Stockholm, Sweden
| | - Geoffrey Masuyer
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Yuankai Wang
- Department of Urology, Boston Children's Hospital, Department of Surgery and Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Pål Stenmark
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Min Dong
- Department of Urology, Boston Children's Hospital, Department of Surgery and Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Gunnar Schulte
- Karolinska Institutet, Department Physiology & Pharmacology, Sec. Receptor Biology & Signaling, Biomedicum, 17165 Stockholm, Sweden.
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123
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He Z, Wu M, Tian H, Wang L, Hu Y, Han F, Zhou J, Wang Y, Zhou L. Euglena's atypical respiratory chain adapts to the discoidal cristae and flexible metabolism. Nat Commun 2024; 15:1628. [PMID: 38388527 PMCID: PMC10884005 DOI: 10.1038/s41467-024-46018-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 02/09/2024] [Indexed: 02/24/2024] Open
Abstract
Euglena gracilis, a model organism of the eukaryotic supergroup Discoba harbouring also clinically important parasitic species, possesses diverse metabolic strategies and an atypical electron transport chain. While structures of the electron transport chain complexes and supercomplexes of most other eukaryotic clades have been reported, no similar structure is currently available for Discoba, limiting the understandings of its core metabolism and leaving a gap in the evolutionary tree of eukaryotic bioenergetics. Here, we report high-resolution cryo-EM structures of Euglena's respirasome I + III2 + IV and supercomplex III2 + IV2. A previously unreported fatty acid synthesis domain locates on the tip of complex I's peripheral arm, providing a clear picture of its atypical subunit composition identified previously. Individual complexes are re-arranged in the respirasome to adapt to the non-uniform membrane curvature of the discoidal cristae. Furthermore, Euglena's conformationally rigid complex I is deactivated by restricting ubiquinone's access to its substrate tunnel. Our findings provide structural insights for therapeutic developments against euglenozoan parasite infections.
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Affiliation(s)
- Zhaoxiang He
- Department of Biophysics and Department of Critical Care Medicine of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Mengchen Wu
- Department of Biophysics and Department of Critical Care Medicine of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Hongtao Tian
- Department of Biophysics and Department of Critical Care Medicine of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Liangdong Wang
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yiqi Hu
- Department of Biophysics and Department of Critical Care Medicine of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Fangzhu Han
- Department of Biophysics and Department of Critical Care Medicine of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Jiancang Zhou
- Department of Critical Care Medicine, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310016, China.
| | - Yong Wang
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.
- The Provincial International Science and Technology Cooperation Base on Engineering Biology, International Campus of Zhejiang University, Haining, 314400, China.
| | - Long Zhou
- Department of Biophysics and Department of Critical Care Medicine of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.
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124
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Park J, Heo Y, Jeon BW, Jung M, Kim YH, Lee HH, Roh SH. Structure of recombinant formate dehydrogenase from Methylobacterium extorquens (MeFDH1). Sci Rep 2024; 14:3819. [PMID: 38360844 PMCID: PMC10869683 DOI: 10.1038/s41598-024-54205-7] [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: 07/27/2023] [Accepted: 02/09/2024] [Indexed: 02/17/2024] Open
Abstract
Formate dehydrogenase (FDH) is critical for the conversion between formate and carbon dioxide. Despite its importance, the structural complexity of FDH and difficulties in the production of the enzyme have made elucidating its unique physicochemical properties challenging. Here, we purified recombinant Methylobacterium extorquens AM1 FDH (MeFDH1) and used cryo-electron microscopy to determine its structure. We resolved a heterodimeric MeFDH1 structure at a resolution of 2.8 Å, showing a noncanonical active site and a well-embedded Fe-S redox chain relay. In particular, the tungsten bis-molybdopterin guanine dinucleotide active site showed an open configuration with a flexible C-terminal cap domain, suggesting structural and dynamic heterogeneity in the enzyme.
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Affiliation(s)
- Junsun Park
- Department of Biological Sciences, Institute of Molecular Biology and Genetics, Seoul National University, Seoul, 08826, Republic of Korea
| | - Yoonyoung Heo
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Byoung Wook Jeon
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea
| | - Mingyu Jung
- Department of Biological Sciences, Institute of Molecular Biology and Genetics, Seoul National University, Seoul, 08826, Republic of Korea
| | - Yong Hwan Kim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea.
| | - Hyung Ho Lee
- Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul, 08826, Republic of Korea.
| | - Soung-Hun Roh
- Department of Biological Sciences, Institute of Molecular Biology and Genetics, Seoul National University, Seoul, 08826, Republic of Korea.
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125
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Schweke H, Pacesa M, Levin T, Goverde CA, Kumar P, Duhoo Y, Dornfeld LJ, Dubreuil B, Georgeon S, Ovchinnikov S, Woolfson DN, Correia BE, Dey S, Levy ED. An atlas of protein homo-oligomerization across domains of life. Cell 2024; 187:999-1010.e15. [PMID: 38325366 DOI: 10.1016/j.cell.2024.01.022] [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: 06/08/2023] [Revised: 11/03/2023] [Accepted: 01/15/2024] [Indexed: 02/09/2024]
Abstract
Protein structures are essential to understanding cellular processes in molecular detail. While advances in artificial intelligence revealed the tertiary structure of proteins at scale, their quaternary structure remains mostly unknown. We devise a scalable strategy based on AlphaFold2 to predict homo-oligomeric assemblies across four proteomes spanning the tree of life. Our results suggest that approximately 45% of an archaeal proteome and a bacterial proteome and 20% of two eukaryotic proteomes form homomers. Our predictions accurately capture protein homo-oligomerization, recapitulate megadalton complexes, and unveil hundreds of homo-oligomer types, including three confirmed experimentally by structure determination. Integrating these datasets with omics information suggests that a majority of known protein complexes are symmetric. Finally, these datasets provide a structural context for interpreting disease mutations and reveal coiled-coil regions as major enablers of quaternary structure evolution in human. Our strategy is applicable to any organism and provides a comprehensive view of homo-oligomerization in proteomes.
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Affiliation(s)
- Hugo Schweke
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Martin Pacesa
- Laboratory of Protein Design and Immunoengineering, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Tal Levin
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Casper A Goverde
- Laboratory of Protein Design and Immunoengineering, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Prasun Kumar
- School of Chemistry, University of Bristol, Bristol BS8 1TS, UK; School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK; Bristol BioDesign Institute, University of Bristol, Life Sciences Building, Bristol BS8 1TQ, UK; Max Planck-Bristol Centre for Minimal Biology, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
| | - Yoan Duhoo
- Protein Production and Structure Characterization Core Facility (PTPSP), School of Life Sciences, École polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Lars J Dornfeld
- Laboratory of Protein Design and Immunoengineering, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Benjamin Dubreuil
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Sandrine Georgeon
- Laboratory of Protein Design and Immunoengineering, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Sergey Ovchinnikov
- John Harvard Distinguished Science Fellowship Program, Harvard University, Cambridge, MA, USA
| | - Derek N Woolfson
- School of Chemistry, University of Bristol, Bristol BS8 1TS, UK; School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK; Bristol BioDesign Institute, University of Bristol, Life Sciences Building, Bristol BS8 1TQ, UK; Max Planck-Bristol Centre for Minimal Biology, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK.
| | - Bruno E Correia
- Laboratory of Protein Design and Immunoengineering, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland.
| | - Sucharita Dey
- Department of Bioscience and Bioengineering, Indian Institute of Technology Jodhpur, Rajasthan, India.
| | - Emmanuel D Levy
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel.
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126
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Mycroft-West CJ, Abdelkarim S, Duyvesteyn HME, Gandhi NS, Skidmore MA, Owens RJ, Wu L. Structural and mechanistic characterization of bifunctional heparan sulfate N-deacetylase-N-sulfotransferase 1. Nat Commun 2024; 15:1326. [PMID: 38351061 PMCID: PMC10864358 DOI: 10.1038/s41467-024-45419-4] [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: 09/07/2023] [Accepted: 01/22/2024] [Indexed: 02/16/2024] Open
Abstract
Heparan sulfate (HS) polysaccharides are major constituents of the extracellular matrix, which are involved in myriad structural and signaling processes. Mature HS polysaccharides contain complex, non-templated patterns of sulfation and epimerization, which mediate interactions with diverse protein partners. Complex HS modifications form around initial clusters of glucosamine-N-sulfate (GlcNS) on nascent polysaccharide chains, but the mechanistic basis underpinning incorporation of GlcNS itself into HS remains unclear. Here, we determine cryo-electron microscopy structures of human N-deacetylase-N-sulfotransferase (NDST)1, the bifunctional enzyme primarily responsible for initial GlcNS modification of HS. Our structures reveal the architecture of both NDST1 deacetylase and sulfotransferase catalytic domains, alongside a non-catalytic N-terminal domain. The two catalytic domains of NDST1 adopt a distinct back-to-back topology that limits direct cooperativity. Binding analyses, aided by activity-modulating nanobodies, suggest that anchoring of the substrate at the sulfotransferase domain initiates the NDST1 catalytic cycle, providing a plausible mechanism for cooperativity despite spatial domain separation. Our data shed light on key determinants of NDST1 activity, and describe tools to probe NDST1 function in vitro and in vivo.
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Affiliation(s)
| | - Sahar Abdelkarim
- The Rosalind Franklin Institute, Harwell Science & Innovation Campus, OX11 0QX, Didcot, UK
| | - Helen M E Duyvesteyn
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, OX3 7BN, Oxford, UK
| | - Neha S Gandhi
- Department of Computer Science and Engineering, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
- School of Chemistry and Physics, Queensland University of Technology, QLD 4000, Brisbane, Australia
- Centre for Genomics and Personalised Health, Queensland University of Technology, Brisbane, QLD 4059, Australia
| | - Mark A Skidmore
- Centre for Glycoscience Research and Training, Keele University, ST5 5BG, Newcastle-Under-Lyme, UK
| | - Raymond J Owens
- The Rosalind Franklin Institute, Harwell Science & Innovation Campus, OX11 0QX, Didcot, UK
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, OX3 7BN, Oxford, UK
| | - Liang Wu
- The Rosalind Franklin Institute, Harwell Science & Innovation Campus, OX11 0QX, Didcot, UK.
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, The Wellcome Centre for Human Genetics, OX3 7BN, Oxford, UK.
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127
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Rochon K, Bauer BL, Roethler NA, Buckley Y, Su CC, Huang W, Ramachandran R, Stoll MSK, Yu EW, Taylor DJ, Mears JA. Structural basis for regulated assembly of the mitochondrial fission GTPase Drp1. Nat Commun 2024; 15:1328. [PMID: 38351080 PMCID: PMC10864337 DOI: 10.1038/s41467-024-45524-4] [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: 06/15/2023] [Accepted: 01/26/2024] [Indexed: 02/16/2024] Open
Abstract
Mitochondrial fission is a critical cellular event to maintain organelle function. This multistep process is initiated by the enhanced recruitment and oligomerization of dynamin-related protein 1 (Drp1) at the surface of mitochondria. As such, Drp1 is essential for inducing mitochondrial division in mammalian cells, and homologous proteins are found in all eukaryotes. As a member of the dynamin superfamily of proteins (DSPs), controlled Drp1 self-assembly into large helical polymers stimulates its GTPase activity to promote membrane constriction. Still, little is known about the mechanisms that regulate correct spatial and temporal assembly of the fission machinery. Here we present a cryo-EM structure of a full-length Drp1 dimer in an auto-inhibited state. This dimer reveals two key conformational rearrangements that must be unlocked through intramolecular rearrangements to achieve the assembly-competent state observed in previous structures. This structural insight provides understanding into the mechanism for regulated self-assembly of the mitochondrial fission machinery.
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Affiliation(s)
- Kristy Rochon
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Brianna L Bauer
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Nathaniel A Roethler
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Yuli Buckley
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Chih-Chia Su
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Wei Huang
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Rajesh Ramachandran
- Cleveland Center for Membrane and Structural Biology, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
- Department of Physiology and Biophysics, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Maria S K Stoll
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
- Center for Mitochondrial Diseases, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Edward W Yu
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
- Cleveland Center for Membrane and Structural Biology, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Derek J Taylor
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
- Cleveland Center for Membrane and Structural Biology, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Jason A Mears
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA.
- Cleveland Center for Membrane and Structural Biology, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA.
- Center for Mitochondrial Diseases, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA.
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128
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Aplin C, Zielinski KA, Pabit S, Ogunribido D, Katt WP, Pollack L, Cerione RA, Milano SK. Defining the conformational states that enable transglutaminase 2 to promote cancer cell survival versus cell death. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.04.578794. [PMID: 38370687 PMCID: PMC10871292 DOI: 10.1101/2024.02.04.578794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Transglutaminase 2 (TG2) is a GTP-binding/protein-crosslinking enzyme that has been investigated as a therapeutic target for Celiac disease, neurological disorders, and aggressive cancers. TG2 has been suggested to adopt two conformational states that regulate its functions: a GTP-bound, closed conformation, and a calcium-bound, crosslinking-active open conformation. TG2 mutants that constitutively adopt an open conformation are cytotoxic to cancer cells. Thus, small molecules that maintain the open conformation of TG2 could offer a new therapeutic strategy. Here, we investigate TG2, using static and time-resolved small-angle X-ray scattering (SAXS) and single-particle cryoelectron microscopy (cryo-EM), to determine the conformational states responsible for conferring its biological effects. We also describe a newly developed TG2 inhibitor, LM11, that potently kills glioblastoma cells and use SAXS to investigate how LM11 affects the conformational states of TG2. Using SAXS and cryo-EM, we show that guanine nucleotide-bound TG2 adopts a monomeric closed conformation while calcium-bound TG2 assumes an open conformational state that can form higher order oligomers. SAXS analysis also suggests how a TG2 mutant that constitutively adopts the open state binds nucleotides through an alternative mechanism to wildtype TG2. Furthermore, we use time-resolved SAXS to show that LM11 increases the ability of calcium to drive TG2 to an open conformation, which is not reversible by guanine nucleotides and is cytotoxic to cancer cells. Taken together, our findings demonstrate that the conformational dynamics of TG2 are more complex than previously suggested and highlight how conformational stabilization of TG2 by LM11 maintains TG2 in a cytotoxic conformational state.
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Affiliation(s)
- Cody Aplin
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853
| | - Kara A. Zielinski
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853
| | - Suzette Pabit
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853
| | - Deborah Ogunribido
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853
| | - William P. Katt
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853
| | - Lois Pollack
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853
| | - Richard A. Cerione
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853
| | - Shawn K. Milano
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853
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129
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Sarson-Lawrence KTG, Hardy JM, Iaria J, Stockwell D, Behrens K, Saiyed T, Tan C, Jebeli L, Scott NE, Dite TA, Nicola NA, Leis AP, Babon JJ, Kershaw NJ. Cryo-EM structure of the extracellular domain of murine Thrombopoietin Receptor in complex with Thrombopoietin. Nat Commun 2024; 15:1135. [PMID: 38326297 PMCID: PMC10850085 DOI: 10.1038/s41467-024-45356-2] [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: 09/01/2023] [Accepted: 01/19/2024] [Indexed: 02/09/2024] Open
Abstract
Thrombopoietin (Tpo) is the primary regulator of megakaryocyte and platelet numbers and is required for haematopoetic stem cell maintenance. Tpo functions by binding its receptor (TpoR, a homodimeric Class I cytokine receptor) and initiating cell proliferation or differentiation. Here we characterise the murine Tpo:TpoR signalling complex biochemically and structurally, using cryo-electron microscopy. Tpo uses opposing surfaces to recruit two copies of receptor, forming a 1:2 complex. Although it binds to the same, membrane-distal site on both receptor chains, it does so with significantly different affinities and its highly glycosylated C-terminal domain is not required. In one receptor chain, a large insertion, unique to TpoR, forms a partially structured loop that contacts cytokine. Tpo binding induces the juxtaposition of the two receptor chains adjacent to the cell membrane. The therapeutic agent romiplostim also targets the cytokine-binding site and the characterisation presented here supports the future development of improved TpoR agonists.
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Affiliation(s)
- Kaiseal T G Sarson-Lawrence
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, 3052, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Royal Parade, Parkville, 3052, Victoria, Australia
| | - Joshua M Hardy
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, 3052, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Royal Parade, Parkville, 3052, Victoria, Australia
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, 3052, Victoria, Australia
| | - Josephine Iaria
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, 3052, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Royal Parade, Parkville, 3052, Victoria, Australia
| | - Dina Stockwell
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, 3052, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Royal Parade, Parkville, 3052, Victoria, Australia
| | - Kira Behrens
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, 3052, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Royal Parade, Parkville, 3052, Victoria, Australia
| | - Tamanna Saiyed
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, 3052, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Royal Parade, Parkville, 3052, Victoria, Australia
| | - Cyrus Tan
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, 3052, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Royal Parade, Parkville, 3052, Victoria, Australia
| | - Leila Jebeli
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, 3000, Victoria, Australia
| | - Nichollas E Scott
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, 3000, Victoria, Australia
| | - Toby A Dite
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, 3052, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Royal Parade, Parkville, 3052, Victoria, Australia
| | - Nicos A Nicola
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, 3052, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Royal Parade, Parkville, 3052, Victoria, Australia
| | - Andrew P Leis
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, 3052, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Royal Parade, Parkville, 3052, Victoria, Australia
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, 3052, Victoria, Australia
| | - Jeffrey J Babon
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, 3052, Victoria, Australia.
- Department of Medical Biology, The University of Melbourne, Royal Parade, Parkville, 3052, Victoria, Australia.
| | - Nadia J Kershaw
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, 3052, Victoria, Australia.
- Department of Medical Biology, The University of Melbourne, Royal Parade, Parkville, 3052, Victoria, Australia.
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130
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Moller E, Britt M, Zhou F, Yang H, Anshkin A, Ernst R, Sukharev S, Matthies D. Polymer-extracted structure of the mechanosensitive channel MscS reveals the role of protein-lipid interactions in the gating cycle. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.22.576751. [PMID: 38328078 PMCID: PMC10849555 DOI: 10.1101/2024.01.22.576751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Membrane protein structure determination is not only technically challenging but is further complicated by the removal or displacement of lipids, which can result in non-native conformations or a strong preference for certain states at the exclusion of others. This is especially applicable to mechanosensitive channels (MSC's) that evolved to gate in response to subtle changes in membrane tension transmitted through the lipid bilayer. E. coli MscS, a model bacterial system, is an ancestral member of the large family of MSCs found across all phyla of walled organisms. As a tension sensor, MscS is very sensitive and highly adaptive; it readily opens under super-threshold tension and closes under no tension, but under lower tensions, it slowly inactivates and can only recover when tension is released. However, existing cryo-EM structures do not explain the entire functional gating cycle of open, closed, and inactivated states. A central question in the field has been the assignment of the frequently observed non-conductive conformation to either a closed or inactivated state. Here, we present a 3 Å MscS structure in native nanodiscs obtained with Glyco-DIBMA polymer extraction, eliminating the lipid removal step that is common to all previous structures. Besides the protein in the non-conductive conformation, we observe well-resolved densities of four endogenous phospholipid molecules intercalating between the lipid-facing and pore-lining helices in preferred orientations. Mutations of positively charged residues coordinating these lipids inhibit MscS inactivation, whereas removal of a negative charge near the lipid-filled crevice increases inactivation. The functional data allows us to assign this class of structures to the inactivated state. This structure reveals preserved lipids in their native locations, and the functional effects of their destabilization illustrate a novel inactivation mechanism based on an uncoupling of the peripheral tension-sensing helices from the gate.
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131
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Bacic L, Gaullier G, Mohapatra J, Mao G, Brackmann K, Panfilov M, Liszczak G, Sabantsev A, Deindl S. Asymmetric nucleosome PARylation at DNA breaks mediates directional nucleosome sliding by ALC1. Nat Commun 2024; 15:1000. [PMID: 38307862 PMCID: PMC10837151 DOI: 10.1038/s41467-024-45237-8] [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: 03/09/2023] [Accepted: 01/16/2024] [Indexed: 02/04/2024] Open
Abstract
The chromatin remodeler ALC1 is activated by DNA damage-induced poly(ADP-ribose) deposited by PARP1/PARP2 and their co-factor HPF1. ALC1 has emerged as a cancer drug target, but how it is recruited to ADP-ribosylated nucleosomes to affect their positioning near DNA breaks is unknown. Here we find that PARP1/HPF1 preferentially initiates ADP-ribosylation on the histone H2B tail closest to the DNA break. To dissect the consequences of such asymmetry, we generate nucleosomes with a defined ADP-ribosylated H2B tail on one side only. The cryo-electron microscopy structure of ALC1 bound to such an asymmetric nucleosome indicates preferential engagement on one side. Using single-molecule FRET, we demonstrate that this asymmetric recruitment gives rise to directed sliding away from the DNA linker closest to the ADP-ribosylation site. Our data suggest a mechanism by which ALC1 slides nucleosomes away from a DNA break to render it more accessible to repair factors.
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Affiliation(s)
- Luka Bacic
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75124, Uppsala, Sweden
| | - Guillaume Gaullier
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75124, Uppsala, Sweden
- Department of Chemistry - Ångström, Uppsala University, 75120, Uppsala, Sweden
| | - Jugal Mohapatra
- Department of Biochemistry, The University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390, USA
| | - Guanzhong Mao
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75124, Uppsala, Sweden
| | - Klaus Brackmann
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75124, Uppsala, Sweden
| | - Mikhail Panfilov
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75124, Uppsala, Sweden
| | - Glen Liszczak
- Department of Biochemistry, The University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390, USA
| | - Anton Sabantsev
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75124, Uppsala, Sweden.
| | - Sebastian Deindl
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75124, Uppsala, Sweden.
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132
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Pumroy RA, De Jesús-Pérez JJ, Protopopova AD, Rocereta JA, Fluck EC, Fricke T, Lee BH, Rohacs T, Leffler A, Moiseenkova-Bell V. Molecular details of ruthenium red pore block in TRPV channels. EMBO Rep 2024; 25:506-523. [PMID: 38225355 PMCID: PMC10897480 DOI: 10.1038/s44319-023-00050-0] [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: 08/24/2023] [Revised: 12/19/2023] [Accepted: 12/21/2023] [Indexed: 01/17/2024] Open
Abstract
Transient receptor potential vanilloid (TRPV) channels play a critical role in calcium homeostasis, pain sensation, immunological response, and cancer progression. TRPV channels are blocked by ruthenium red (RR), a universal pore blocker for a wide array of cation channels. Here we use cryo-electron microscopy to reveal the molecular details of RR block in TRPV2 and TRPV5, members of the two TRPV subfamilies. In TRPV2 activated by 2-aminoethoxydiphenyl borate, RR is tightly coordinated in the open selectivity filter, blocking ion flow and preventing channel inactivation. In TRPV5 activated by phosphatidylinositol 4,5-bisphosphate, RR blocks the selectivity filter and closes the lower gate through an interaction with polar residues in the pore vestibule. Together, our results provide a detailed understanding of TRPV subfamily pore block, the dynamic nature of the selectivity filter and allosteric communication between the selectivity filter and lower gate.
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Affiliation(s)
- Ruth A Pumroy
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - José J De Jesús-Pérez
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Anna D Protopopova
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Julia A Rocereta
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Edwin C Fluck
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Tabea Fricke
- Institute for Neurophysiology, Hannover Medical School, 30625, Hannover, Germany
| | - Bo-Hyun Lee
- Department of Physiology and Convergence Medical Science, Institute of Health Sciences, Gyeongsang National University Medical School, Jinju, Korea
- Department of Pharmacology, Physiology and Neuroscience, New Jersey Medical School, Rutgers University, Newark, NJ, 07103, USA
| | - Tibor Rohacs
- Department of Pharmacology, Physiology and Neuroscience, New Jersey Medical School, Rutgers University, Newark, NJ, 07103, USA
| | - Andreas Leffler
- Institute for Neurophysiology, Hannover Medical School, 30625, Hannover, Germany
| | - Vera Moiseenkova-Bell
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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133
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Hehl LA, Horn-Ghetko D, Prabu JR, Vollrath R, Vu DT, Pérez Berrocal DA, Mulder MPC, van der Heden van Noort GJ, Schulman BA. Structural snapshots along K48-linked ubiquitin chain formation by the HECT E3 UBR5. Nat Chem Biol 2024; 20:190-200. [PMID: 37620400 PMCID: PMC10830417 DOI: 10.1038/s41589-023-01414-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 07/30/2023] [Indexed: 08/26/2023]
Abstract
Ubiquitin (Ub) chain formation by homologous to E6AP C-terminus (HECT)-family E3 ligases regulates vast biology, yet the structural mechanisms remain unknown. We used chemistry and cryo-electron microscopy (cryo-EM) to visualize stable mimics of the intermediates along K48-linked Ub chain formation by the human E3, UBR5. The structural data reveal a ≈ 620 kDa UBR5 dimer as the functional unit, comprising a scaffold with flexibly tethered Ub-associated (UBA) domains, and elaborately arranged HECT domains. Chains are forged by a UBA domain capturing an acceptor Ub, with its K48 lured into the active site by numerous interactions between the acceptor Ub, manifold UBR5 elements and the donor Ub. The cryo-EM reconstructions allow defining conserved HECT domain conformations catalyzing Ub transfer from E2 to E3 and from E3. Our data show how a full-length E3, ubiquitins to be adjoined, E2 and intermediary products guide a feed-forward HECT domain conformational cycle establishing a highly efficient, broadly targeting, K48-linked Ub chain forging machine.
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Affiliation(s)
- Laura A Hehl
- Department of Chemistry, School of Natural Sciences, Technical University of Munich, Garching, Germany
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Daniel Horn-Ghetko
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - J Rajan Prabu
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Ronnald Vollrath
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - D Tung Vu
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - David A Pérez Berrocal
- Department of Cell and Chemical Biology, Leiden University Medical Centre, Leiden, the Netherlands
| | - Monique P C Mulder
- Department of Cell and Chemical Biology, Leiden University Medical Centre, Leiden, the Netherlands
| | | | - Brenda A Schulman
- Department of Chemistry, School of Natural Sciences, Technical University of Munich, Garching, Germany.
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany.
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134
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Acar DD, Witkowski W, Wejda M, Wei R, Desmet T, Schepens B, De Cae S, Sedeyn K, Eeckhaut H, Fijalkowska D, Roose K, Vanmarcke S, Poupon A, Jochmans D, Zhang X, Abdelnabi R, Foo CS, Weynand B, Reiter D, Callewaert N, Remaut H, Neyts J, Saelens X, Gerlo S, Vandekerckhove L. Integrating artificial intelligence-based epitope prediction in a SARS-CoV-2 antibody discovery pipeline: caution is warranted. EBioMedicine 2024; 100:104960. [PMID: 38232633 PMCID: PMC10803917 DOI: 10.1016/j.ebiom.2023.104960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 12/22/2023] [Accepted: 12/22/2023] [Indexed: 01/19/2024] Open
Abstract
BACKGROUND SARS-CoV-2-neutralizing antibodies (nABs) showed great promise in the early phases of the COVID-19 pandemic. The emergence of resistant strains, however, quickly rendered the majority of clinically approved nABs ineffective. This underscored the imperative to develop nAB cocktails targeting non-overlapping epitopes. METHODS Undertaking a nAB discovery program, we employed a classical workflow, while integrating artificial intelligence (AI)-based prediction to select non-competing nABs very early in the pipeline. We identified and in vivo validated (in female Syrian hamsters) two highly potent nABs. FINDINGS Despite the promising results, in depth cryo-EM structural analysis demonstrated that the AI-based prediction employed with the intention to ensure non-overlapping epitopes was inaccurate. The two nABs in fact bound to the same receptor-binding epitope in a remarkably similar manner. INTERPRETATION Our findings indicate that, even in the Alphafold era, AI-based predictions of paratope-epitope interactions are rough and experimental validation of epitopes remains an essential cornerstone of a successful nAB lead selection. FUNDING Full list of funders is provided at the end of the manuscript.
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Affiliation(s)
- Delphine Diana Acar
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, Ghent 9000, Belgium
| | - Wojciech Witkowski
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, Ghent 9000, Belgium
| | - Magdalena Wejda
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, Ghent 9000, Belgium
| | - Ruifang Wei
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, Ghent 9000, Belgium
| | - Tim Desmet
- Department of Basic and Applied Medical Sciences, Ghent University, Ghent 9000, Belgium
| | - Bert Schepens
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent 9052, Belgium; Department of Biochemistry and Microbiology, Ghent University, Ghent 9052, Belgium
| | - Sieglinde De Cae
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent 9052, Belgium; Department of Biochemistry and Microbiology, Ghent University, Ghent 9052, Belgium
| | - Koen Sedeyn
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent 9052, Belgium; Department of Biochemistry and Microbiology, Ghent University, Ghent 9052, Belgium
| | - Hannah Eeckhaut
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent 9052, Belgium; Department of Biochemistry and Microbiology, Ghent University, Ghent 9052, Belgium
| | - Daria Fijalkowska
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent 9052, Belgium; Department of Biochemistry and Microbiology, Ghent University, Ghent 9052, Belgium
| | - Kenny Roose
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent 9052, Belgium; Department of Biochemistry and Microbiology, Ghent University, Ghent 9052, Belgium
| | - Sandrine Vanmarcke
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent 9052, Belgium; Department of Biochemistry and Microbiology, Ghent University, Ghent 9052, Belgium
| | | | - Dirk Jochmans
- Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven 3000, Belgium
| | - Xin Zhang
- Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven 3000, Belgium
| | - Rana Abdelnabi
- Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven 3000, Belgium
| | - Caroline S Foo
- Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven 3000, Belgium
| | - Birgit Weynand
- Department of Imaging and Pathology, Translational Cell and Tissue Research, KU Leuven, Leuven 3000, Belgium
| | - Dirk Reiter
- Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels 1050, Belgium
| | - Nico Callewaert
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent 9052, Belgium; Department of Biochemistry and Microbiology, Ghent University, Ghent 9052, Belgium
| | - Han Remaut
- Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels 1050, Belgium; VIB-VUB Center for Structural Biology, VIB, Brussels 1050, Belgium
| | - Johan Neyts
- Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven 3000, Belgium
| | - Xavier Saelens
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent 9052, Belgium; Department of Biochemistry and Microbiology, Ghent University, Ghent 9052, Belgium
| | - Sarah Gerlo
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, Ghent 9000, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent 9000, Belgium
| | - Linos Vandekerckhove
- HIV Cure Research Center, Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent University, Ghent 9000, Belgium.
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Hao A, Suo Y, Lee SY. Structural insights into the FtsEX-EnvC complex regulation on septal peptidoglycan hydrolysis in Vibrio cholerae. Structure 2024; 32:188-199.e5. [PMID: 38070498 DOI: 10.1016/j.str.2023.11.007] [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: 08/28/2023] [Revised: 10/02/2023] [Accepted: 11/14/2023] [Indexed: 02/04/2024]
Abstract
During bacterial cell division, hydrolysis of septal peptidoglycan (sPG) is crucial for cell separation. This sPG hydrolysis is performed by the enzyme amidases whose activity is regulated by the integral membrane protein complex FtsEX-EnvC. FtsEX is an ATP-binding cassette transporter, and EnvC is a long coiled-coil protein that interacts with and activates the amidases. The molecular mechanism by which the FtsEX-EnvC complex activates amidases remains largely unclear. We present the cryo-electron microscopy structure of the FtsEX-EnvC complex from the pathogenic bacteria V. cholerae (FtsEX-EnvCVC). FtsEX-EnvCVC in the presence of ADP adopts a distinct conformation where EnvC is "horizontally extended" rather than "vertically extended". Subsequent structural studies suggest that EnvC can swing between these conformations in space in a nucleotide-dependent manner. Our structural analysis and functional studies suggest that FtsEX-EnvCVC employs spatial control of EnvC for amidase activation, providing mechanistic insights into the FtsEX-EnvC regulation on septal peptidoglycan hydrolysis.
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Affiliation(s)
- Aili Hao
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
| | - Yang Suo
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
| | - Seok-Yong Lee
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA.
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Hickey CM, Digianantonio KM, Zimmermann K, Harbin A, Quinn C, Patel A, Gareiss P, Chapman A, Tiberi B, Dobrodziej J, Corradi J, Cacace AM, Langley DR, Békés M. Co-opting the E3 ligase KLHDC2 for targeted protein degradation by small molecules. Nat Struct Mol Biol 2024; 31:311-322. [PMID: 38177675 DOI: 10.1038/s41594-023-01146-w] [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: 04/14/2023] [Accepted: 10/04/2023] [Indexed: 01/06/2024]
Abstract
Targeted protein degradation (TPD) by PROTAC (proteolysis-targeting chimera) and molecular glue small molecules is an emerging therapeutic strategy. To expand the roster of E3 ligases that can be utilized for TPD, we describe the discovery and biochemical characterization of small-molecule ligands targeting the E3 ligase KLHDC2. Furthermore, we functionalize these KLHDC2-targeting ligands into KLHDC2-based BET-family and AR PROTAC degraders and demonstrate KLHDC2-dependent target-protein degradation. Additionally, we offer insight into the assembly of the KLHDC2 E3 ligase complex. Using biochemical binding studies, X-ray crystallography and cryo-EM, we show that the KLHDC2 E3 ligase assembles into a dynamic tetramer held together via its own C terminus, and that this assembly can be modulated by substrate and ligand engagement.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Bernadette Tiberi
- Arvinas, Inc, New Haven, CT, USA
- Genetics, Genomics and Cancer Biology Graduate Program, Thomas Jefferson University, Philadelphia, PA, USA
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137
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Dalton MP, Cheng MH, Bahar I, Coleman JA. Structural mechanisms for VMAT2 inhibition by tetrabenazine. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.05.556211. [PMID: 37732203 PMCID: PMC10508774 DOI: 10.1101/2023.09.05.556211] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
The vesicular monoamine transporter 2 (VMAT2) is a proton-dependent antiporter responsible for loading monoamine neurotransmitters into synaptic vesicles. Dysregulation of VMAT2 can lead to several neuropsychiatric disorders including Parkinson's disease and schizophrenia. Furthermore, drugs such as amphetamine and MDMA are known to act on VMAT2, exemplifying its role in the mechanisms of actions for drugs of abuse. Despite VMAT2's importance, there remains a critical lack of mechanistic understanding, largely driven by a lack of structural information. Here we report a 3.1 Å resolution cryo-EM structure of VMAT2 complexed with tetrabenazine (TBZ), a non-competitive inhibitor used in the treatment of Huntington's chorea. We find TBZ interacts with residues in a central binding site, locking VMAT2 in an occluded conformation and providing a mechanistic basis for non-competitive inhibition. We further identify residues critical for cytosolic and lumenal gating, including a cluster of hydrophobic residues which are involved in a lumenal gating strategy. Our structure also highlights three distinct polar networks that may determine VMAT2 conformational dynamics and play a role in proton transduction. The structure elucidates mechanisms of VMAT2 inhibition and transport, providing insights into VMAT2 architecture, function, and the design of small-molecule therapeutics.
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Affiliation(s)
- Michael P Dalton
- Department of Structural Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA
| | - Mary Hongying Cheng
- Laufer Center for Physical and Quantitative Biology, and Department of Biochemistry and Cell Biology, School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA
| | - Ivet Bahar
- Laufer Center for Physical and Quantitative Biology, and Department of Biochemistry and Cell Biology, School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA
| | - Jonathan A Coleman
- Department of Structural Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA
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138
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Aplin C, Cerione RA. Probing the mechanism by which the retinal G protein transducin activates its biological effector PDE6. J Biol Chem 2024; 300:105608. [PMID: 38159849 PMCID: PMC10838916 DOI: 10.1016/j.jbc.2023.105608] [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: 10/22/2023] [Revised: 11/23/2023] [Accepted: 12/14/2023] [Indexed: 01/03/2024] Open
Abstract
Phototransduction in retinal rods occurs when the G protein-coupled photoreceptor rhodopsin triggers the activation of phosphodiesterase 6 (PDE6) by GTP-bound alpha subunits of the G protein transducin (GαT). Recently, we presented a cryo-EM structure for a complex between two GTP-bound recombinant GαT subunits and native PDE6, that included a bivalent antibody bound to the C-terminal ends of GαT and the inhibitor vardenafil occupying the active sites on the PDEα and PDEβ subunits. We proposed GαT-activated PDE6 by inducing a striking reorientation of the PDEγ subunits away from the catalytic sites. However, questions remained including whether in the absence of the antibody GαT binds to PDE6 in a similar manner as observed when the antibody is present, does GαT activate PDE6 by enabling the substrate cGMP to access the catalytic sites, and how does the lipid membrane enhance PDE6 activation? Here, we demonstrate that 2:1 GαT-PDE6 complexes form with either recombinant or retinal GαT in the absence of the GαT antibody. We show that GαT binding is not necessary for cGMP nor competitive inhibitors to access the active sites; instead, occupancy of the substrate binding sites enables GαT to bind and reposition the PDE6γ subunits to promote catalytic activity. Moreover, we demonstrate by reconstituting GαT-stimulated PDE6 activity in lipid bilayer nanodiscs that the membrane-induced enhancement results from an increase in the apparent binding affinity of GαT for PDE6. These findings provide new insights into how the retinal G protein stimulates rapid catalytic turnover by PDE6 required for dim light vision.
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Affiliation(s)
- Cody Aplin
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, USA
| | - Richard A Cerione
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, USA; Department of Molecular Medicine, Cornell University, Ithaca, New York, USA.
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139
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De Jesús-Pérez JJ, Gabrielle M, Raheem S, Fluck EC, Rohacs T, Moiseenkova-Bell VY. Structural mechanism of TRPV5 inhibition by econazole. Structure 2024; 32:148-156.e5. [PMID: 38141613 PMCID: PMC10872542 DOI: 10.1016/j.str.2023.11.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 11/01/2023] [Accepted: 11/28/2023] [Indexed: 12/25/2023]
Abstract
The calcium-selective TRPV5 channel activated by phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2] is involved in calcium homeostasis. Recently, cryoelectron microscopy (cryo-EM) provided molecular details of TRPV5 modulation by exogenous and endogenous molecules. However, the details of TRPV5 inhibition by the antifungal agent econazole (ECN) remain elusive due to the low resolution of the currently available structure. In this study, we employ cryo-EM to comprehensively examine how the ECN inhibits TRPV5. By combining our structural findings with site-directed mutagenesis, calcium measurements, electrophysiology, and molecular dynamics simulations, we determined that residues F472 and L475 on the S4 helix, along with residue W495 on the S5 helix, collectively constitute the ECN-binding site. Additionally, the structure of TRPV5 in the presence of ECN and PI(4,5)P2, which does not show the bound activator, reveals a potential inhibition mechanism in which ECN competes with PI(4,5)P2, preventing the latter from binding, and ultimately pore closure.
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Affiliation(s)
- José J De Jesús-Pérez
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Matthew Gabrielle
- Department of Pharmacology, Physiology and Neuroscience, New Jersey Medical School, Rutgers University, Newark, NJ 07103, USA
| | - Sumiyya Raheem
- Department of Pharmacology, Physiology and Neuroscience, New Jersey Medical School, Rutgers University, Newark, NJ 07103, USA
| | - Edwin C Fluck
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Tibor Rohacs
- Department of Pharmacology, Physiology and Neuroscience, New Jersey Medical School, Rutgers University, Newark, NJ 07103, USA
| | - Vera Y Moiseenkova-Bell
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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140
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Jing T, Shan Z, Dinh T, Biswas A, Jang S, Greenwood J, Li M, Zhang Z, Gray G, Shin HJ, Zhou B, Passos D, Aiyer S, Li Z, Craigie R, Engelman AN, Kvaratskhelia M, Lyumkis D. Oligomeric HIV-1 Integrase Structures Reveal Functional Plasticity for Intasome Assembly and RNA Binding. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.26.577436. [PMID: 38328132 PMCID: PMC10849644 DOI: 10.1101/2024.01.26.577436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Integrase (IN) performs dual essential roles during HIV-1 replication. During ingress, IN functions within an oligomeric "intasome" assembly to catalyze viral DNA integration into host chromatin. During late stages of infection, tetrameric IN binds viral RNA and orchestrates the condensation of ribonucleoprotein complexes into the capsid core. The molecular architectures of HIV-1 IN assemblies that mediate these distinct events remain unknown. Furthermore, the tetramer is an important antiviral target for allosteric IN inhibitors. Here, we determined cryo-EM structures of wildtype HIV-1 IN tetramers and intasome hexadecamers. Our structures unveil a remarkable plasticity that leverages IN C-terminal domains and abutting linkers to assemble functionally distinct oligomeric forms. Alteration of a newly recognized conserved interface revealed that both IN functions track with tetramerization in vitro and during HIV-1 infection. Collectively, our findings reveal how IN plasticity orchestrates its diverse molecular functions, suggest a working model for IN-viral RNA binding, and provide atomic blueprints for allosteric IN inhibitor development.
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Affiliation(s)
- Tao Jing
- The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Zelin Shan
- The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Tung Dinh
- Division of Infectious Diseases, Anschutz Medical Campus, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Avik Biswas
- The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Sooin Jang
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Juliet Greenwood
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Min Li
- National Institutes of Health, National Institute of Diabetes and Digestive Diseases, Bethesda, MD, 20892, USA
| | - Zeyuan Zhang
- The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Gennavieve Gray
- The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Hye Jeong Shin
- The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Bo Zhou
- The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Dario Passos
- The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Sriram Aiyer
- The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Zhen Li
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Robert Craigie
- National Institutes of Health, National Institute of Diabetes and Digestive Diseases, Bethesda, MD, 20892, USA
| | - Alan N. Engelman
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Mamuka Kvaratskhelia
- Division of Infectious Diseases, Anschutz Medical Campus, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Dmitry Lyumkis
- The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
- Graduate School of Biological Sciences, Section of Molecular Biology, University of California San Diego, La Jolla, CA 92093, USA
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141
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Ghanim GE, Sekne Z, Balch S, van Roon AMM, Nguyen THD. 2.7 Å cryo-EM structure of human telomerase H/ACA ribonucleoprotein. Nat Commun 2024; 15:746. [PMID: 38272871 PMCID: PMC10811338 DOI: 10.1038/s41467-024-45002-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: 06/27/2023] [Accepted: 01/03/2024] [Indexed: 01/27/2024] Open
Abstract
Telomerase is a ribonucleoprotein (RNP) enzyme that extends telomeric repeats at eukaryotic chromosome ends to counterbalance telomere loss caused by incomplete genome replication. Human telomerase is comprised of two distinct functional lobes tethered by telomerase RNA (hTR): a catalytic core, responsible for DNA extension; and a Hinge and ACA (H/ACA) box RNP, responsible for telomerase biogenesis. H/ACA RNPs also have a general role in pseudouridylation of spliceosomal and ribosomal RNAs, which is critical for the biogenesis of the spliceosome and ribosome. Much of our structural understanding of eukaryotic H/ACA RNPs comes from structures of the human telomerase H/ACA RNP. Here we report a 2.7 Å cryo-electron microscopy structure of the telomerase H/ACA RNP. The significant improvement in resolution over previous 3.3 Å to 8.2 Å structures allows us to uncover new molecular interactions within the H/ACA RNP. Many disease mutations are mapped to these interaction sites. The structure also reveals unprecedented insights into a region critical for pseudouridylation in canonical H/ACA RNPs. Together, our work advances understanding of telomerase-related disease mutations and the mechanism of pseudouridylation by eukaryotic H/ACA RNPs.
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Affiliation(s)
| | - Zala Sekne
- MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
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142
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Esfahani BG, Randolph PS, Peng R, Grant T, Stroupe ME, Stagg SM. SPOT-RASTR - a cryo-EM specimen preparation technique that overcomes problems with preferred orientation and the air/water interface. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.24.577038. [PMID: 38501120 PMCID: PMC10945588 DOI: 10.1101/2024.01.24.577038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
In cryogenic electron microscopy (cryo-EM), specimen preparation remains a bottleneck despite recent advancements. Classical plunge freezing methods often result in issues like aggregation and preferred orientations at the air/water interface. Many alternative methods have been proposed, but there remains a lack a universal solution, and multiple techniques are often required for challenging samples. Here, we demonstrate the use of lipid nanotubes with nickel NTA headgroups as a platform for cryo-EM sample preparation. His-tagged specimens of interest are added to the tubules, and they can be frozen by conventional plunge freezing. We show that the nanotubes protect samples from the air/water interface and promote a wider range of orientations. The reconstruction of average subtracted tubular regions (RASTR) method allows for the removal of the nanotubule signal from the cryo-EM images resulting in isolated images of specimens of interest. Testing with β-galactosidase validates the method's ability to capture particles at lower concentrations, overcome preferred orientations, and achieve near-atomic resolution reconstructions. Since the nanotubules can be identified and targeted automatically at low magnification, the method enables fully automated data collection. Furthermore, the particles on the tubes can be automatically identified and centered using 2D classification enabling particle picking without requiring prior information. Altogether, our approach that we call specimen preparation on a tube RASTR (SPOT-RASTR) holds promise for overcoming air-water interface and preferred orientation challenges and offers the potential for fully automated cryo-EM data collection and structure determination.
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143
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Bruch EM, Zhu S, Szymkowicz L, Blake T, Kiss T, James DA, Rak A, Narayan K, Balmer MT, Chicz RM. Structural and biochemical rationale for Beta variant protein booster vaccine broad cross-neutralization of SARS-CoV-2. Sci Rep 2024; 14:2038. [PMID: 38263191 PMCID: PMC10805794 DOI: 10.1038/s41598-024-52499-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 01/19/2024] [Indexed: 01/25/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), responsible for the COVID-19 pandemic, uses a surface expressed trimeric spike glycoprotein for cell entry. This trimer is the primary target for neutralizing antibodies making it a key candidate for vaccine development. During the global pandemic circulating variants of concern (VOC) caused several waves of infection, severe disease, and death. The reduced efficacy of the ancestral trimer-based vaccines against emerging VOC led to the need for booster vaccines. Here we present a detailed characterization of the Sanofi Beta trimer, utilizing cryo-EM for structural elucidation. We investigate the conformational dynamics and stabilizing features using orthogonal SPR, SEC, nanoDSF, and HDX-MS techniques to better understand how this antigen elicits superior broad neutralizing antibodies as a variant booster vaccine. This structural analysis confirms the Beta trimer preference for canonical quaternary structure with two RBD in the up position and the reversible equilibrium between the canonical spike and open trimer conformations. Moreover, this report provides a better understanding of structural differences between spike antigens contributing to differential vaccine efficacy.
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144
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Gewering T, Waghray D, Parey K, Jung H, Tran NNB, Zapata J, Zhao P, Chen H, Januliene D, Hummer G, Urbatsch I, Moeller A, Zhang Q. Tracing the substrate translocation mechanism in P-glycoprotein. eLife 2024; 12:RP90174. [PMID: 38259172 PMCID: PMC10945689 DOI: 10.7554/elife.90174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2024] Open
Abstract
P-glycoprotein (Pgp) is a prototypical ATP-binding cassette (ABC) transporter of great biological and clinical significance.Pgp confers cancer multidrug resistance and mediates the bioavailability and pharmacokinetics of many drugs (Juliano and Ling, 1976; Ueda et al., 1986; Sharom, 2011). Decades of structural and biochemical studies have provided insights into how Pgp binds diverse compounds (Loo and Clarke, 2000; Loo et al., 2009; Aller et al., 2009; Alam et al., 2019; Nosol et al., 2020; Chufan et al., 2015), but how they are translocated through the membrane has remained elusive. Here, we covalently attached a cyclic substrate to discrete sites of Pgp and determined multiple complex structures in inward- and outward-facing states by cryoEM. In conjunction with molecular dynamics simulations, our structures trace the substrate passage across the membrane and identify conformational changes in transmembrane helix 1 (TM1) as regulators of substrate transport. In mid-transport conformations, TM1 breaks at glycine 72. Mutation of this residue significantly impairs drug transport of Pgp in vivo, corroborating the importance of its regulatory role. Importantly, our data suggest that the cyclic substrate can exit Pgp without the requirement of a wide-open outward-facing conformation, diverting from the common efflux model for Pgp and other ABC exporters. The substrate transport mechanism of Pgp revealed here pinpoints critical targets for future drug discovery studies of this medically relevant system.
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Affiliation(s)
- Theresa Gewering
- Osnabrück University, Department of Biology/Chemistry, Structural Biology SectionOsnabrückGermany
- Department of Structural Biology, Max Planck Institute of BiophysicsFrankfurtGermany
| | - Deepali Waghray
- Department of Integrative Structural and Computational Biology, The Scripps Research InstituteLa JollaUnited States
| | - Kristian Parey
- Osnabrück University, Department of Biology/Chemistry, Structural Biology SectionOsnabrückGermany
- Department of Structural Biology, Max Planck Institute of BiophysicsFrankfurtGermany
- Osnabrück University, Center of Cellular Nanoanalytic Osnabrück (CellNanOs)OsnabrückGermany
| | - Hendrik Jung
- Department of Theoretical Biophysics, Max Planck Institute of BiophysicsFrankfurtGermany
| | - Nghi NB Tran
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences CenterLubbockUnited States
| | - Joel Zapata
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences CenterLubbockUnited States
| | - Pengyi Zhao
- Department of Chemistry & Environmental Science, New Jersey Institute of TechnologyNewarkUnited States
| | - Hao Chen
- Department of Chemistry & Environmental Science, New Jersey Institute of TechnologyNewarkUnited States
| | - Dovile Januliene
- Osnabrück University, Department of Biology/Chemistry, Structural Biology SectionOsnabrückGermany
- Department of Structural Biology, Max Planck Institute of BiophysicsFrankfurtGermany
- Osnabrück University, Center of Cellular Nanoanalytic Osnabrück (CellNanOs)OsnabrückGermany
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of BiophysicsFrankfurtGermany
- Institute for Biophysics, Goethe University FrankfurtFrankfurtGermany
| | - Ina Urbatsch
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences CenterLubbockUnited States
| | - Arne Moeller
- Osnabrück University, Department of Biology/Chemistry, Structural Biology SectionOsnabrückGermany
- Department of Structural Biology, Max Planck Institute of BiophysicsFrankfurtGermany
- Osnabrück University, Center of Cellular Nanoanalytic Osnabrück (CellNanOs)OsnabrückGermany
| | - Qinghai Zhang
- Department of Integrative Structural and Computational Biology, The Scripps Research InstituteLa JollaUnited States
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145
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Tang N, Wu Z, Gao Y, Chen W, Wang Z, Su M, Ji W, Ji Q. Molecular Basis and Genome Editing Applications of a Compact Eubacterium ventriosum CRISPR-Cas9 System. ACS Synth Biol 2024; 13:269-281. [PMID: 38061052 DOI: 10.1021/acssynbio.3c00501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2024]
Abstract
CRISPR-Cas9 systems have been widely harnessed for diverse genome editing applications because of their ease of use and high efficiency. However, the large molecular sizes and strict PAM requirements of commonly used CRISPR-Cas9 systems restrict their broad applications in therapeutics. Here, we report the molecular basis and genome editing applications of a novel compact type II-A Eubacterium ventriosum CRISPR-Cas9 system (EvCas9) with 1107 residues and distinct 5'-NNGDGN-3' (where D represents A, T, or G) PAM specificity. We determine the cryo-EM structure of EvCas9 in a complex with an sgRNA and a target DNA, revealing the detailed PAM recognition and sgRNA and target DNA association mechanisms. Additionally, we demonstrate the robust genome editing capacity of EvCas9 in bacteria and human cells with superior fidelity compared to SaCas9 and SpCas9, and we engineer it to be efficient base editors by fusing a cytidine or adenosine deaminase. Collectively, our results facilitate further understanding of CRISPR-Cas9 working mechanisms and expand the compact CRISPR-Cas9 toolbox.
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Affiliation(s)
- Na Tang
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Zhaowei Wu
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yan Gao
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Weizhong Chen
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Zixiao Wang
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Mengjiao Su
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Wenxin Ji
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Quanjiang Ji
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- Shanghai Clinical Research and Trial Center, Shanghai 201210, China
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146
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Kavčič L, Kežar A, Koritnik N, Žnidarič MT, Klobučar T, Vičič Ž, Merzel F, Holden E, Benesch JLP, Podobnik M. From structural polymorphism to structural metamorphosis of the coat protein of flexuous filamentous potato virus Y. Commun Chem 2024; 7:14. [PMID: 38233506 PMCID: PMC10794713 DOI: 10.1038/s42004-024-01100-x] [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: 09/20/2023] [Accepted: 01/05/2024] [Indexed: 01/19/2024] Open
Abstract
The structural diversity and tunability of the capsid proteins (CPs) of various icosahedral and rod-shaped viruses have been well studied and exploited in the development of smart hybrid nanoparticles. However, the potential of CPs of the wide-spread flexuous filamentous plant viruses remains to be explored. Here, we show that we can control the shape, size, RNA encapsidation ability, symmetry, stability and surface functionalization of nanoparticles through structure-based design of CP from potato virus Y (PVY). We provide high-resolution insight into CP-based self-assemblies, ranging from large polymorphic or monomorphic filaments to smaller annular, cubic or spherical particles. Furthermore, we show that we can prevent CP self-assembly in bacteria by fusion with a cleavable protein, enabling controlled nanoparticle formation in vitro. Understanding the remarkable structural diversity of PVY CP not only provides possibilities for the production of biodegradable nanoparticles, but may also advance future studies of CP's polymorphism in a biological context.
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Affiliation(s)
- Luka Kavčič
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Ljubljana, Slovenia
- PhD Program 'Chemical Sciences', Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
| | - Andreja Kežar
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Neža Koritnik
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Ljubljana, Slovenia
- PhD Program 'Biomedicine', Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Magda Tušek Žnidarič
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Tajda Klobučar
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Ljubljana, Slovenia
- PhD Program 'Biosciences', Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Žiga Vičič
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Franci Merzel
- Theory Department, National Institute of Chemistry, Ljubljana, Slovenia
| | - Ellie Holden
- Department of Chemistry, University of Oxford, Oxford, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK
| | - Justin L P Benesch
- Department of Chemistry, University of Oxford, Oxford, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK
| | - Marjetka Podobnik
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Ljubljana, Slovenia.
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147
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Sarsam RD, Xu J, Lahiri I, Gong W, Li Q, Oh J, Zhou Z, Hou P, Chong J, Hao N, Li S, Wang D, Leschziner AE. Elf1 promotes Rad26's interaction with lesion-arrested Pol II for transcription-coupled repair. Proc Natl Acad Sci U S A 2024; 121:e2314245121. [PMID: 38194460 PMCID: PMC10801861 DOI: 10.1073/pnas.2314245121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 11/27/2023] [Indexed: 01/11/2024] Open
Abstract
Transcription-coupled nucleotide excision repair (TC-NER) is a highly conserved DNA repair pathway that removes bulky lesions in the transcribed genome. Cockayne syndrome B protein (CSB), or its yeast ortholog Rad26, has been known for decades to play important roles in the lesion-recognition steps of TC-NER. Another conserved protein ELOF1, or its yeast ortholog Elf1, was recently identified as a core transcription-coupled repair factor. How Rad26 distinguishes between RNA polymerase II (Pol II) stalled at a DNA lesion or other obstacles and what role Elf1 plays in this process remains unknown. Here, we present cryo-EM structures of Pol II-Rad26 complexes stalled at different obstacles that show that Rad26 uses a common mechanism to recognize a stalled Pol II, with additional interactions when Pol II is arrested at a lesion. A cryo-EM structure of lesion-arrested Pol II-Rad26 bound to Elf1 revealed that Elf1 induces further interactions between Rad26 and a lesion-arrested Pol II. Biochemical and genetic data support the importance of the interplay between Elf1 and Rad26 in TC-NER initiation. Together, our results provide important mechanistic insights into how two conserved transcription-coupled repair factors, Rad26/CSB and Elf1/ELOF1, work together at the initial lesion recognition steps of transcription-coupled repair.
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Affiliation(s)
- Reta D. Sarsam
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA92093
| | - Jun Xu
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA92093
| | - Indrajit Lahiri
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA92093
| | - Wenzhi Gong
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA70803
| | - Qingrong Li
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA92093
| | - Juntaek Oh
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA92093
| | - Zhen Zhou
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA92093
| | - Peini Hou
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA92093
| | - Jenny Chong
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA92093
| | - Nan Hao
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA92093
| | - Shisheng Li
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA70803
| | - Dong Wang
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA92093
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA92093
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA92093
| | - Andres E. Leschziner
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA92093
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA92093
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148
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Driggers CM, Kuo YY, Zhu P, ElSheikh A, Shyng SL. Structure of an open K ATP channel reveals tandem PIP 2 binding sites mediating the Kir6.2 and SUR1 regulatory interface. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.08.01.551546. [PMID: 37577494 PMCID: PMC10418277 DOI: 10.1101/2023.08.01.551546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
ATP-sensitive potassium (K ATP ) channels, composed of four pore-lining Kir6.2 subunits and four regulatory sulfonylurea receptor 1 (SUR1) subunits, control insulin secretion in pancreatic β-cells. K ATP channel opening is stimulated by PIP 2 and inhibited by ATP. Mutations that increase channel opening by PIP 2 reduce ATP inhibition and cause neonatal diabetes. Although considerable evidence has indicated PIP 2 in K ATP channel function, previously solved open-channel structures have lacked bound PIP 2 , and mechanisms by which PIP 2 regulates K ATP channels remain unresolved. Here, we report the cryoEM structure of a K ATP channel harboring the neonatal diabetes mutation Kir6.2-Q52R, bound to natural C18:0/C20:4 long-chain PIP 2 in an open conformation. The structure reveals two adjacent PIP 2 molecules between SUR1 and Kir6.2. The first PIP 2 binding site is conserved among PIP 2 -gated Kir channels. The second site forms uniquely in K ATP at the interface of Kir6.2 and SUR1. Functional studies demonstrate both binding sites determine channel activity. Kir6.2 pore opening is associated with a twist of the Kir6.2 cytoplasmic domain and a rotation of the N-terminal transmembrane domain of SUR1, which widens the inhibitory ATP binding pocket to disfavor ATP binding. The open conformation is particularly stabilized by the Kir6.2-Q52R residue through cation-π bonding with SUR1-W51. Together, these results uncover the cooperation between SUR1 and Kir6.2 in PIP 2 binding and gating, explain the antagonistic regulation of K ATP channels by PIP 2 and ATP, and provide the mechanism by which Kir6.2-Q52R stabilizes an open channel to cause neonatal diabetes.
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149
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McCallum M, Park YJ, Stewart C, Sprouse KR, Brown J, Tortorici MA, Gibson C, Wong E, Ieven M, Telenti A, Veesler D. Human coronavirus HKU1 recognition of the TMPRSS2 host receptor. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.09.574565. [PMID: 38260518 PMCID: PMC10802434 DOI: 10.1101/2024.01.09.574565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
The human coronavirus HKU1 spike (S) glycoprotein engages host cell surface sialoglycans and transmembrane protease serine 2 (TMPRSS2) to initiate infection. The molecular basis of HKU1 binding to TMPRSS2 and determinants of host receptor tropism remain elusive. Here, we designed an active human TMPRSS2 construct enabling high-yield recombinant production in human cells of this key therapeutic target. We determined a cryo-electron microscopy structure of the HKU1 RBD bound to human TMPRSS2 providing a blueprint of the interactions supporting viral entry and explaining the specificity for TMPRSS2 among human type 2 transmembrane serine proteases. We found that human, rat, hamster and camel TMPRSS2 promote HKU1 S-mediated entry into cells and identified key residues governing host receptor usage. Our data show that serum antibodies targeting the HKU1 RBD TMPRSS2 binding-site are key for neutralization and that HKU1 uses conformational masking and glycan shielding to balance immune evasion and receptor engagement.
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Affiliation(s)
- Matthew McCallum
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Young-Jun Park
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Cameron Stewart
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | | | - Jack Brown
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | | | - Cecily Gibson
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Emily Wong
- Vir Biotechnology, San Francisco, CA 94158, USA
| | - Margareta Ieven
- Laboratory of Clinical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | | | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
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150
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Botsch JJ, Junker R, Sorgenfrei M, Ogger PP, Stier L, von Gronau S, Murray PJ, Seeger MA, Schulman BA, Bräuning B. Doa10/MARCH6 architecture interconnects E3 ligase activity with lipid-binding transmembrane channel to regulate SQLE. Nat Commun 2024; 15:410. [PMID: 38195637 PMCID: PMC10776854 DOI: 10.1038/s41467-023-44670-5] [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: 06/12/2023] [Accepted: 12/19/2023] [Indexed: 01/11/2024] Open
Abstract
Transmembrane E3 ligases play crucial roles in homeostasis. Much protein and organelle quality control, and metabolic regulation, are determined by ER-resident MARCH6 E3 ligases, including Doa10 in yeast. Here, we present Doa10/MARCH6 structural analysis by cryo-EM and AlphaFold predictions, and a structure-based mutagenesis campaign. The majority of Doa10/MARCH6 adopts a unique circular structure within the membrane. This channel is established by a lipid-binding scaffold, and gated by a flexible helical bundle. The ubiquitylation active site is positioned over the channel by connections between the cytosolic E3 ligase RING domain and the membrane-spanning scaffold and gate. Here, by assaying 95 MARCH6 variants for effects on stability of the well-characterized substrate SQLE, which regulates cholesterol levels, we reveal crucial roles of the gated channel and RING domain consistent with AlphaFold-models of substrate-engaged and ubiquitylation complexes. SQLE degradation further depends on connections between the channel and RING domain, and lipid binding sites, revealing how interconnected Doa10/MARCH6 elements could orchestrate metabolic signals, substrate binding, and E3 ligase activity.
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Affiliation(s)
- J Josephine Botsch
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
- Technical University of Munich, School of Natural Sciences, Munich, Germany
| | - Roswitha Junker
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Michèle Sorgenfrei
- Institute of Medical Microbiology, University of Zurich, Gloriastrasse 28/30, 8006, Zurich, Switzerland
| | - Patricia P Ogger
- Research Group of Immunoregulation, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Luca Stier
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
- Technical University of Munich, School of Natural Sciences, Munich, Germany
| | - Susanne von Gronau
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Peter J Murray
- Research Group of Immunoregulation, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Markus A Seeger
- Institute of Medical Microbiology, University of Zurich, Gloriastrasse 28/30, 8006, Zurich, Switzerland
| | - Brenda A Schulman
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany.
| | - Bastian Bräuning
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany.
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