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Moiseenko A, Zhang Y, Vorovitch MF, Ivanova AL, Liu Z, Osolodkin DI, Egorov AM, Ishmukhametov AA, Sokolova OS. Structural diversity of tick-borne encephalitis virus particles in the inactivated vaccine based on strain Sofjin. Emerg Microbes Infect 2024; 13:2290833. [PMID: 38073510 DOI: 10.1080/22221751.2023.2290833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 11/29/2023] [Indexed: 03/12/2024]
Abstract
The main approach to preventing tick-borne encephalitis (TBE) is vaccination. Formaldehyde-inactivated TBE vaccines have a proven record of safety and efficiency but have never been characterized structurally with atomic resolution. We report a cryoelectron microscopy (cryo-EM) structure of the formaldehyde-inactivated TBE virus (TBEV) of Sofjin-Chumakov strain representing the Far-Eastern subtype. A 3.8 Å resolution reconstruction reveals the structural integrity of the envelope E proteins, specifically the E protein ectodomains. The comparative study shows a high structural similarity to the previously published structures of the TBEV European subtype strains Hypr and Kuutsalo-14. A fraction of inactivated virions exhibits asymmetric features including the deformations of the membrane profile. We propose that the heterogeneity is caused by inactivation and perform a local variability analysis on the small parts of the envelope protein shell to reveal membrane curvature features possibly induced by the inactivation. The results of this study will have implications for the design of novel vaccines against diseases caused by flaviviruses.
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Affiliation(s)
- Andrey Moiseenko
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Yichen Zhang
- Faculty of Biology, Shenzhen MSU-BIT University, Shenzhen, People's Republic of China
| | - Mikhail F Vorovitch
- FSASI "Chumakov FSC R&D IBP RAS" (Institute of Poliomyelitis), Moscow, Russia
- Sechenov First Moscow State Medical University, Moscow, Russia
| | - Alla L Ivanova
- FSASI "Chumakov FSC R&D IBP RAS" (Institute of Poliomyelitis), Moscow, Russia
| | - Zheng Liu
- Kobilka Institute of Innovative Drug Discovery, School of Medicine, Chinese University of Hong Kong, Shenzhen, People's Republic of China
| | - Dmitry I Osolodkin
- FSASI "Chumakov FSC R&D IBP RAS" (Institute of Poliomyelitis), Moscow, Russia
- Sechenov First Moscow State Medical University, Moscow, Russia
| | - Alexey M Egorov
- FSASI "Chumakov FSC R&D IBP RAS" (Institute of Poliomyelitis), Moscow, Russia
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Aydar A Ishmukhametov
- FSASI "Chumakov FSC R&D IBP RAS" (Institute of Poliomyelitis), Moscow, Russia
- Sechenov First Moscow State Medical University, Moscow, Russia
| | - Olga S Sokolova
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
- Faculty of Biology, Shenzhen MSU-BIT University, Shenzhen, People's Republic of China
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2
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Lee N, Kim S, Lee NY, Jo H, Jeong P, Pagire HS, Pagire SH, Ahn JH, Jin MS, Park CS. Activation mechanism and novel binding sites of the BK Ca channel activator CTIBD. Life Sci Alliance 2024; 7:e202402621. [PMID: 39089879 PMCID: PMC11294680 DOI: 10.26508/lsa.202402621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 07/12/2024] [Accepted: 07/15/2024] [Indexed: 08/04/2024] Open
Abstract
The large-conductance calcium-activated potassium (BKCa) channel, which is crucial for urinary bladder smooth muscle relaxation, is a potential target for overactive bladder treatment. Our prior work unveiled CTIBD as a promising BKCa channel activator, altering V 1/2 and G max This study investigates CTIBD's activation mechanism, revealing its independence from the Ca2+ and membrane voltage sensing of the BKCa channel. Cryo-electron microscopy disclosed that two CTIBD molecules bind to hydrophobic regions on the extracellular side of the lipid bilayer. Key residues (W22, W203, and F266) are important for CTIBD binding, and their replacement with alanine reduces CTIBD-mediated channel activation. The triple-mutant (W22A/W203A/F266A) channel showed the smallest V 1/2 shift with a minimal impact on activation and deactivation kinetics by CTIBD. At the single-channel level, CTIBD treatment was much less effective at increasing P o in the triple mutant, mainly because of a drastically increased dissociation rate compared with the WT. These findings highlight CTIBD's mechanism, offering crucial insights for developing small-molecule treatments for BKCa-related pathophysiological conditions.
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Affiliation(s)
- Narasaem Lee
- https://ror.org/024kbgz78 School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
| | - Subin Kim
- https://ror.org/024kbgz78 School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
| | - Na Young Lee
- https://ror.org/024kbgz78 School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
| | - Heeji Jo
- https://ror.org/024kbgz78 School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
| | | | - Haushabhau S Pagire
- https://ror.org/024kbgz78 Department of Chemistry, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
| | - Suvarna H Pagire
- https://ror.org/024kbgz78 Department of Chemistry, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
| | - Jin Hee Ahn
- https://ror.org/024kbgz78 Department of Chemistry, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
| | - Mi Sun Jin
- https://ror.org/024kbgz78 School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
| | - Chul-Seung Park
- https://ror.org/024kbgz78 School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
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3
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Navratna V, Kumar A, Rana JK, Mosalaganti S. Structure of the human systemic RNAi defective transmembrane protein 1 (hSIDT1) reveals the conformational flexibility of its lipid binding domain. Life Sci Alliance 2024; 7:e202402624. [PMID: 38925866 PMCID: PMC11208740 DOI: 10.26508/lsa.202402624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 06/10/2024] [Accepted: 06/12/2024] [Indexed: 06/28/2024] Open
Abstract
In Caenorhabditis elegans, inter-cellular transport of the small non-coding RNA causing systemic RNAi is mediated by the transmembrane protein SID1, encoded by the sid1 gene in the systemic RNAi defective (sid) loci. SID1 shares structural and sequence similarity with cholesterol uptake protein 1 (CHUP1) and is classified as a member of the ChUP family. Although systemic RNAi is not an evolutionarily conserved process, the sid gene products are found across the animal kingdom, suggesting the existence of other novel gene regulatory mechanisms mediated by small non-coding RNAs. Human homologs of sid gene products-hSIDT1 and hSIDT2-mediate contact-dependent lipophilic small non-coding dsRNA transport. Here, we report the structure of recombinant human SIDT1. We find that the extra-cytosolic domain of hSIDT1 adopts a double jelly roll fold, and the transmembrane domain exists as two modules-a flexible lipid binding domain and a rigid transmembrane domain core. Our structural analyses provide insights into the inherent conformational dynamics within the lipid binding domain in ChUP family members.
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Affiliation(s)
- Vikas Navratna
- https://ror.org/00jmfr291 Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
- https://ror.org/00jmfr291 Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | | | - Jaimin K Rana
- https://ror.org/00jmfr291 Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
- https://ror.org/00jmfr291 Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Shyamal Mosalaganti
- https://ror.org/00jmfr291 Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
- https://ror.org/00jmfr291 Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
- https://ror.org/00jmfr291 Department of Biophysics, College of Literature, Science and the Arts, University of Michigan, Ann Arbor, MI, USA
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4
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Rowland RJ, Korolchuk S, Salamina M, Tatum NJ, Ault JR, Hart S, Turkenburg JP, Blaza JN, Noble MEM, Endicott JA. Cryo-EM structure of the CDK2-cyclin A-CDC25A complex. Nat Commun 2024; 15:6807. [PMID: 39122719 PMCID: PMC11316097 DOI: 10.1038/s41467-024-51135-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 07/22/2024] [Indexed: 08/12/2024] Open
Abstract
The cell division cycle 25 phosphatases CDC25A, B and C regulate cell cycle transitions by dephosphorylating residues in the conserved glycine-rich loop of CDKs to activate their activity. Here, we present the cryo-EM structure of CDK2-cyclin A in complex with CDC25A at 2.7 Å resolution, providing a detailed structural analysis of the overall complex architecture and key protein-protein interactions that underpin this 86 kDa complex. We further identify a CDC25A C-terminal helix that is critical for complex formation. Sequence conservation analysis suggests CDK1/2-cyclin A, CDK1-cyclin B and CDK2/3-cyclin E are suitable binding partners for CDC25A, whilst CDK4/6-cyclin D complexes appear unlikely substrates. A comparative structural analysis of CDK-containing complexes also confirms the functional importance of the conserved CDK1/2 GDSEID motif. This structure improves our understanding of the roles of CDC25 phosphatases in CDK regulation and may inform the development of CDC25-targeting anticancer strategies.
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Affiliation(s)
- Rhianna J Rowland
- Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle University, Paul O'Gorman Building, Framlington Place, Newcastle upon Tyne, NE2 4HH, UK
| | - Svitlana Korolchuk
- Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle University, Paul O'Gorman Building, Framlington Place, Newcastle upon Tyne, NE2 4HH, UK
- Fujifilm, Belasis Ave, Stockton-on-Tees, Billingham, TS23 1LH, UK
| | - Marco Salamina
- Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle University, Paul O'Gorman Building, Framlington Place, Newcastle upon Tyne, NE2 4HH, UK
- Evotec (UK) Ltd., Milton, Abingdon, OX14 4RZ, UK
| | - Natalie J Tatum
- Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle University, Paul O'Gorman Building, Framlington Place, Newcastle upon Tyne, NE2 4HH, UK
| | - James R Ault
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Sam Hart
- York Structural Biology Laboratory and York Biomedical Research Institute, Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK
| | - Johan P Turkenburg
- York Structural Biology Laboratory and York Biomedical Research Institute, Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK
| | - James N Blaza
- York Structural Biology Laboratory and York Biomedical Research Institute, Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK
| | - Martin E M Noble
- Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle University, Paul O'Gorman Building, Framlington Place, Newcastle upon Tyne, NE2 4HH, UK.
| | - Jane A Endicott
- Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle University, Paul O'Gorman Building, Framlington Place, Newcastle upon Tyne, NE2 4HH, UK.
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5
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McCallum M, Park YJ, Stewart C, Sprouse KR, Addetia A, Brown J, Tortorici MA, Gibson C, Wong E, Ieven M, Telenti A, Veesler D. Human coronavirus HKU1 recognition of the TMPRSS2 host receptor. Cell 2024; 187:4231-4245.e13. [PMID: 38964328 DOI: 10.1016/j.cell.2024.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 04/26/2024] [Accepted: 06/05/2024] [Indexed: 07/06/2024]
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. 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 orthologous proteases. We identified TMPRSS2 orthologs from five mammalian orders promoting HKU1 S-mediated entry into cells along with key residues governing host receptor usage. Our data show that the TMPRSS2 binding motif is a site of vulnerability to neutralizing antibodies and suggest that HKU1 uses S 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, WA, USA
| | - Young-Jun Park
- Department of Biochemistry, University of Washington, Seattle, WA, USA; Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Cameron Stewart
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Kaitlin R Sprouse
- Department of Biochemistry, University of Washington, Seattle, WA, USA; Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Amin Addetia
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Jack Brown
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | | | - Cecily Gibson
- Department of Biochemistry, University of Washington, Seattle, WA, 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, WA, USA; Howard Hughes Medical Institute, Seattle, WA 98195, USA.
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6
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Knight KM, Krumm BE, Kapolka NJ, Ludlam WG, Cui M, Mani S, Prytkova I, Obarow EG, Lefevre TJ, Wei W, Ma N, Huang XP, Fay JF, Vaidehi N, Smrcka AV, Slesinger PA, Logothetis DE, Martemyanov KA, Roth BL, Dohlman HG. A neurodevelopmental disorder mutation locks G proteins in the transitory pre-activated state. Nat Commun 2024; 15:6643. [PMID: 39103320 DOI: 10.1038/s41467-024-50964-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 07/25/2024] [Indexed: 08/07/2024] Open
Abstract
Many neurotransmitter receptors activate G proteins through exchange of GDP for GTP. The intermediate nucleotide-free state has eluded characterization, due largely to its inherent instability. Here we characterize a G protein variant associated with a rare neurological disorder in humans. GαoK46E has a charge reversal that clashes with the phosphate groups of GDP and GTP. As anticipated, the purified protein binds poorly to guanine nucleotides yet retains wild-type affinity for G protein βγ subunits. In cells with physiological concentrations of nucleotide, GαoK46E forms a stable complex with receptors and Gβγ, impeding effector activation. Further, we demonstrate that the mutant can be easily purified in complex with dopamine-bound D2 receptors, and use cryo-electron microscopy to determine the structure, including both domains of Gαo, without nucleotide or stabilizing nanobodies. These findings reveal the molecular basis for the first committed step of G protein activation, establish a mechanistic basis for a neurological disorder, provide a simplified strategy to determine receptor-G protein structures, and a method to detect high affinity agonist binding in cells.
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Affiliation(s)
- Kevin M Knight
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Neuroscience, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, University of Florida, Jupiter, FL, USA
| | - Brian E Krumm
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Nicholas J Kapolka
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - W Grant Ludlam
- Department of Neuroscience, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, University of Florida, Jupiter, FL, USA
| | - Meng Cui
- Department of Pharmaceutical Sciences Northeastern University, Boston, MA, USA
| | - Sepehr Mani
- Department of Pharmaceutical Sciences Northeastern University, Boston, MA, USA
| | - Iya Prytkova
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Elizabeth G Obarow
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Tyler J Lefevre
- Department of Pharmacology, University of Michigan, Ann Arbor, MI, USA
| | - Wenyuan Wei
- Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, CA, USA
| | - Ning Ma
- Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, CA, USA
| | - Xi-Ping Huang
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jonathan F Fay
- Department of Biochemistry and Molecular Biology, School of Medicine, University of Maryland, Baltimore, Baltimore, MD, USA
| | - Nagarajan Vaidehi
- Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, CA, USA
| | - Alan V Smrcka
- Department of Pharmacology, University of Michigan, Ann Arbor, MI, USA
| | - Paul A Slesinger
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Kirill A Martemyanov
- Department of Neuroscience, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, University of Florida, Jupiter, FL, USA
| | - Bryan L Roth
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Henrik G Dohlman
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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7
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Yin Y, Park CG, Zhang F, G. Fedor J, Feng S, Suo Y, Im W, Lee SY. Mechanisms of sensory adaptation and inhibition of the cold and menthol receptor TRPM8. SCIENCE ADVANCES 2024; 10:eadp2211. [PMID: 39093967 PMCID: PMC11296349 DOI: 10.1126/sciadv.adp2211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 06/28/2024] [Indexed: 08/04/2024]
Abstract
Our sensory adaptation to cold and chemically induced coolness is mediated by the intrinsic property of TRPM8 channels to desensitize. TRPM8 is also implicated in cold-evoked pain disorders and migraine, highlighting its inhibitors as an avenue for pain relief. Despite the importance, the mechanisms of TRPM8 desensitization and inhibition remained unclear. We found, using cryo-electron microscopy, electrophysiology, and molecular dynamics simulations, that TRPM8 inhibitors bind selectively to the desensitized state of the channel. These inhibitors were used to reveal the overlapping mechanisms of desensitization and inhibition and that cold and cooling agonists share a common desensitization pathway. Furthermore, we identified the structural determinants crucial for the conformational change in TRPM8 desensitization. Our study illustrates how receptor-level conformational changes alter cold sensation, providing insights into therapeutic development.
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Affiliation(s)
- Ying Yin
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Cheon-Gyu Park
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Feng Zhang
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Justin G. Fedor
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Shasha Feng
- Department of Biological Sciences, Lehigh University, Bethlehem, PA 18015, USA
| | - Yang Suo
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
| | - Wonpil Im
- Department of Biological Sciences, Lehigh University, Bethlehem, PA 18015, USA
| | - Seok-Yong Lee
- Department of Biochemistry, Duke University School of Medicine, Durham, NC 27710, USA
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8
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Lyu Y, Fu C, Ma H, Su Z, Sun Z, Zhou X. Engineering of a mammalian VMAT2 for cryo-EM analysis results in non-canonical protein folding. Nat Commun 2024; 15:6511. [PMID: 39095428 PMCID: PMC11297040 DOI: 10.1038/s41467-024-50934-5] [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: 01/12/2024] [Accepted: 07/24/2024] [Indexed: 08/04/2024] Open
Abstract
Vesicular monoamine transporter 2 (VMAT2) belongs to the major facilitator superfamily (MFS), and mediates cytoplasmic monoamine packaging into presynaptic vesicles. Here, we present two cryo-EM structures of VMAT2, with a frog VMAT2 adopting a canonical MFS fold and an engineered sheep VMAT2 adopting a non-canonical fold. Both VMAT2 proteins mediate uptake of a selective fluorescent VMAT2 substrate into cells. Molecular docking, substrate binding and transport analysis reveal potential substrate binding mechanism in VMAT2. Meanwhile, caution is advised when interpreting engineered membrane protein structures.
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Affiliation(s)
- Ying Lyu
- Department of Integrated Traditional Chinese and Western Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Chunting Fu
- Department of Integrated Traditional Chinese and Western Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Haiyun Ma
- State Key Laboratory of Biotherapy, Department of Geriatrics and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Zhaoming Su
- State Key Laboratory of Biotherapy, Department of Geriatrics and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China.
| | - Ziyi Sun
- Department of Integrated Traditional Chinese and Western Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China.
| | - Xiaoming Zhou
- Department of Integrated Traditional Chinese and Western Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China.
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9
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Ravala SK, Adame-Garcia SR, Li S, Chen CL, Cianfrocco MA, Silvio Gutkind J, Cash JN, Tesmer JJG. Structural and dynamic changes in P-Rex1 upon activation by PIP 3 and inhibition by IP 4. eLife 2024; 12:RP92822. [PMID: 39082940 PMCID: PMC11290822 DOI: 10.7554/elife.92822] [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: 08/02/2024] Open
Abstract
PIP3-dependent Rac exchanger 1 (P-Rex1) is abundantly expressed in neutrophils and plays central roles in chemotaxis and cancer metastasis by serving as a guanine-nucleotide exchange factor (GEF) for Rac. The enzyme is synergistically activated by PIP3 and heterotrimeric Gβγ subunits, but mechanistic details remain poorly understood. While investigating the regulation of P-Rex1 by PIP3, we discovered that Ins(1,3,4,5)P4 (IP4) inhibits P-Rex1 activity and induces large decreases in backbone dynamics in diverse regions of the protein. Cryo-electron microscopy analysis of the P-Rex1·IP4 complex revealed a conformation wherein the pleckstrin homology (PH) domain occludes the active site of the Dbl homology (DH) domain. This configuration is stabilized by interactions between the first DEP domain (DEP1) and the DH domain and between the PH domain and a 4-helix bundle (4HB) subdomain that extends from the C-terminal domain of P-Rex1. Disruption of the DH-DEP1 interface in a DH/PH-DEP1 fragment enhanced activity and led to a more extended conformation in solution, whereas mutations that constrain the occluded conformation led to decreased GEF activity. Variants of full-length P-Rex1 in which the DH-DEP1 and PH-4HB interfaces were disturbed exhibited enhanced activity during chemokine-induced cell migration, confirming that the observed structure represents the autoinhibited state in living cells. Interactions with PIP3-containing liposomes led to disruption of these interfaces and increased dynamics protein-wide. Our results further suggest that inositol phosphates such as IP4 help to inhibit basal P-Rex1 activity in neutrophils, similar to their inhibitory effects on phosphatidylinositol-3-kinase.
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Affiliation(s)
- Sandeep K Ravala
- Departments of Biological Sciences and of Medicinal Chemistry and Molecular Pharmacology, Purdue UniversityWest LafayetteUnited States
| | - Sendi Rafael Adame-Garcia
- Department of Pharmacology and Moores Cancer Center, University of California, San DiegoSan DiegoUnited States
| | - Sheng Li
- Department of Medicine, University of California, San DiegoLa JollaUnited States
| | - Chun-Liang Chen
- Departments of Biological Sciences and of Medicinal Chemistry and Molecular Pharmacology, Purdue UniversityWest LafayetteUnited States
| | - Michael A Cianfrocco
- Department of Biological Chemistry, University of MichiganAnn ArborUnited States
| | - J Silvio Gutkind
- Department of Pharmacology and Moores Cancer Center, University of California, San DiegoSan DiegoUnited States
| | - Jennifer N Cash
- Department of Molecular and Cellular Biology, University of California, DavisDavisUnited States
| | - John JG Tesmer
- Departments of Biological Sciences and of Medicinal Chemistry and Molecular Pharmacology, Purdue UniversityWest LafayetteUnited States
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10
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Zhou BR, Feng H, Huang F, Zhu I, Portillo-Ledesma S, Shi D, Zaret KS, Schlick T, Landsman D, Wang Q, Bai Y. Structural insights into the cooperative nucleosome recognition and chromatin opening by FOXA1 and GATA4. Mol Cell 2024:S1097-2765(24)00592-6. [PMID: 39121853 DOI: 10.1016/j.molcel.2024.07.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 06/10/2024] [Accepted: 07/16/2024] [Indexed: 08/12/2024]
Abstract
Mouse FOXA1 and GATA4 are prototypes of pioneer factors, initiating liver cell development by binding to the N1 nucleosome in the enhancer of the ALB1 gene. Using cryoelectron microscopy (cryo-EM), we determined the structures of the free N1 nucleosome and its complexes with FOXA1 and GATA4, both individually and in combination. We found that the DNA-binding domains of FOXA1 and GATA4 mainly recognize the linker DNA and an internal site in the nucleosome, respectively, whereas their intrinsically disordered regions interact with the acidic patch on histone H2A-H2B. FOXA1 efficiently enhances GATA4 binding by repositioning the N1 nucleosome. In vivo DNA editing and bioinformatics analyses suggest that the co-binding mode of FOXA1 and GATA4 plays important roles in regulating genes involved in liver cell functions. Our results reveal the mechanism whereby FOXA1 and GATA4 cooperatively bind to the nucleosome through nucleosome repositioning, opening chromatin by bending linker DNA and obstructing nucleosome packing.
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Affiliation(s)
- Bing-Rui Zhou
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Hanqiao Feng
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Furong Huang
- Department of Pathology and Duke Cancer Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Iris Zhu
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20892, USA
| | - Stephanie Portillo-Ledesma
- Department of Chemistry, New York University, 100 Washington Square East, Silver Building, New York, NY 10003, USA; Simons Center for Computational Physical Chemistry, New York University, 24 Waverly Place, Silver Building, New York, NY 10003, USA
| | - Dan Shi
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Kenneth S Zaret
- Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Cell and Development Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Tamar Schlick
- Department of Chemistry, New York University, 100 Washington Square East, Silver Building, New York, NY 10003, USA; Simons Center for Computational Physical Chemistry, New York University, 24 Waverly Place, Silver Building, New York, NY 10003, USA; Courant Institute of Mathematical Sciences, New York University, 251 Mercer St., New York, NY 10012, USA; New York University-East China Normal University Center for Computational Chemistry, New York University Shanghai, Shanghai 200122, China
| | - David Landsman
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20892, USA
| | - Qianben Wang
- Department of Pathology and Duke Cancer Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Yawen Bai
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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11
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Li H, Teng J, Hibbs RE. Structural switch in acetylcholine receptors in developing muscle. Nature 2024:10.1038/s41586-024-07774-6. [PMID: 39085615 DOI: 10.1038/s41586-024-07774-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 07/02/2024] [Indexed: 08/02/2024]
Abstract
During development, motor neurons originating in the brainstem and spinal cord form elaborate synapses with skeletal muscle fibres1. These neurons release acetylcholine (ACh), which binds to nicotinic ACh receptors (AChRs) on the muscle, initiating contraction. Two types of AChR are present in developing muscle cells, and their differential expression serves as a hallmark of neuromuscular synapse maturation2-4. The structural principles underlying the switch from fetal to adult muscle receptors are unknown. Here, we present high-resolution structures of both fetal and adult muscle nicotinic AChRs, isolated from bovine skeletal muscle in developmental transition. These structures, obtained in the absence and presence of ACh, provide a structural context for understanding how fetal versus adult receptor isoforms are tuned for synapse development versus the all-or-none signalling required for high-fidelity skeletal muscle contraction. We find that ACh affinity differences are driven by binding site access, channel conductance is tuned by widespread surface electrostatics and open duration changes result from intrasubunit interactions and structural flexibility. The structures further reveal pathogenic mechanisms underlying congenital myasthenic syndromes.
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Affiliation(s)
- Huanhuan Li
- Department of Neurobiology, University of California San Diego, La Jolla, CA, USA
| | - Jinfeng Teng
- Department of Neurobiology, University of California San Diego, La Jolla, CA, USA
| | - Ryan E Hibbs
- Department of Neurobiology, University of California San Diego, La Jolla, CA, USA.
- Department of Pharmacology, University of California San Diego, La Jolla, CA, USA.
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12
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Li X, Huang G, Zhu L, Hao C, Sui SF, Qin X. Structure of the red-shifted Fittonia albivenis photosystem I. Nat Commun 2024; 15:6325. [PMID: 39060282 PMCID: PMC11282222 DOI: 10.1038/s41467-024-50655-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 07/11/2024] [Indexed: 07/28/2024] Open
Abstract
Photosystem I (PSI) from Fittonia albivenis, an Acanthaceae ornamental plant, is notable among green plants for its red-shifted emission spectrum. Here, we solved the structure of a PSI-light harvesting complex I (LHCI) supercomplex from F. albivenis at 2.46-Å resolution using cryo-electron microscopy. The supercomplex contains a core complex of 14 subunits and an LHCI belt with four antenna subunits (Lhca1-4) similar to previously reported angiosperm PSI-LHCI structures; however, Lhca3 differs in three regions surrounding a dimer of low-energy chlorophylls (Chls) termed red Chls, which absorb far-red beyond visible light. The unique amino acid sequences within these regions are exclusively shared by plants with strongly red-shifted fluorescence emission, suggesting candidate structural elements for regulating the energy state of red Chls. These results provide a structural basis for unraveling the mechanisms of light harvest and transfer in PSI-LHCI of under canopy plants and for designing Lhc to harness longer-wavelength light in the far-red spectral range.
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Affiliation(s)
- Xiuxiu Li
- School of Chemistry and Chemical Engineering, School of Biological Science and Technology, University of Jinan, Jinan, China
| | - Guoqiang Huang
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China
- Multiscale Research Institute of Complex Systems, Fudan University, Shanghai, China
| | - Lixia Zhu
- School of Chemistry and Chemical Engineering, School of Biological Science and Technology, University of Jinan, Jinan, China
| | - Chenyang Hao
- School of Chemistry and Chemical Engineering, School of Biological Science and Technology, University of Jinan, Jinan, China
| | - Sen-Fang Sui
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing, China.
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.
| | - Xiaochun Qin
- School of Chemistry and Chemical Engineering, School of Biological Science and Technology, University of Jinan, Jinan, China.
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13
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Zhan X, Lu Y, Shi Y. Molecular basis for the activation of human spliceosome. Nat Commun 2024; 15:6348. [PMID: 39068178 PMCID: PMC11283556 DOI: 10.1038/s41467-024-50785-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Accepted: 07/20/2024] [Indexed: 07/30/2024] Open
Abstract
The spliceosome executes pre-mRNA splicing through four sequential stages: assembly, activation, catalysis, and disassembly. Activation of the spliceosome, namely remodeling of the pre-catalytic spliceosome (B complex) into the activated spliceosome (Bact complex) and the catalytically activated spliceosome (B* complex), involves major flux of protein components and structural rearrangements. Relying on a splicing inhibitor, we have captured six intermediate states between the B and B* complexes: pre-Bact, Bact-I, Bact-II, Bact-III, Bact-IV, and post-Bact. Their cryo-EM structures, together with an improved structure of the catalytic step I spliceosome (C complex), reveal how the catalytic center matures around the internal stem loop of U6 snRNA, how the branch site approaches 5'-splice site, how the RNA helicase PRP2 rearranges to bind pre-mRNA, and how U2 snRNP undergoes remarkable movement to facilitate activation. We identify a previously unrecognized key role of PRP2 in spliceosome activation. Our study recapitulates a molecular choreography of the human spliceosome during its catalytic activation.
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Affiliation(s)
- Xiechao Zhan
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China.
- Research Center for Industries of the Future, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China.
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China.
| | - Yichen Lu
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
- Research Center for Industries of the Future, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China
- College of Life Sciences, Fudan University, Shanghai, China
| | - Yigong Shi
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China.
- Research Center for Industries of the Future, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China.
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China.
- Beijing Frontier Research Center for Biological Structure, Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China.
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14
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Zhu D, Cao W, Li J, Wu C, Cao D, Zhang X. Correction of preferred orientation-induced distortion in cryo-electron microscopy maps. SCIENCE ADVANCES 2024; 10:eadn0092. [PMID: 39058771 DOI: 10.1126/sciadv.adn0092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 06/06/2024] [Indexed: 07/28/2024]
Abstract
Reconstruction maps of cryo-electron microscopy (cryo-EM) exhibit distortion when the cryo-EM dataset is incomplete, usually caused by unevenly distributed orientations. Prior efforts had been attempted to address this preferred orientation problem using tilt-collection strategy and modifications to grids or to air-water interfaces. However, these approaches often require time-consuming experiments, and the effect was always protein dependent. Here, we developed a procedure containing removing misaligned particles and an iterative reconstruction method based on signal-to-noise ratio of Fourier component to correct this distortion by recovering missing data using a purely computational algorithm. This procedure called signal-to-noise ratio iterative reconstruction method (SIRM) was applied on incomplete datasets of various proteins to fix distortion in cryo-EM maps and to a more isotropic resolution. In addition, SIRM provides a better reference map for further reconstruction refinements, resulting in an improved alignment, which ultimately improves map quality and benefits model building.
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Affiliation(s)
- Dongjie Zhu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101 Beijing, China
| | - Weili Cao
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101 Beijing, China
- University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Junxi Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101 Beijing, China
- University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Chunling Wu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101 Beijing, China
- University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Duanfang Cao
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101 Beijing, China
- University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Xinzheng Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 100101 Beijing, China
- University of Chinese Academy of Sciences, 100049 Beijing, China
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15
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Fan W, Xu Y, He X, Luo P, Zhu J, Li J, Wang R, Yuan Q, Wu K, Hu W, Zhao Y, Xu S, Cheng X, Wang Y, Xu HE, Zhuang Y. Molecular basis for the activation of PAF receptor by PAF. Cell Rep 2024; 43:114422. [PMID: 38943642 DOI: 10.1016/j.celrep.2024.114422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 05/07/2024] [Accepted: 06/14/2024] [Indexed: 07/01/2024] Open
Abstract
Platelet-activating factor (PAF) is a potent phospholipid mediator crucial in multiple inflammatory and immune responses through binding and activating the PAF receptor (PAFR). However, drug development targeting the PAFR has been limited, partly due to an incomplete understanding of its activation mechanism. Here, we present a 2.9-Å structure of the PAF-bound PAFR-Gi complex. Structural and mutagenesis analyses unveil a specific binding mode of PAF, with the choline head forming cation-π interactions within PAFR hydrophobic pocket, while the alkyl tail penetrates deeply into an aromatic cleft between TM4 and TM5. Binding of PAF modulates conformational changes in key motifs of PAFR, triggering the outward movement of TM6, TM7, and helix 8 for G protein coupling. Molecular dynamics simulation suggests a membrane-side pathway for PAF entry into PAFR via the TM4-TM5 cavity. By providing molecular insights into PAFR signaling, this work contributes a foundation for developing therapeutic interventions targeting PAF signal axis.
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Affiliation(s)
- Wenjia Fan
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210046, China; The State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Youwei Xu
- The State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Xinheng He
- The State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ping Luo
- The State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Jingpeng Zhu
- The State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Junrui Li
- The State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Ruolan Wang
- The State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qingning Yuan
- The State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; The Shanghai Advanced Electron Microscope Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Kai Wu
- The State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; The Shanghai Advanced Electron Microscope Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Wen Hu
- The State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; The Shanghai Advanced Electron Microscope Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Yuxi Zhao
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210046, China; The State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Shiqi Xu
- The State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Xi Cheng
- The State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yue Wang
- The State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.
| | - H Eric Xu
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210046, China; The State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Youwen Zhuang
- The State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; Medicinal Bioinformatics Center, School of Medicine, Shanghai Jiao Tong University, Shanghai 200025, China.
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16
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Planchais C, Fernández I, Chalopin B, Bruel T, Rosenbaum P, Beretta M, Dimitrov JD, Conquet L, Donati F, Prot M, Porrot F, Planas D, Staropoli I, Guivel-Benhassine F, Baquero E, van der Werf S, Haouz A, Simon-Lorière E, Montagutelli X, Maillère B, Rey FA, Guardado-Calvo P, Nozach H, Schwartz O, Mouquet H. Broad sarbecovirus neutralization by combined memory B cell antibodies to ancestral SARS-CoV-2. iScience 2024; 27:110354. [PMID: 39071888 PMCID: PMC11277385 DOI: 10.1016/j.isci.2024.110354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 05/27/2024] [Accepted: 06/20/2024] [Indexed: 07/30/2024] Open
Abstract
Antibodies play a pivotal role in protecting from SARS-CoV-2 infection, but their efficacy is challenged by the continuous emergence of viral variants. In this study, we describe two broadly neutralizing antibodies cloned from the memory B cells of a single convalescent individual after infection with ancestral SARS-CoV-2. Cv2.3194, a resilient class 1 anti-RBD antibody, remains active against Omicron sub-variants up to BA.2.86. Cv2.3132, a near pan-Sarbecovirus neutralizer, targets the heptad repeat 2 membrane proximal region. When combined, Cv2.3194 and Cv2.3132 form a complementary SARS-CoV-2 neutralizing antibody cocktail exhibiting a local dose-dependent synergy. Thus, remarkably robust neutralizing memory B cell antibodies elicited in response to ancestral SARS-CoV-2 infection can withstand viral evolution and immune escape. The cooperative effect of such antibody combination may confer a certain level of protection against the latest SARS-CoV-2 variants.
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Affiliation(s)
- Cyril Planchais
- Institut Pasteur, Université Paris Cité, INSERM U1222, Humoral Immunology Unit, 75015 Paris, France
| | - Ignacio Fernández
- Institut Pasteur, Université Paris Cité, Structural Virology Unit, 75015 Paris, France
- CNRS UMR3569, 75015 Paris, France
| | - Benjamin Chalopin
- CEA, INRAE, Medicines and Healthcare Technologies Department, SIMoS, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Timothée Bruel
- CNRS UMR3569, 75015 Paris, France
- Institut Pasteur, Université Paris Cité, Virus & Immunity Unit, 75015 Paris, France
| | - Pierre Rosenbaum
- Institut Pasteur, Université Paris Cité, INSERM U1222, Humoral Immunology Unit, 75015 Paris, France
| | - Maxime Beretta
- Institut Pasteur, Université Paris Cité, INSERM U1222, Humoral Immunology Unit, 75015 Paris, France
| | - Jordan D. Dimitrov
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université de Paris, 75006 Paris, France
| | - Laurine Conquet
- Institut Pasteur, Université Paris Cité, Mouse Genetics Laboratory, 75015 Paris, France
| | - Flora Donati
- Institut Pasteur, Université Paris Cité, G5 Evolutionary Genomics of RNA Viruses, 75015 Paris, France
- National Reference Center for Respiratory Viruses, Institut Pasteur, 75015 Paris, France
| | - Matthieu Prot
- Institut Pasteur, Université Paris Cité, G5 Evolutionary Genomics of RNA Viruses, 75015 Paris, France
| | - Françoise Porrot
- CNRS UMR3569, 75015 Paris, France
- Institut Pasteur, Université Paris Cité, Virus & Immunity Unit, 75015 Paris, France
| | - Delphine Planas
- CNRS UMR3569, 75015 Paris, France
- Institut Pasteur, Université Paris Cité, Virus & Immunity Unit, 75015 Paris, France
| | - Isabelle Staropoli
- CNRS UMR3569, 75015 Paris, France
- Institut Pasteur, Université Paris Cité, Virus & Immunity Unit, 75015 Paris, France
| | - Florence Guivel-Benhassine
- CNRS UMR3569, 75015 Paris, France
- Institut Pasteur, Université Paris Cité, Virus & Immunity Unit, 75015 Paris, France
| | - Eduard Baquero
- Institut Pasteur, Université Paris Cité, Structural Virology Unit, 75015 Paris, France
- CNRS UMR3569, 75015 Paris, France
| | - Sylvie van der Werf
- CNRS UMR3569, 75015 Paris, France
- National Reference Center for Respiratory Viruses, Institut Pasteur, 75015 Paris, France
- Institut Pasteur, Université Paris Cité, Molecular Genetics of RNA Viruses, 75015 Paris, France
| | - Ahmed Haouz
- Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Cristallography Platform-C2RT, 75015 Paris, France
| | - Etienne Simon-Lorière
- Institut Pasteur, Université Paris Cité, G5 Evolutionary Genomics of RNA Viruses, 75015 Paris, France
- National Reference Center for Respiratory Viruses, Institut Pasteur, 75015 Paris, France
| | - Xavier Montagutelli
- Institut Pasteur, Université Paris Cité, Mouse Genetics Laboratory, 75015 Paris, France
| | - Bernard Maillère
- CEA, INRAE, Medicines and Healthcare Technologies Department, SIMoS, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Félix A. Rey
- Institut Pasteur, Université Paris Cité, Structural Virology Unit, 75015 Paris, France
- CNRS UMR3569, 75015 Paris, France
| | - Pablo Guardado-Calvo
- Institut Pasteur, Université Paris Cité, Structural Virology Unit, 75015 Paris, France
- CNRS UMR3569, 75015 Paris, France
| | - Hervé Nozach
- CEA, INRAE, Medicines and Healthcare Technologies Department, SIMoS, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Olivier Schwartz
- CNRS UMR3569, 75015 Paris, France
- Institut Pasteur, Université Paris Cité, Virus & Immunity Unit, 75015 Paris, France
| | - Hugo Mouquet
- Institut Pasteur, Université Paris Cité, INSERM U1222, Humoral Immunology Unit, 75015 Paris, France
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17
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Wang H, Tarsio M, Kane PM, Rubinstein JL. Structure of yeast RAVE bound to a partial V 1 complex. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.18.604153. [PMID: 39071316 PMCID: PMC11275763 DOI: 10.1101/2024.07.18.604153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Vacuolar-type ATPases (V-ATPases) are membrane-embedded proton pumps that acidify intracellular compartments in almost all eukaryotic cells. Homologous with ATP synthases, these multi-subunit enzymes consist of a soluble catalytic V 1 subcomplex and a membrane-embedded proton-translocating V O subcomplex. The V 1 and V O subcomplexes can undergo reversible dissociation to regulate proton pumping, with reassociation of V 1 and V O requiring the protein complex known as RAVE (regulator of the A TPase of v acuoles and e ndosomes). In the yeast Saccharomyces cerevisiae , RAVE consists of subunits Rav1p, Rav2p, and Skp1p. We used electron cryomicroscopy (cryo-EM) to determine a structure of yeast RAVE bound to V 1 . In the structure, RAVE is a L-shaped complex with Rav2p pointing toward the membrane and Skp1p distant from both the membrane and V 1 . Only Rav1p interacts with V 1 , binding to a region of subunit A not found in the corresponding ATP synthase subunit. When bound to RAVE, V 1 is in a rotational state suitable for binding the free V O complex, but it is partially disrupted in the structure, missing five of its 16 subunits. Other than these missing subunits and the conformation of the inhibitory subunit H, the V 1 complex with RAVE appears poised for reassembly with V O .
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18
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Pedersen CN, Yang F, Ita S, Xu Y, Akunuri R, Trampari S, Neumann CMT, Desdorf LM, Schiøtt B, Salvino JM, Mortensen OV, Nissen P, Shahsavar A. Cryo-EM structure of the dopamine transporter with a novel atypical non-competitive inhibitor bound to the orthosteric site. J Neurochem 2024. [PMID: 39010681 DOI: 10.1111/jnc.16179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Revised: 06/28/2024] [Accepted: 07/01/2024] [Indexed: 07/17/2024]
Abstract
The regulation of dopamine (DA) removal from the synaptic cleft is a crucial process in neurotransmission and is facilitated by the sodium- and chloride-coupled dopamine transporter DAT. Psychostimulant drugs, cocaine, and amphetamine, both block the uptake of DA, while amphetamine also triggers the release of DA. As a result, they prolong or even amplify neurotransmitter signaling. Atypical inhibitors of DAT lack cocaine-like rewarding effects and offer a promising strategy for the treatment of drug use disorders. Here, we present the 3.2 Å resolution cryo-electron microscopy structure of the Drosophila melanogaster dopamine transporter (dDAT) in complex with the atypical non-competitive inhibitor AC-4-248. The inhibitor partially binds at the central binding site, extending into the extracellular vestibule, and locks the transporter in an outward open conformation. Our findings propose mechanisms for the non-competitive inhibition of DAT and attenuation of cocaine potency by AC-4-248 and provide a basis for the rational design of more efficacious atypical inhibitors.
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Affiliation(s)
- Clara Nautrup Pedersen
- DANDRITE, Nordic EMBL Partnership for Molecular Medicine, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Fuyu Yang
- Department of Pharmacology and Physiology, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA
| | - Samantha Ita
- Department of Pharmacology and Physiology, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA
| | - Yibin Xu
- Department of Pharmacology and Physiology, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA
| | | | - Sofia Trampari
- DANDRITE, Nordic EMBL Partnership for Molecular Medicine, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Caroline Marie Teresa Neumann
- DANDRITE, Nordic EMBL Partnership for Molecular Medicine, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | | | - Birgit Schiøtt
- Department of Chemistry, Aarhus University, Aarhus, Denmark
| | | | - Ole Valente Mortensen
- Department of Pharmacology and Physiology, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA
| | - Poul Nissen
- DANDRITE, Nordic EMBL Partnership for Molecular Medicine, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Azadeh Shahsavar
- DANDRITE, Nordic EMBL Partnership for Molecular Medicine, Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
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19
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Drulyte I, Ghai R, Ow SY, Kapp EA, Quek AJ, Panousis C, Wilson MJ, Nash AD, Pelzing M. Structural basis for the inhibition of βFXIIa by garadacimab. Structure 2024:S0969-2126(24)00239-9. [PMID: 39059382 DOI: 10.1016/j.str.2024.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 05/24/2024] [Accepted: 07/01/2024] [Indexed: 07/28/2024]
Abstract
Activated FXII (FXIIa) is the principal initiator of the plasma contact system and can activate both procoagulant and proinflammatory pathways. Its activity is important in the pathophysiology of hereditary angioedema (HAE). Here, we describe a high-resolution cryoelectron microscopy (cryo-EM) structure of the beta-chain from FXIIa (βFXIIa) complexed with the Fab fragment of garadacimab. Garadacimab binds to βFXIIa through an unusually long CDR-H3 that inserts into the S1 pocket in a non-canonical way. This structural mechanism is likely the primary contributor to the inhibition of activated FXIIa proteolytic activity in HAE. Garadacimab Fab-βFXIIa structure also reveals critical determinants of high-affinity binding of garadacimab to activated FXIIa. Structural analysis with other bona fide FXIIa inhibitors, such as benzamidine and C1-INH, reveals a surprisingly similar mechanism of βFXIIa inhibition by garadacimab. In summary, the garadacimab Fab-βFXIIa structure provides crucial insights into its mechanism of action and delineates primary and auxiliary paratopes/epitopes.
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Affiliation(s)
- Ieva Drulyte
- Materials and Structural Analysis, Thermo Fisher Scientific, Eindhoven, the Netherlands
| | - Rajesh Ghai
- Research and Development, CSL Limited, Bio21 Molecular Science and Biotechnology Institute, Parkville, Victoria, Australia
| | - Saw Yen Ow
- Research and Development, CSL Limited, Bio21 Molecular Science and Biotechnology Institute, Parkville, Victoria, Australia
| | - Eugene A Kapp
- Research and Development, CSL Limited, Bio21 Molecular Science and Biotechnology Institute, Parkville, Victoria, Australia
| | - Adam J Quek
- Research and Development, CSL Limited, Bio21 Molecular Science and Biotechnology Institute, Parkville, Victoria, Australia
| | - Con Panousis
- Research and Development, CSL Limited, Bio21 Molecular Science and Biotechnology Institute, Parkville, Victoria, Australia
| | - Michael J Wilson
- Research and Development, CSL Limited, Bio21 Molecular Science and Biotechnology Institute, Parkville, Victoria, Australia
| | - Andrew D Nash
- Research and Development, CSL Limited, Bio21 Molecular Science and Biotechnology Institute, Parkville, Victoria, Australia
| | - Matthias Pelzing
- Research and Development, CSL Limited, Bio21 Molecular Science and Biotechnology Institute, Parkville, Victoria, Australia.
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20
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Coupland CE, Karimi R, Bueler SA, Liang Y, Courbon GM, Di Trani JM, Wong CJ, Saghian R, Youn JY, Wang LY, Rubinstein JL. High-resolution electron cryomicroscopy of V-ATPase in native synaptic vesicles. Science 2024; 385:168-174. [PMID: 38900912 DOI: 10.1126/science.adp5577] [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: 04/01/2024] [Accepted: 05/16/2024] [Indexed: 06/22/2024]
Abstract
Intercellular communication in the nervous system occurs through the release of neurotransmitters into the synaptic cleft between neurons. In the presynaptic neuron, the proton pumping vesicular- or vacuolar-type ATPase (V-ATPase) powers neurotransmitter loading into synaptic vesicles (SVs), with the V1 complex dissociating from the membrane region of the enzyme before exocytosis. We isolated SVs from rat brain using SidK, a V-ATPase-binding bacterial effector protein. Single-particle electron cryomicroscopy allowed high-resolution structure determination of V-ATPase within the native SV membrane. In the structure, regularly spaced cholesterol molecules decorate the enzyme's rotor and the abundant SV protein synaptophysin binds the complex stoichiometrically. ATP hydrolysis during vesicle loading results in a loss of the V1 region of V-ATPase from the SV membrane, suggesting that loading is sufficient to induce dissociation of the enzyme.
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Affiliation(s)
- Claire E Coupland
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 1X1, Canada
| | - Ryan Karimi
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 1X1, Canada
- Department of Medical Biophysics, The University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Stephanie A Bueler
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 1X1, Canada
| | - Yingke Liang
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 1X1, Canada
- Department of Biochemistry, The University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Gautier M Courbon
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 1X1, Canada
- Department of Medical Biophysics, The University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Justin M Di Trani
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 1X1, Canada
| | - Cassandra J Wong
- Lunenfeld-Tanenbaum Research Institute, Toronto, ON M5G 1X5, Canada
| | - Rayan Saghian
- Neuroscience and Mental Health Program, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
- Department of Physiology, The University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Ji-Young Youn
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 1X1, Canada
- Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
- Department of Molecular Genetics, The University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Lu-Yang Wang
- Neuroscience and Mental Health Program, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
- Department of Physiology, The University of Toronto, Toronto, ON M5S 1A8, Canada
| | - John L Rubinstein
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 1X1, Canada
- Department of Medical Biophysics, The University of Toronto, Toronto, ON M5G 1L7, Canada
- Department of Biochemistry, The University of Toronto, Toronto, ON M5S 1A8, Canada
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21
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Kang H, Han AR, Zhang A, Jeong H, Koh W, Lee JM, Lee H, Jo HY, Maria-Solano MA, Bhalla M, Kwon J, Roh WS, Yang J, An HJ, Choi S, Kim HM, Lee CJ. GolpHCat (TMEM87A), a unique voltage-dependent cation channel in Golgi apparatus, contributes to Golgi-pH maintenance and hippocampus-dependent memory. Nat Commun 2024; 15:5830. [PMID: 38992057 PMCID: PMC11239671 DOI: 10.1038/s41467-024-49297-8] [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: 12/14/2023] [Accepted: 05/30/2024] [Indexed: 07/13/2024] Open
Abstract
Impaired ion channels regulating Golgi pH lead to structural alterations in the Golgi apparatus, such as fragmentation, which is found, along with cognitive impairment, in Alzheimer's disease. However, the causal relationship between altered Golgi structure and cognitive impairment remains elusive due to the lack of understanding of ion channels in the Golgi apparatus of brain cells. Here, we identify that a transmembrane protein TMEM87A, renamed Golgi-pH-regulating cation channel (GolpHCat), expressed in astrocytes and neurons that contributes to hippocampus-dependent memory. We find that GolpHCat displays unique voltage-dependent currents, which is potently inhibited by gluconate. Additionally, we gain structural insights into the ion conduction through GolpHCat at the molecular level by determining three high-resolution cryogenic-electron microscopy structures of human GolpHCat. GolpHCat-knockout mice show fragmented Golgi morphology and altered protein glycosylation and functions in the hippocampus, leading to impaired spatial memory. These findings suggest a molecular target for Golgi-related diseases and cognitive impairment.
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Affiliation(s)
- Hyunji Kang
- Center for Cognition and Sociality, Life Science Cluster, Institute for Basic Science (IBS), 55 Expo-ro, Yuseong-gu, Daejeon, 34126, Republic of Korea
- IBS School, University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, 34113, Republic of Korea
| | - Ah-Reum Han
- Center for Biomolecular and Cellular Structure, Life Science Cluster, Institute for Basic Science (IBS), 55 Expo-ro, Yuseong-gu, Daejeon, 34126, Republic of Korea
| | - Aihua Zhang
- Global AI Drug Discovery Center, College of Pharmacy and Graduate School of Pharmaceutical Science, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - Heejin Jeong
- Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, 34134, Korea
| | - Wuhyun Koh
- Center for Cognition and Sociality, Life Science Cluster, Institute for Basic Science (IBS), 55 Expo-ro, Yuseong-gu, Daejeon, 34126, Republic of Korea
| | - Jung Moo Lee
- Center for Cognition and Sociality, Life Science Cluster, Institute for Basic Science (IBS), 55 Expo-ro, Yuseong-gu, Daejeon, 34126, Republic of Korea
| | - Hayeon Lee
- Center for Cognition and Sociality, Life Science Cluster, Institute for Basic Science (IBS), 55 Expo-ro, Yuseong-gu, Daejeon, 34126, Republic of Korea
| | - Hee Young Jo
- Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, 34134, Korea
| | - Miguel A Maria-Solano
- Global AI Drug Discovery Center, College of Pharmacy and Graduate School of Pharmaceutical Science, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - Mridula Bhalla
- Center for Cognition and Sociality, Life Science Cluster, Institute for Basic Science (IBS), 55 Expo-ro, Yuseong-gu, Daejeon, 34126, Republic of Korea
| | - Jea Kwon
- Center for Cognition and Sociality, Life Science Cluster, Institute for Basic Science (IBS), 55 Expo-ro, Yuseong-gu, Daejeon, 34126, Republic of Korea
| | - Woo Suk Roh
- Center for Cognition and Sociality, Life Science Cluster, Institute for Basic Science (IBS), 55 Expo-ro, Yuseong-gu, Daejeon, 34126, Republic of Korea
| | - Jimin Yang
- Center for Biomolecular and Cellular Structure, Life Science Cluster, Institute for Basic Science (IBS), 55 Expo-ro, Yuseong-gu, Daejeon, 34126, Republic of Korea
| | - Hyun Joo An
- Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, 34134, Korea
| | - Sun Choi
- Global AI Drug Discovery Center, College of Pharmacy and Graduate School of Pharmaceutical Science, Ewha Womans University, Seoul, 03760, Republic of Korea.
| | - Ho Min Kim
- Center for Biomolecular and Cellular Structure, Life Science Cluster, Institute for Basic Science (IBS), 55 Expo-ro, Yuseong-gu, Daejeon, 34126, Republic of Korea.
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea.
| | - C Justin Lee
- Center for Cognition and Sociality, Life Science Cluster, Institute for Basic Science (IBS), 55 Expo-ro, Yuseong-gu, Daejeon, 34126, Republic of Korea.
- IBS School, University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, 34113, Republic of Korea.
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22
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Ma CX, Li Y, Liu WT, Li Y, Zhao F, Lian XT, Ding J, Liu SM, Liu XP, Fan BZ, Liu LY, Xue F, Li J, Zhang JR, Xue Z, Pei XT, Lin JZ, Liang JH. Synthetic macrolides overcoming MLS BK-resistant pathogens. Cell Discov 2024; 10:75. [PMID: 38992047 PMCID: PMC11239830 DOI: 10.1038/s41421-024-00702-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Accepted: 06/26/2024] [Indexed: 07/13/2024] Open
Abstract
Conventional macrolide-lincosamide-streptogramin B-ketolide (MLSBK) antibiotics are unable to counter the growing challenge of antibiotic resistance that is conferred by the constitutive methylation of rRNA base A2058 or its G2058 mutation, while the presence of unmodified A2058 is crucial for high selectivity of traditional MLSBK in targeting pathogens over human cells. The absence of effective modes of action reinforces the prevailing belief that constitutively antibiotic-resistant Staphylococcus aureus remains impervious to existing macrolides including telithromycin. Here, we report the design and synthesis of a novel series of macrolides, featuring the strategic fusion of ketolide and quinolone moieties. Our effort led to the discovery of two potent compounds, MCX-219 and MCX-190, demonstrating enhanced antibacterial efficacy against a broad spectrum of formidable pathogens, including A2058-methylated Staphylococcus aureus, Streptococcus pneumoniae, Streptococcus pyogenes, and notably, the clinical Mycoplasma pneumoniae isolates harboring A2058G mutations which are implicated in the recent pneumonia outbreak in China. Mechanistic studies reveal that the modified quinolone moiety of MCX-190 establishes a distinctive secondary binding site within the nascent peptide exit tunnel. Structure-activity relationship analysis underscores the importance of this secondary binding, maintained by a sandwich-like π-π stacking interaction and a water-magnesium bridge, for effective engagement with A2058-methylated ribosomes rather than topoisomerases targeted by quinolone antibiotics. Our findings not only highlight MCX-219 and MCX-190 as promising candidates for next-generation MLSBK antibiotics to combat antibiotic resistance, but also pave the way for the future rational design of the class of MLSBK antibiotics, offering a strategic framework to overcome the challenges posed by escalating antibiotic resistance.
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Affiliation(s)
- Cong-Xuan Ma
- Key Laboratory of Medicinal Molecule Science and Pharmaceutical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
| | - Ye Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
- Center for mRNA Translational Research, Fudan University, Shanghai, China
| | - Wen-Tian Liu
- Key Laboratory of Medicinal Molecule Science and Pharmaceutical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
| | - Yun Li
- Institute of Clinical Pharmacology, Peking University First Hospital, Beijing, China
| | - Fei Zhao
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, State Key Laboratory of Infectious Disease Prevention and Control, Beijing, China
| | - Xiao-Tian Lian
- Key Laboratory of Medicinal Molecule Science and Pharmaceutical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
| | - Jing Ding
- Key Laboratory of Medicinal Molecule Science and Pharmaceutical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
| | - Si-Meng Liu
- Key Laboratory of Medicinal Molecule Science and Pharmaceutical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
| | - Xie-Peng Liu
- Key Laboratory of Medicinal Molecule Science and Pharmaceutical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
| | - Bing-Zhi Fan
- Key Laboratory of Medicinal Molecule Science and Pharmaceutical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
| | - Li-Yong Liu
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, State Key Laboratory of Infectious Disease Prevention and Control, Beijing, China
| | - Feng Xue
- Institute of Clinical Pharmacology, Peking University First Hospital, Beijing, China
| | - Jian Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
- Center for mRNA Translational Research, Fudan University, Shanghai, China
| | - Jue-Ru Zhang
- Key Laboratory of Medicinal Molecule Science and Pharmaceutical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China
| | - Zhao Xue
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
- Center for mRNA Translational Research, Fudan University, Shanghai, China
| | - Xiao-Tong Pei
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
- Center for mRNA Translational Research, Fudan University, Shanghai, China
| | - Jin-Zhong Lin
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai, China.
- Center for mRNA Translational Research, Fudan University, Shanghai, China.
| | - Jian-Hua Liang
- Key Laboratory of Medicinal Molecule Science and Pharmaceutical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, China.
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23
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Vadakkepat AK, Xue S, Redzej A, Smith TK, Ho BT, Waksman G. Cryo-EM structure of the R388 plasmid conjugative pilus reveals a helical polymer characterized by an unusual pilin/phospholipid binary complex. Structure 2024:S0969-2126(24)00227-2. [PMID: 39002540 DOI: 10.1016/j.str.2024.06.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 05/14/2024] [Accepted: 06/18/2024] [Indexed: 07/15/2024]
Abstract
Bacterial conjugation is a process by which DNA is transferred unidirectionally from a donor cell to a recipient cell. It is the main means by which antibiotic resistance genes spread among bacterial populations. It is crucially dependent upon the elaboration of an extracellular appendage, termed "pilus," by a large double-membrane-spanning secretion system termed conjugative "type IV secretion system." Here we present the structure of the conjugative pilus encoded by the R388 plasmid. We demonstrate that, as opposed to all conjugative pili produced so far for cryoelectron microscopy (cryo-EM) structure determination, the conjugative pilus encoded by the R388 plasmid is greatly stimulated by the presence of recipient cells. Comparison of its cryo-EM structure with existing conjugative pilus structures highlights a number of important differences between the R388 pilus structure and that of its homologs, the most prominent being the highly distinctive conformation of its bound lipid.
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Affiliation(s)
- Abhinav K Vadakkepat
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, Malet Street, London WC1E 7HX, UK.
| | - Songlin Xue
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London WC1E 6BT, UK
| | - Adam Redzej
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, Malet Street, London WC1E 7HX, UK
| | - Terry K Smith
- BSRC, School of Biology, University of St Andrews, St Andrews KY16 9AJ, UK
| | - Brian T Ho
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, Malet Street, London WC1E 7HX, UK; Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London WC1E 6BT, UK
| | - Gabriel Waksman
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, Malet Street, London WC1E 7HX, UK; Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London WC1E 6BT, UK.
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24
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Karuppan S, Schrag LG, Pastrano CM, Jara-Oseguera A, Zubcevic L. Structural dynamics at cytosolic interprotomer interfaces control gating of a mammalian TRPM5 channel. Proc Natl Acad Sci U S A 2024; 121:e2403333121. [PMID: 38923985 PMCID: PMC11228501 DOI: 10.1073/pnas.2403333121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 05/15/2024] [Indexed: 06/28/2024] Open
Abstract
The transient receptor potential melastatin (TRPM) tetrameric cation channels are involved in a wide range of biological functions, from temperature sensing and taste transduction to regulation of cardiac function, inflammatory pain, and insulin secretion. The structurally conserved TRPM cytoplasmic domains make up >70 % of the total protein. To investigate the mechanism by which the TRPM cytoplasmic domains contribute to gating, we employed electrophysiology and cryo-EM to study TRPM5-a channel that primarily relies on activation via intracellular Ca2+. Here, we show that activation of mammalian TRPM5 channels is strongly altered by Ca2+-dependent desensitization. Structures of rat TRPM5 identify a series of conformational transitions triggered by Ca2+ binding, whereby formation and dissolution of cytoplasmic interprotomer interfaces appear to control activation and desensitization of the channel. This study shows the importance of the cytoplasmic assembly in TRPM5 channel function and sets the stage for future investigations of other members of the TRPM family.
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Affiliation(s)
- Sebastian Karuppan
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, KS66160
| | - Lynn Goss Schrag
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, KS66160
| | - Caroline M. Pastrano
- Department of Molecular Biosciences, College of Natural Sciences, The University of Texas at Austin, Austin, TX78712
| | - Andrés Jara-Oseguera
- Department of Molecular Biosciences, College of Natural Sciences, The University of Texas at Austin, Austin, TX78712
| | - Lejla Zubcevic
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, KS66160
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25
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Zheng W, Chai P, Zhu J, Zhang K. High-resolution in situ structures of mammalian respiratory supercomplexes. Nature 2024; 631:232-239. [PMID: 38811722 PMCID: PMC11222160 DOI: 10.1038/s41586-024-07488-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 04/30/2024] [Indexed: 05/31/2024]
Abstract
Mitochondria play a pivotal part in ATP energy production through oxidative phosphorylation, which occurs within the inner membrane through a series of respiratory complexes1-4. Despite extensive in vitro structural studies, determining the atomic details of their molecular mechanisms in physiological states remains a major challenge, primarily because of loss of the native environment during purification. Here we directly image porcine mitochondria using an in situ cryo-electron microscopy approach. This enables us to determine the structures of various high-order assemblies of respiratory supercomplexes in their native states. We identify four main supercomplex organizations: I1III2IV1, I1III2IV2, I2III2IV2 and I2III4IV2, which potentially expand into higher-order arrays on the inner membranes. These diverse supercomplexes are largely formed by 'protein-lipids-protein' interactions, which in turn have a substantial impact on the local geometry of the surrounding membranes. Our in situ structures also capture numerous reactive intermediates within these respiratory supercomplexes, shedding light on the dynamic processes of the ubiquinone/ubiquinol exchange mechanism in complex I and the Q-cycle in complex III. Structural comparison of supercomplexes from mitochondria treated under different conditions indicates a possible correlation between conformational states of complexes I and III, probably in response to environmental changes. By preserving the native membrane environment, our approach enables structural studies of mitochondrial respiratory supercomplexes in reaction at high resolution across multiple scales, from atomic-level details to the broader subcellular context.
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Affiliation(s)
- Wan Zheng
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Pengxin Chai
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Jiapeng Zhu
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China.
| | - Kai Zhang
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.
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26
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Saecker RM, Mueller AU, Malone B, Chen J, Budell WC, Dandey VP, Maruthi K, Mendez JH, Molina N, Eng ET, Yen LY, Potter CS, Carragher B, Darst SA. Early intermediates in bacterial RNA polymerase promoter melting visualized by time-resolved cryo-electron microscopy. Nat Struct Mol Biol 2024:10.1038/s41594-024-01349-9. [PMID: 38951624 DOI: 10.1038/s41594-024-01349-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 06/06/2024] [Indexed: 07/03/2024]
Abstract
During formation of the transcription-competent open complex (RPo) by bacterial RNA polymerases (RNAPs), transient intermediates pile up before overcoming a rate-limiting step. Structural descriptions of these interconversions in real time are unavailable. To address this gap, here we use time-resolved cryogenic electron microscopy (cryo-EM) to capture four intermediates populated 120 ms or 500 ms after mixing Escherichia coli σ70-RNAP and the λPR promoter. Cryo-EM snapshots revealed that the upstream edge of the transcription bubble unpairs rapidly, followed by stepwise insertion of two conserved nontemplate strand (nt-strand) bases into RNAP pockets. As the nt-strand 'read-out' extends, the RNAP clamp closes, expelling an inhibitory σ70 domain from the active-site cleft. The template strand is fully unpaired by 120 ms but remains dynamic, indicating that yet unknown conformational changes complete RPo formation in subsequent steps. Given that these events likely describe DNA opening at many bacterial promoters, this study provides insights into how DNA sequence regulates steps of RPo formation.
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Affiliation(s)
- Ruth M Saecker
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY, USA
| | - Andreas U Mueller
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY, USA
| | - Brandon Malone
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY, USA
- Memorial Sloan Kettering Cancer Center, Sloan Kettering Institute, New York, NY, USA
| | - James Chen
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY, USA
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY, USA
| | - William C Budell
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Venkata P Dandey
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
- National Institute of Environmental Health Sciences, Durham, NC, USA
| | - Kashyap Maruthi
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Joshua H Mendez
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Nina Molina
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY, USA
| | - Edward T Eng
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Laura Y Yen
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Clinton S Potter
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
- Chan Zuckerberg Imaging Institute, San Francisco, CA, USA
| | - Bridget Carragher
- The National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
- Chan Zuckerberg Imaging Institute, San Francisco, CA, USA
| | - Seth A Darst
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY, USA.
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27
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Kimanius D, Jamali K, Wilkinson ME, Lövestam S, Velazhahan V, Nakane T, Scheres SHW. Data-driven regularization lowers the size barrier of cryo-EM structure determination. Nat Methods 2024; 21:1216-1221. [PMID: 38862790 PMCID: PMC11239489 DOI: 10.1038/s41592-024-02304-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 05/08/2024] [Indexed: 06/13/2024]
Abstract
Macromolecular structure determination by electron cryo-microscopy (cryo-EM) is limited by the alignment of noisy images of individual particles. Because smaller particles have weaker signals, alignment errors impose size limitations on its applicability. Here, we explore how image alignment is improved by the application of deep learning to exploit prior knowledge about biological macromolecular structures that would otherwise be difficult to express mathematically. We train a denoising convolutional neural network on pairs of half-set reconstructions from the electron microscopy data bank (EMDB) and use this denoiser as an alternative to a commonly used smoothness prior. We demonstrate that this approach, which we call Blush regularization, yields better reconstructions than do existing algorithms, in particular for data with low signal-to-noise ratios. The reconstruction of a protein-nucleic acid complex with a molecular weight of 40 kDa, which was previously intractable, illustrates that denoising neural networks will expand the applicability of cryo-EM structure determination for a wide range of biological macromolecules.
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Affiliation(s)
- Dari Kimanius
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, UK.
- CZ Imaging Institute, Redwood City, CA, USA.
| | - Kiarash Jamali
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, UK
| | - Max E Wilkinson
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Howard Hughes Medical Institute, Cambridge, MA, USA
| | - Sofia Lövestam
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, UK
| | - Vaithish Velazhahan
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, UK
- School of Medicine, Stanford University, Stanford, CA, USA
| | - Takanori Nakane
- Institute for Protein Research, Osaka University, Suita-shi, Osaka, Japan
| | - Sjors H W Scheres
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, UK.
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28
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Jungnickel KEJ, Guelle O, Iguchi M, Dong W, Kotov V, Gabriel F, Debacker C, Dairou J, McCort-Tranchepain I, Laqtom NN, Chan SH, Ejima A, Sato K, Massa López D, Saftig P, Mehdipour AR, Abu-Remaileh M, Gasnier B, Löw C, Damme M. MFSD1 with its accessory subunit GLMP functions as a general dipeptide uniporter in lysosomes. Nat Cell Biol 2024; 26:1047-1061. [PMID: 38839979 PMCID: PMC11252000 DOI: 10.1038/s41556-024-01436-5] [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: 01/22/2024] [Accepted: 05/07/2024] [Indexed: 06/07/2024]
Abstract
The lysosomal degradation of macromolecules produces diverse small metabolites exported by specific transporters for reuse in biosynthetic pathways. Here we deorphanized the major facilitator superfamily domain containing 1 (MFSD1) protein, which forms a tight complex with the glycosylated lysosomal membrane protein (GLMP) in the lysosomal membrane. Untargeted metabolomics analysis of MFSD1-deficient mouse lysosomes revealed an increase in cationic dipeptides. Purified MFSD1 selectively bound diverse dipeptides, while electrophysiological, isotope tracer and fluorescence-based studies in Xenopus oocytes and proteoliposomes showed that MFSD1-GLMP acts as a uniporter for cationic, neutral and anionic dipeptides. Cryoelectron microscopy structure of the dipeptide-bound MFSD1-GLMP complex in outward-open conformation characterized the heterodimer interface and, in combination with molecular dynamics simulations, provided a structural basis for its selectivity towards diverse dipeptides. Together, our data identify MFSD1 as a general lysosomal dipeptide uniporter, providing an alternative route to recycle lysosomal proteolysis products when lysosomal amino acid exporters are overloaded.
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Affiliation(s)
| | - Océane Guelle
- Saints-Pères Paris Institute for the Neurosciences, Université Paris Cité, Centre National de la Recherche Scientifique, Paris, France
| | - Miharu Iguchi
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
- The Institute for Chemistry, Engineering and Medicine for Human Health, Stanford University, Stanford, CA, USA
| | - Wentao Dong
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
- The Institute for Chemistry, Engineering and Medicine for Human Health, Stanford University, Stanford, CA, USA
| | - Vadim Kotov
- Centre for Structural Systems Biology, Hamburg, Germany
- European Molecular Biology Laboratory Hamburg, Hamburg, Germany
| | - Florian Gabriel
- Centre for Structural Systems Biology, Hamburg, Germany
- European Molecular Biology Laboratory Hamburg, Hamburg, Germany
| | - Cécile Debacker
- Saints-Pères Paris Institute for the Neurosciences, Université Paris Cité, Centre National de la Recherche Scientifique, Paris, France
| | - Julien Dairou
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, CNRS UMR 8601, Université Paris Cité, Paris, France
| | - Isabelle McCort-Tranchepain
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, CNRS UMR 8601, Université Paris Cité, Paris, France
| | - Nouf N Laqtom
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
- The Institute for Chemistry, Engineering and Medicine for Human Health, Stanford University, Stanford, CA, USA
| | - Sze Ham Chan
- Department of Pharmacology, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Akika Ejima
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Kenji Sato
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - David Massa López
- Institute of Biochemistry, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Paul Saftig
- Institute of Biochemistry, Christian-Albrechts-University Kiel, Kiel, Germany
| | | | - Monther Abu-Remaileh
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
- The Institute for Chemistry, Engineering and Medicine for Human Health, Stanford University, Stanford, CA, USA
| | - Bruno Gasnier
- Saints-Pères Paris Institute for the Neurosciences, Université Paris Cité, Centre National de la Recherche Scientifique, Paris, France.
| | - Christian Löw
- Centre for Structural Systems Biology, Hamburg, Germany.
- European Molecular Biology Laboratory Hamburg, Hamburg, Germany.
| | - Markus Damme
- Institute of Biochemistry, Christian-Albrechts-University Kiel, Kiel, Germany.
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29
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Shuto Y, Nakagawa R, Zhu S, Hoki M, Omura SN, Hirano H, Itoh Y, Zhang F, Nureki O. Structural basis for pegRNA-guided reverse transcription by a prime editor. Nature 2024; 631:224-231. [PMID: 38811740 PMCID: PMC11222144 DOI: 10.1038/s41586-024-07497-8] [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: 10/24/2023] [Accepted: 04/30/2024] [Indexed: 05/31/2024]
Abstract
The prime editor system composed of Streptococcus pyogenes Cas9 nickase (nSpCas9) and engineered Moloney murine leukaemia virus reverse transcriptase (M-MLV RT) collaborates with a prime editing guide RNA (pegRNA) to facilitate a wide variety of precise genome edits in living cells1. However, owing to a lack of structural information, the molecular mechanism of pegRNA-guided reverse transcription by the prime editor remains poorly understood. Here we present cryo-electron microscopy structures of the SpCas9-M-MLV RTΔRNaseH-pegRNA-target DNA complex in multiple states. The termination structure, along with our functional analysis, reveals that M-MLV RT extends reverse transcription beyond the expected site, resulting in scaffold-derived incorporations that cause undesired edits at the target loci. Furthermore, structural comparisons among the pre-initiation, initiation and elongation states show that M-MLV RT remains in a consistent position relative to SpCas9 during reverse transcription, whereas the pegRNA-synthesized DNA heteroduplex builds up along the surface of SpCas9. On the basis of our structural insights, we rationally engineered pegRNA variants and prime-editor variants in which M-MLV RT is fused within SpCas9. Collectively, our findings provide structural insights into the stepwise mechanism of prime editing, and will pave the way for the development of a versatile prime editing toolbox.
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Affiliation(s)
- Yutaro Shuto
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Ryoya Nakagawa
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.
| | - Shiyou Zhu
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Mizuki Hoki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Satoshi N Omura
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Hisato Hirano
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Yuzuru Itoh
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Feng Zhang
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.
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30
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Soppela S, Plavec Z, Gröhn S, Jartti M, Oikarinen S, Laajala M, Marjomaki V, Butcher SJ, Hankaniemi MM. Comparison of structure and immunogenicity of CVB1-VLP and inactivated CVB1 vaccine candidates. RESEARCH SQUARE 2024:rs.3.rs-4545395. [PMID: 38978565 PMCID: PMC11230480 DOI: 10.21203/rs.3.rs-4545395/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Coxsackievirus B1 (CVB1) is a common cause of acute and chronic myocarditis, dilated cardiomyopathy and aseptic meningitis. However, no CVB-vaccines are available for human use. In this study, we investigated the immunogenicity of virus-like particle (VLP) and inactivated whole-virus vaccines for CVB1 when administrated to mice via either subcutaneous or intranasal routes formulated with and without commercial and experimental adjuvants. Here, the potential of utilizing epigallocatechin-3-gallate (EGCG) as a mucosal adjuvant synergistically with its ability to inactivate the virus were investigated. EGCG had promising adjuvant properties for CVB1-VLP when administered via the parenteral route but limited efficacy via intranasal administration. However, intranasal administration of the formalin-inactivated virus induced high CVB1-specific humoral, cellular, and mucosal immune responses. Also, based on CVB1-specific IgG-antibody responses, we conclude that CVB1-VLP can be taken up by immune cells when administrated intranasally and further structural engineering for the VLP may increase the mucosal immunogenicity. The preparations contained mixtures of compact and expanded A particles with 85% expanded in the formalin-inactivated virus, but only 52% in the VLP observed by cryogenic electron microscopy. To correlate the structure to immunogenicity, we solved the structures of the CVB1-VLP and the formalin-inactivated CVB1 virus at resolutions ranging from 2.15 A to 4.1 A for the expanded and compact VLP and virus particles by image reconstruction. These structures can be used in designing mutations increasing the stability and immunogenicity of CVB1-VLP in the future. Overall, our results highlight the potential of using formalin inactivated CVB1 vaccine in mucosal immunization programs and provide important information for future development of VLP-based vaccines against all enteroviruses.
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31
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Lee J, Stewart C, Schäfer A, Leaf EM, Park YJ, Asarnow D, Powers JM, Treichel C, Sprouse KR, Corti D, Baric R, King NP, Veesler D. A broadly generalizable stabilization strategy for sarbecovirus fusion machinery vaccines. Nat Commun 2024; 15:5496. [PMID: 38944664 PMCID: PMC11214633 DOI: 10.1038/s41467-024-49656-5] [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: 01/04/2024] [Accepted: 06/13/2024] [Indexed: 07/01/2024] Open
Abstract
Evolution of SARS-CoV-2 alters the antigenicity of the immunodominant spike (S) receptor-binding domain and N-terminal domain, undermining the efficacy of vaccines and antibody therapies. To overcome this challenge, we set out to develop a vaccine focusing antibody responses on the highly conserved but metastable S2 subunit, which folds as a spring-loaded fusion machinery. We describe a strategy for prefusion-stabilization and high yield recombinant production of SARS-CoV-2 S2 trimers with native structure and antigenicity. We demonstrate that our design strategy is broadly generalizable to sarbecoviruses, as exemplified with the SARS-CoV-1 (clade 1a) and PRD-0038 (clade 3) S2 subunits. Immunization of mice with a prefusion-stabilized SARS-CoV-2 S2 trimer elicits broadly reactive sarbecovirus antibodies and neutralizing antibody titers of comparable magnitude against Wuhan-Hu-1 and the immune evasive XBB.1.5 variant. Vaccinated mice were protected from weight loss and disease upon challenge with XBB.1.5, providing proof-of-principle for fusion machinery sarbecovirus vaccines.
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Affiliation(s)
- Jimin Lee
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Cameron Stewart
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - Alexandra Schäfer
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
| | - Elizabeth M Leaf
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Young-Jun Park
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
- Howard Hughes Medical Institute, Seattle, WA, USA
| | - Daniel Asarnow
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
| | - John M Powers
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
| | - Catherine Treichel
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Kaitlin R Sprouse
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
- Howard Hughes Medical Institute, Seattle, WA, USA
| | - Davide Corti
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Ralph Baric
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
| | - Neil P King
- Department of Biochemistry, University of Washington, Seattle, Washington, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, Washington, USA.
- Howard Hughes Medical Institute, Seattle, WA, USA.
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32
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Lodwick JE, Shen R, Erramilli S, Xie Y, Roganowicz K, Kossiakoff AA, Zhao M. Structural Insights into the Roles of PARP4 and NAD + in the Human Vault Cage. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.27.601040. [PMID: 38979142 PMCID: PMC11230398 DOI: 10.1101/2024.06.27.601040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Vault is a massive ribonucleoprotein complex found across Eukaryota. The major vault protein (MVP) oligomerizes into an ovular cage, which contains several minor vault components (MVCs) and is thought to transport transiently bound "cargo" molecules. Vertebrate vaults house a poly (ADP-ribose) polymerase (known as PARP4 in humans), which is the only MVC with known enzymatic activity. Despite being discovered decades ago, the molecular basis for PARP4's interaction with MVP remains unclear. In this study, we determined the structure of the human vault cage in complex with PARP4 and its enzymatic substrate NAD + . The structures reveal atomic-level details of the protein-binding interface, as well as unexpected NAD + -binding pockets within the interior of the vault cage. In addition, proteomics data show that human vaults purified from wild-type and PARP4-depleted cells interact with distinct subsets of proteins. Our results thereby support a model in which PARP4's specific incorporation into the vault cage helps to regulate vault's selection of cargo and its subcellular localization. Further, PARP4's proximity to MVP's NAD + -binding sites could support its enzymatic function within the vault.
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33
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Mindrebo JT, Lander GC. Structural and mechanistic studies on human LONP1 redefine the hand-over-hand translocation mechanism. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.24.600538. [PMID: 38979310 PMCID: PMC11230189 DOI: 10.1101/2024.06.24.600538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
AAA+ enzymes use energy from ATP hydrolysis to remodel diverse cellular targets. Structures of substrate-bound AAA+ complexes suggest that these enzymes employ a conserved hand-over-hand mechanism to thread substrates through their central pore. However, the fundamental aspects of the mechanisms governing motor function and substrate processing within specific AAA+ families remain unresolved. We used cryo-electron microscopy to structurally interrogate reaction intermediates from in vitro biochemical assays to inform the underlying regulatory mechanisms of the human mitochondrial AAA+ protease, LONP1. Our results demonstrate that substrate binding allosterically regulates proteolytic activity, and that LONP1 can adopt a configuration conducive to substrate translocation even when the ATPases are bound to ADP. These results challenge the conventional understanding of the hand-over-hand translocation mechanism, giving rise to an alternative model that aligns more closely with biochemical and biophysical data on related enzymes like ClpX, ClpA, the 26S proteasome, and Lon protease.
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Affiliation(s)
- Jeffrey T. Mindrebo
- Department of Integrative Structural and Computational Biology, Scripps Research; La Jolla, CA, USA
| | - Gabriel C. Lander
- Department of Integrative Structural and Computational Biology, Scripps Research; La Jolla, CA, USA
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34
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Throll P, G Dolce L, Rico-Lastres P, Arnold K, Tengo L, Basu S, Kaiser S, Schneider R, Kowalinski E. Structural basis of tRNA recognition by the m 3C RNA methyltransferase METTL6 in complex with SerRS seryl-tRNA synthetase. Nat Struct Mol Biol 2024:10.1038/s41594-024-01341-3. [PMID: 38918637 DOI: 10.1038/s41594-024-01341-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 05/29/2024] [Indexed: 06/27/2024]
Abstract
Methylation of cytosine 32 in the anticodon loop of tRNAs to 3-methylcytosine (m3C) is crucial for cellular translation fidelity. Misregulation of the RNA methyltransferases setting this modification can cause aggressive cancers and metabolic disturbances. Here, we report the cryo-electron microscopy structure of the human m3C tRNA methyltransferase METTL6 in complex with seryl-tRNA synthetase (SerRS) and their common substrate tRNASer. Through the complex structure, we identify the tRNA-binding domain of METTL6. We show that SerRS acts as the tRNASer substrate selection factor for METTL6. We demonstrate that SerRS augments the methylation activity of METTL6 and that direct contacts between METTL6 and SerRS are necessary for efficient tRNASer methylation. Finally, on the basis of the structure of METTL6 in complex with SerRS and tRNASer, we postulate a universal tRNA-binding mode for m3C RNA methyltransferases, including METTL2 and METTL8, suggesting that these mammalian paralogs use similar ways to engage their respective tRNA substrates and cofactors.
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Affiliation(s)
| | | | - Palma Rico-Lastres
- Institute of Functional Epigenetics, Helmholtz Zentrum Munich, Neuherberg, Germany
| | - Katharina Arnold
- Institute of Functional Epigenetics, Helmholtz Zentrum Munich, Neuherberg, Germany
| | - Laura Tengo
- European Molecular Biology Laboratory, Grenoble, France
| | - Shibom Basu
- European Molecular Biology Laboratory, Grenoble, France
| | - Stefanie Kaiser
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt, Germany
| | - Robert Schneider
- Institute of Functional Epigenetics, Helmholtz Zentrum Munich, Neuherberg, Germany
| | - Eva Kowalinski
- European Molecular Biology Laboratory, Grenoble, France.
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35
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Du W, Debski-Antoniak O, Drabek D, van Haperen R, van Dortmondt M, van der Lee J, Drulyte I, van Kuppeveld FJM, Grosveld F, Hurdiss DL, Bosch BJ. Neutralizing antibodies reveal cryptic vulnerabilities and interdomain crosstalk in the porcine deltacoronavirus spike protein. Nat Commun 2024; 15:5330. [PMID: 38909062 PMCID: PMC11193727 DOI: 10.1038/s41467-024-49693-0] [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: 12/08/2023] [Accepted: 06/11/2024] [Indexed: 06/24/2024] Open
Abstract
Porcine deltacoronavirus (PDCoV) is an emerging enteric pathogen that has recently been detected in humans. Despite this zoonotic concern, the antigenic structure of PDCoV remains unknown. The virus relies on its spike (S) protein for cell entry, making it a prime target for neutralizing antibodies. Here, we generate and characterize a set of neutralizing antibodies targeting the S protein, shedding light on PDCoV S interdomain crosstalk and its vulnerable sites. Among the four identified antibodies, one targets the S1A domain, causing local and long-range conformational changes, resulting in partial exposure of the S1B domain. The other antibodies bind the S1B domain, disrupting binding to aminopeptidase N (APN), the entry receptor for PDCoV. Notably, the epitopes of these S1B-targeting antibodies are concealed in the prefusion S trimer conformation, highlighting the necessity for conformational changes for effective antibody binding. The binding footprint of one S1B binder entirely overlaps with APN-interacting residues and thus targets a highly conserved epitope. These findings provide structural insights into the humoral immune response against the PDCoV S protein, potentially guiding vaccine and therapeutic development for this zoonotic pathogen.
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Affiliation(s)
- Wenjuan Du
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Oliver Debski-Antoniak
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Dubravka Drabek
- Department of Cell Biology, Erasmus Medical Center, Rotterdam, The Netherlands
- Harbour BioMed, Rotterdam, The Netherlands
| | - Rien van Haperen
- Department of Cell Biology, Erasmus Medical Center, Rotterdam, The Netherlands
- Harbour BioMed, Rotterdam, The Netherlands
| | - Melissa van Dortmondt
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Joline van der Lee
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Ieva Drulyte
- Thermo Fisher Scientific, Materials and Structural Analysis, Eindhoven, The Netherlands
| | - Frank J M van Kuppeveld
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Frank Grosveld
- Department of Cell Biology, Erasmus Medical Center, Rotterdam, The Netherlands
- Harbour BioMed, Rotterdam, The Netherlands
| | - Daniel L Hurdiss
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands.
| | - Berend-Jan Bosch
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands.
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36
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Hugener J, Xu J, Wettstein R, Ioannidi L, Velikov D, Wollweber F, Henggeler A, Matos J, Pilhofer M. FilamentID reveals the composition and function of metabolic enzyme polymers during gametogenesis. Cell 2024; 187:3303-3318.e18. [PMID: 38906101 DOI: 10.1016/j.cell.2024.04.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 02/06/2024] [Accepted: 04/19/2024] [Indexed: 06/23/2024]
Abstract
Gamete formation and subsequent offspring development often involve extended phases of suspended cellular development or even dormancy. How cells adapt to recover and resume growth remains poorly understood. Here, we visualized budding yeast cells undergoing meiosis by cryo-electron tomography (cryoET) and discovered elaborate filamentous assemblies decorating the nucleus, cytoplasm, and mitochondria. To determine filament composition, we developed a "filament identification" (FilamentID) workflow that combines multiscale cryoET/cryo-electron microscopy (cryoEM) analyses of partially lysed cells or organelles. FilamentID identified the mitochondrial filaments as being composed of the conserved aldehyde dehydrogenase Ald4ALDH2 and the nucleoplasmic/cytoplasmic filaments as consisting of acetyl-coenzyme A (CoA) synthetase Acs1ACSS2. Structural characterization further revealed the mechanism underlying polymerization and enabled us to genetically perturb filament formation. Acs1 polymerization facilitates the recovery of chronologically aged spores and, more generally, the cell cycle re-entry of starved cells. FilamentID is broadly applicable to characterize filaments of unknown identity in diverse cellular contexts.
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Affiliation(s)
- Jannik Hugener
- Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland; Institute of Biochemistry, ETH Zürich, 8093 Zürich, Switzerland; Max Perutz Labs, University of Vienna, 1030 Vienna, Austria
| | - Jingwei Xu
- Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland
| | - Rahel Wettstein
- Institute of Biochemistry, ETH Zürich, 8093 Zürich, Switzerland; Max Perutz Labs, University of Vienna, 1030 Vienna, Austria
| | - Lydia Ioannidi
- Max Perutz Labs, University of Vienna, 1030 Vienna, Austria
| | - Daniel Velikov
- Max Perutz Labs, University of Vienna, 1030 Vienna, Austria; Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, 1030 Vienna, Austria
| | - Florian Wollweber
- Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland
| | - Adrian Henggeler
- Institute of Biochemistry, ETH Zürich, 8093 Zürich, Switzerland; Max Perutz Labs, University of Vienna, 1030 Vienna, Austria
| | - Joao Matos
- Institute of Biochemistry, ETH Zürich, 8093 Zürich, Switzerland; Max Perutz Labs, University of Vienna, 1030 Vienna, Austria.
| | - Martin Pilhofer
- Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland.
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37
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Eggers AR, Chen K, Soczek KM, Tuck OT, Doherty EE, Xu B, Trinidad MI, Thornton BW, Yoon PH, Doudna JA. Rapid DNA unwinding accelerates genome editing by engineered CRISPR-Cas9. Cell 2024; 187:3249-3261.e14. [PMID: 38781968 DOI: 10.1016/j.cell.2024.04.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 02/20/2024] [Accepted: 04/24/2024] [Indexed: 05/25/2024]
Abstract
Thermostable clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas9) enzymes could improve genome-editing efficiency and delivery due to extended protein lifetimes. However, initial experimentation demonstrated Geobacillus stearothermophilus Cas9 (GeoCas9) to be virtually inactive when used in cultured human cells. Laboratory-evolved variants of GeoCas9 overcome this natural limitation by acquiring mutations in the wedge (WED) domain that produce >100-fold-higher genome-editing levels. Cryoelectron microscopy (cryo-EM) structures of the wild-type and improved GeoCas9 (iGeoCas9) enzymes reveal extended contacts between the WED domain of iGeoCas9 and DNA substrates. Biochemical analysis shows that iGeoCas9 accelerates DNA unwinding to capture substrates under the magnesium-restricted conditions typical of mammalian but not bacterial cells. These findings enabled rational engineering of other Cas9 orthologs to enhance genome-editing levels, pointing to a general strategy for editing enzyme improvement. Together, these results uncover a new role for the Cas9 WED domain in DNA unwinding and demonstrate how accelerated target unwinding dramatically improves Cas9-induced genome-editing activity.
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Affiliation(s)
- Amy R Eggers
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Kai Chen
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Katarzyna M Soczek
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Owen T Tuck
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Erin E Doherty
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Bryant Xu
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Marena I Trinidad
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Brittney W Thornton
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Peter H Yoon
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jennifer A Doudna
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Gladstone Institutes, San Francisco, CA 94158, USA; Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA 94158, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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38
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Riepl D, Gamiz-Hernandez AP, Kovalova T, Król SM, Mader SL, Sjöstrand D, Högbom M, Brzezinski P, Kaila VRI. Long-range charge transfer mechanism of the III 2IV 2 mycobacterial supercomplex. Nat Commun 2024; 15:5276. [PMID: 38902248 PMCID: PMC11189923 DOI: 10.1038/s41467-024-49628-9] [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: 11/16/2023] [Accepted: 06/12/2024] [Indexed: 06/22/2024] Open
Abstract
Aerobic life is powered by membrane-bound redox enzymes that shuttle electrons to oxygen and transfer protons across a biological membrane. Structural studies suggest that these energy-transducing enzymes operate as higher-order supercomplexes, but their functional role remains poorly understood and highly debated. Here we resolve the functional dynamics of the 0.7 MDa III2IV2 obligate supercomplex from Mycobacterium smegmatis, a close relative of M. tuberculosis, the causative agent of tuberculosis. By combining computational, biochemical, and high-resolution (2.3 Å) cryo-electron microscopy experiments, we show how the mycobacterial supercomplex catalyses long-range charge transport from its menaquinol oxidation site to the binuclear active site for oxygen reduction. Our data reveal proton and electron pathways responsible for the charge transfer reactions, mechanistic principles of the quinone catalysis, and how unique molecular adaptations, water molecules, and lipid interactions enable the proton-coupled electron transfer (PCET) reactions. Our combined findings provide a mechanistic blueprint of mycobacterial supercomplexes and a basis for developing drugs against pathogenic bacteria.
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Affiliation(s)
- Daniel Riepl
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Ana P Gamiz-Hernandez
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Terezia Kovalova
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Sylwia M Król
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Sophie L Mader
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Dan Sjöstrand
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Martin Högbom
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Peter Brzezinski
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Ville R I Kaila
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91, Stockholm, Sweden.
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39
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Mittal A, Martin MF, Levin EJ, Adams C, Yang M, Provins L, Hall A, Procter M, Ledecq M, Hillisch A, Wolff C, Gillard M, Horanyi PS, Coleman JA. Structures of synaptic vesicle protein 2A and 2B bound to anticonvulsants. Nat Struct Mol Biol 2024:10.1038/s41594-024-01335-1. [PMID: 38898101 DOI: 10.1038/s41594-024-01335-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 05/14/2024] [Indexed: 06/21/2024]
Abstract
Epilepsy is a common neurological disorder characterized by abnormal activity of neuronal networks, leading to seizures. The racetam class of anti-seizure medications bind specifically to a membrane protein found in the synaptic vesicles of neurons called synaptic vesicle protein 2 (SV2) A (SV2A). SV2A belongs to an orphan subfamily of the solute carrier 22 organic ion transporter family that also includes SV2B and SV2C. The molecular basis for how anti-seizure medications act on SV2s remains unknown. Here we report cryo-electron microscopy structures of SV2A and SV2B captured in a luminal-occluded conformation complexed with anticonvulsant ligands. The conformation bound by anticonvulsants resembles an inhibited transporter with closed luminal and intracellular gates. Anticonvulsants bind to a highly conserved central site in SV2s. These structures provide blueprints for future drug design and will facilitate future investigations into the biological function of SV2s.
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Affiliation(s)
- Anshumali Mittal
- Department of Structural Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Matthew F Martin
- Department of Structural Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | | | | | | | | | | | | | | | | | | | | | | | - Jonathan A Coleman
- Department of Structural Biology, University of Pittsburgh, Pittsburgh, PA, USA.
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40
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Shvarev D, König C, Susan N, Langemeyer L, Walter S, Perz A, Fröhlich F, Ungermann C, Moeller A. Structure of the endosomal CORVET tethering complex. Nat Commun 2024; 15:5227. [PMID: 38898033 PMCID: PMC11187117 DOI: 10.1038/s41467-024-49137-9] [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: 11/09/2023] [Accepted: 05/24/2024] [Indexed: 06/21/2024] Open
Abstract
Cells depend on their endolysosomal system for nutrient uptake and downregulation of plasma membrane proteins. These processes rely on endosomal maturation, which requires multiple membrane fusion steps. Early endosome fusion is promoted by the Rab5 GTPase and its effector, the hexameric CORVET tethering complex, which is homologous to the lysosomal HOPS. How these related complexes recognize their specific target membranes remains entirely elusive. Here, we solve the structure of CORVET by cryo-electron microscopy and revealed its minimal requirements for membrane tethering. As expected, the core of CORVET and HOPS resembles each other. However, the function-defining subunits show marked structural differences. Notably, we discover that unlike HOPS, CORVET depends not only on Rab5 but also on phosphatidylinositol-3-phosphate (PI3P) and membrane lipid packing defects for tethering, implying that an organelle-specific membrane code enables fusion. Our data suggest that both shape and membrane interactions of CORVET and HOPS are conserved in metazoans, thus providing a paradigm how tethering complexes function.
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Affiliation(s)
- Dmitry Shvarev
- Department of Biology/Chemistry, Structural Biology Section, Osnabrück University, 49076, Osnabrück, Germany
| | - Caroline König
- Department of Biology/Chemistry, Biochemistry Section, Osnabrück University, 49076, Osnabrück, Germany
| | - Nicole Susan
- Department of Biology/Chemistry, Biochemistry Section, Osnabrück University, 49076, Osnabrück, Germany
| | - Lars Langemeyer
- Department of Biology/Chemistry, Biochemistry Section, Osnabrück University, 49076, Osnabrück, Germany
- Center of Cellular Nanoanalytics Osnabrück (CellNanOs), Osnabrück University, 49076, Osnabrück, Germany
| | - Stefan Walter
- Center of Cellular Nanoanalytics Osnabrück (CellNanOs), Osnabrück University, 49076, Osnabrück, Germany
| | - Angela Perz
- Department of Biology/Chemistry, Biochemistry Section, Osnabrück University, 49076, Osnabrück, Germany
| | - Florian Fröhlich
- Center of Cellular Nanoanalytics Osnabrück (CellNanOs), Osnabrück University, 49076, Osnabrück, Germany
- Department of Biology/Chemistry, Bioanalytical Chemistry Section, Osnabrück University, 49076, Osnabrück, Germany
| | - Christian Ungermann
- Department of Biology/Chemistry, Biochemistry Section, Osnabrück University, 49076, Osnabrück, Germany.
- Center of Cellular Nanoanalytics Osnabrück (CellNanOs), Osnabrück University, 49076, Osnabrück, Germany.
| | - Arne Moeller
- Department of Biology/Chemistry, Structural Biology Section, Osnabrück University, 49076, Osnabrück, Germany.
- Center of Cellular Nanoanalytics Osnabrück (CellNanOs), Osnabrück University, 49076, Osnabrück, Germany.
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41
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Karimullina E, Guo Y, Khan HM, Emde T, Quade B, Leo RD, Otwinowski Z, Tieleman Peter D, Borek D, Savchenko A. Structural architecture of TolQ-TolR inner membrane protein complex from opportunistic pathogen Acinetobacter baumannii. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.19.599759. [PMID: 38948712 PMCID: PMC11212960 DOI: 10.1101/2024.06.19.599759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Gram-negative bacteria harness the proton motive force (PMF) within their inner membrane (IM) to uphold the integrity of their cell envelope, an indispensable aspect for both division and survival. The IM TolQ-TolR complex is the essential part of the Tol-Pal system, serving as a conduit for PMF energy transfer to the outer membrane. Here we present cryo-EM reconstructions of Acinetobacter baumannii TolQ in apo and TolR- bound forms at atomic resolution. The apo TolQ configuration manifests as a symmetric pentameric pore, featuring a trans-membrane funnel leading towards a cytoplasmic chamber. In contrast, the TolQ-TolR complex assumes a proton non-permeable stance, characterized by the TolQ pentamer's flexure to accommodate the TolR dimer, where two protomers undergo a translation-based relationship. Our structure-guided analysis and simulations support the rotor-stator mechanism of action, wherein the rotation of the TolQ pentamer harmonizes with the TolR protomers' interplay. These findings broaden our mechanistic comprehension of molecular stator units empowering critical functions within the Gram-negative bacterial cell envelope. Teaser Apo TolQ and TolQ-TolR structures depict structural rearrangements required for cell envelope organization in bacterial cell division.
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42
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Bakker AT, Kotsogianni I, Avalos M, Punt JM, Liu B, Piermarini D, Gagestein B, Slingerland CJ, Zhang L, Willemse JJ, Ghimire LB, van den Berg RJHBN, Janssen APA, Ottenhoff THM, van Boeckel CAA, van Wezel GP, Ghilarov D, Martin NI, van der Stelt M. Discovery of isoquinoline sulfonamides as allosteric gyrase inhibitors with activity against fluoroquinolone-resistant bacteria. Nat Chem 2024:10.1038/s41557-024-01516-x. [PMID: 38898213 DOI: 10.1038/s41557-024-01516-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 03/22/2024] [Indexed: 06/21/2024]
Abstract
Bacteria have evolved resistance to nearly all known antibacterials, emphasizing the need to identify antibiotics that operate via novel mechanisms. Here we report a class of allosteric inhibitors of DNA gyrase with antibacterial activity against fluoroquinolone-resistant clinical isolates of Escherichia coli. Screening of a small-molecule library revealed an initial isoquinoline sulfonamide hit, which was optimized via medicinal chemistry efforts to afford the more potent antibacterial LEI-800. Target identification studies, including whole-genome sequencing of in vitro selected mutants with resistance to isoquinoline sulfonamides, unanimously pointed to the DNA gyrase complex, an essential bacterial topoisomerase and an established antibacterial target. Using single-particle cryogenic electron microscopy, we determined the structure of the gyrase-LEI-800-DNA complex. The compound occupies an allosteric, hydrophobic pocket in the GyrA subunit and has a mode of action that is distinct from the clinically used fluoroquinolones or any other gyrase inhibitor reported to date. LEI-800 provides a chemotype suitable for development to counter the increasingly widespread bacterial resistance to fluoroquinolones.
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Affiliation(s)
- Alexander T Bakker
- Department of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - Ioli Kotsogianni
- Biological Chemistry Group, Institute of Biology, Leiden University, Leiden, the Netherlands
| | - Mariana Avalos
- Department of Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, the Netherlands
| | - Jeroen M Punt
- Department of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - Bing Liu
- Department of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - Diana Piermarini
- Department of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - Berend Gagestein
- Department of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - Cornelis J Slingerland
- Biological Chemistry Group, Institute of Biology, Leiden University, Leiden, the Netherlands
| | - Le Zhang
- Department of Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, the Netherlands
| | - Joost J Willemse
- Department of Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, the Netherlands
| | - Leela B Ghimire
- Department of Molecular Microbiology, John Innes Centre, Norwich, UK
| | | | - Antonius P A Janssen
- Department of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - Tom H M Ottenhoff
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, the Netherlands
| | - Constant A A van Boeckel
- Department of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
| | - Gilles P van Wezel
- Department of Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, the Netherlands
| | - Dmitry Ghilarov
- Department of Molecular Microbiology, John Innes Centre, Norwich, UK.
| | - Nathaniel I Martin
- Biological Chemistry Group, Institute of Biology, Leiden University, Leiden, the Netherlands.
| | - Mario van der Stelt
- Department of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands.
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43
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Burtscher V, Mount J, Huang J, Cowgill J, Chang Y, Bickel K, Chen J, Yuan P, Chanda B. Structural basis for hyperpolarization-dependent opening of human HCN1 channel. Nat Commun 2024; 15:5216. [PMID: 38890331 PMCID: PMC11189445 DOI: 10.1038/s41467-024-49599-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: 08/14/2023] [Accepted: 06/11/2024] [Indexed: 06/20/2024] Open
Abstract
Hyperpolarization and cyclic nucleotide (HCN) activated ion channels are critical for the automaticity of action potentials in pacemaking and rhythmic electrical circuits in the human body. Unlike most voltage-gated ion channels, the HCN and related plant ion channels activate upon membrane hyperpolarization. Although functional studies have identified residues in the interface between the voltage-sensing and pore domain as crucial for inverted electromechanical coupling, the structural mechanisms for this unusual voltage-dependence remain unclear. Here, we present cryo-electron microscopy structures of human HCN1 corresponding to Closed, Open, and a putative Intermediate state. Our structures reveal that the downward motion of the gating charges past the charge transfer center is accompanied by concomitant unwinding of the inner end of the S4 and S5 helices, disrupting the tight gating interface observed in the Closed state structure. This helix-coil transition at the intracellular gating interface accompanies a concerted iris-like dilation of the pore helices and underlies the reversed voltage dependence of HCN channels.
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Affiliation(s)
- Verena Burtscher
- Department of Anesthesiology, Washington University School of Medicine, Saint Louis, MO, USA
- Center for the Investigation of Membrane Excitability Diseases, Washington University School of Medicine, Saint Louis, MO, USA
| | - Jonathan Mount
- Center for the Investigation of Membrane Excitability Diseases, Washington University School of Medicine, Saint Louis, MO, USA
- Department of Cell Biology and Physiology, Washington University School of Medicine, Saint Louis, MO, USA
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jian Huang
- Department of Chemistry, University of Massachusetts, Amherst, MA, USA
| | - John Cowgill
- Department of Anesthesiology, Washington University School of Medicine, Saint Louis, MO, USA
- Center for the Investigation of Membrane Excitability Diseases, Washington University School of Medicine, Saint Louis, MO, USA
- Department of Applied Physics, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Yongchang Chang
- Department of Anesthesiology, Washington University School of Medicine, Saint Louis, MO, USA
- Center for the Investigation of Membrane Excitability Diseases, Washington University School of Medicine, Saint Louis, MO, USA
| | - Kathleen Bickel
- Department of Anesthesiology, Washington University School of Medicine, Saint Louis, MO, USA
- Center for the Investigation of Membrane Excitability Diseases, Washington University School of Medicine, Saint Louis, MO, USA
| | - Jianhan Chen
- Department of Chemistry, University of Massachusetts, Amherst, MA, USA
| | - Peng Yuan
- Center for the Investigation of Membrane Excitability Diseases, Washington University School of Medicine, Saint Louis, MO, USA.
- Department of Cell Biology and Physiology, Washington University School of Medicine, Saint Louis, MO, USA.
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Baron Chanda
- Department of Anesthesiology, Washington University School of Medicine, Saint Louis, MO, USA.
- Center for the Investigation of Membrane Excitability Diseases, Washington University School of Medicine, Saint Louis, MO, USA.
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Saint Louis, MO, USA.
- Department of Neuroscience, Washington University School of Medicine, Saint Louis, MO, USA.
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44
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Zhang L, Einsle O. Architecture of the RNF1 complex that drives biological nitrogen fixation. Nat Chem Biol 2024:10.1038/s41589-024-01641-1. [PMID: 38890433 DOI: 10.1038/s41589-024-01641-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 05/10/2024] [Indexed: 06/20/2024]
Abstract
Biological nitrogen fixation requires substantial metabolic energy in form of ATP as well as low-potential electrons that must derive from central metabolism. During aerobic growth, the free-living soil diazotroph Azotobacter vinelandii transfers electrons from the key metabolite NADH to the low-potential ferredoxin FdxA that serves as a direct electron donor to the dinitrogenase reductases. This process is mediated by the RNF complex that exploits the proton motive force over the cytoplasmic membrane to lower the midpoint potential of the transferred electron. Here we report the cryogenic electron microscopy structure of the nitrogenase-associated RNF complex of A. vinelandii, a seven-subunit membrane protein assembly that contains four flavin cofactors and six iron-sulfur centers. Its function requires the strict coupling of electron and proton transfer but also involves major conformational changes within the assembly that can be traced with a combination of electron microscopy and modeling.
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Affiliation(s)
- Lin Zhang
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Oliver Einsle
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany.
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45
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Yamamoto K, Sato T, Hao A, Asao K, Kaguchi R, Kusaka S, Ruddarraju RR, Kazamori D, Seo K, Takahashi S, Horiuchi M, Yokota SI, Lee SY, Ichikawa S. Development of a natural product optimization strategy for inhibitors against MraY, a promising antibacterial target. Nat Commun 2024; 15:5085. [PMID: 38877016 PMCID: PMC11178787 DOI: 10.1038/s41467-024-49484-7] [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: 04/30/2023] [Accepted: 06/06/2024] [Indexed: 06/16/2024] Open
Abstract
MraY (phospho-N-acetylmuramoyl-pentapeptide-transferase) inhibitory natural products are attractive molecules as candidates for a new class of antibacterial agents to combat antimicrobial-resistant bacteria. Structural optimization of these natural products is required to improve their drug-like properties for therapeutic use. However, chemical modifications of these natural products are painstaking tasks due to complex synthetic processes, which is a bottleneck in advancing natural products to the clinic. Here, we develop a strategy for a comprehensive in situ evaluation of the build-up library, which enables us to streamline the preparation of the analogue library and directly assess its biological activities. We apply this approach to a series of MraY inhibitory natural products. Through construction and evaluation of the 686-compound library, we identify promising analogues that exhibit potent and broad-spectrum antibacterial activity against highly drug-resistant strains in vitro as well as in vivo in an acute thigh infection model. Structures of the MraY-analogue complexes reveal distinct interaction patterns, suggesting that these analogues represent MraY inhibitors with unique binding modes. We further demonstrate the generality of our strategy by applying it to tubulin-binding natural products to modulate their tubulin polymerization activities.
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Grants
- 22K20704 MEXT | Japan Society for the Promotion of Science (JSPS)
- 21H03622 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP19K16648 MEXT | Japan Society for the Promotion of Science (JSPS)
- 19H03345 MEXT | Japan Society for the Promotion of Science (JSPS)
- 18H04599 MEXT | Japan Society for the Promotion of Science (JSPS)
- 20H04757 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP19ak0101118h0001 Japan Agency for Medical Research and Development (AMED)
- 21ak0101118h9903 Japan Agency for Medical Research and Development (AMED)
- JP18am0101093j0002 Japan Agency for Medical Research and Development (AMED)
- JP22ama121039 Japan Agency for Medical Research and Development (AMED)
- JP23gm1610012 Japan Agency for Medical Research and Development (AMED)
- JP23gm1610013 Japan Agency for Medical Research and Development (AMED)
- JST START Program: ST211004JO Japan Initiative for Global Research Network on Infectious Diseases (J-GRID) from the Ministry of Education, Culture, Sport, Science, and Technology in Japan, MEXT for the Joint Research Program of the Research Center for Zoonosis Control, Hokkaido University
- the Duke Science Technology Scholar Fund
- Takeda Foundation, The Tokyo Biomedical Research Foundation and was partly supported by Hokkaido University, Global Facility Center (GFC), Pharma Science Open Unit (PSOU), funded by MEXT under "Support Program for Implementation of New Equipment Sharing System"
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Affiliation(s)
- Kazuki Yamamoto
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, 060-0812, Japan.
- Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, 060-0812, Japan.
| | - Toyotaka Sato
- Laboratory of Veterinary Hygiene, School/Faculty of Veterinary Medicine, Hokkaido University, Kita-18, Nishi-9, Kita-ku, Sapporo, 060-0818, Japan
- Graduate School of Infectious Diseases, Hokkaido University, Kita-18, Nishi-9, Kita-ku, Sapporo, 060-0818, Japan
- One Health Research Center, Hokkaido University, Kita-18, Nishi-9, Kita-ku, Sapporo, 060-0818, Japan
| | - Aili Hao
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Kenta Asao
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, 060-0812, Japan
| | - Rintaro Kaguchi
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, 060-0812, Japan
| | - Shintaro Kusaka
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, 060-0812, Japan
| | | | - Daichi Kazamori
- Drug Discovery Laboratory, Wakunaga Pharmaceutical Co., Ltd., 1624, Shimokotachi, Koda-cho, Akitakata-shi, Hiroshima, 739-1195, Japan
| | - Kiki Seo
- Drug Discovery Laboratory, Wakunaga Pharmaceutical Co., Ltd., 1624, Shimokotachi, Koda-cho, Akitakata-shi, Hiroshima, 739-1195, Japan
| | - Satoshi Takahashi
- Division of Laboratory Medicine, Sapporo Medical University Hospital, Minami-1, Nishi-16, Chuo-ku, Sapporo, 060-8543, Japan
- Department of Infection Control and Laboratory Medicine, Sapporo Medical University School of Medicine, Minami-1, Nishi-16, Chuo-ku, Sapporo, 060-8543, Japan
| | - Motohiro Horiuchi
- Laboratory of Veterinary Hygiene, School/Faculty of Veterinary Medicine, Hokkaido University, Kita-18, Nishi-9, Kita-ku, Sapporo, 060-0818, Japan
- Graduate School of Infectious Diseases, Hokkaido University, Kita-18, Nishi-9, Kita-ku, Sapporo, 060-0818, Japan
- One Health Research Center, Hokkaido University, Kita-18, Nishi-9, Kita-ku, Sapporo, 060-0818, Japan
| | - Shin-Ichi Yokota
- Department of Microbiology, Sapporo Medical University School of Medicine, Minami-1, Nishi-17, Chuo-ku, Sapporo, 060-8556, Japan
| | - Seok-Yong Lee
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Satoshi Ichikawa
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, 060-0812, Japan.
- Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo, 060-0812, Japan.
- Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Sapporo, Japan.
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46
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Esfahani BG, Walia N, Neselu K, Aragon M, Askenasy I, Wei A, Mendez JH, Stroupe ME. Dimerization of assimilatory NADPH-dependent sulfite reductase reveals elements for diflavin reductase binding at a minimal interface. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.14.599029. [PMID: 38915618 PMCID: PMC11195156 DOI: 10.1101/2024.06.14.599029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Escherichia coli NADPH-dependent assimilatory sulfite reductase is responsible for fixing sulfur for incorporation into sulfur-containing biomolecules. The oxidoreductase is composed of two subunits, an NADPH, FMN, and FAD-binding diflavin reductase and an iron siroheme and Fe4S4-containing oxidase. How they interact has been an unknown for over 50 years because the complex is highly flexible, thus has been intransigent for traditional X-ray or cryo-EM structural analysis. Using a combination of the chameleon plunging system with a fluorinated lipid we overcame the challenge of preserving the minimal dimer between the subunits for high-resolution cryo-EM analysis. Here, we report the first structure of the complex between the reductase and oxidase, revealing how they interact in a minimal interface. Further, we determined the structural elements that discriminate between the pairing of a siroheme-containing oxidase with a diflavin reductase or a ferredoxin partner to channel the six electrons that reduce sulfite to sulfide.
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Affiliation(s)
- Behrouz Ghazi Esfahani
- Department of Biological Science and Institute of Molecular Biophysics, Florida State University, Tallahassee, FL, 32303, USA
| | - Nidhi Walia
- Department of Biological Science and Institute of Molecular Biophysics, Florida State University, Tallahassee, FL, 32303, USA
- Current Location: Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Kasahun Neselu
- New York Structural Biology Center, New York, NY, 10027, USA
| | - Mahira Aragon
- New York Structural Biology Center, New York, NY, 10027, USA
| | - Isabel Askenasy
- Department of Biological Science and Institute of Molecular Biophysics, Florida State University, Tallahassee, FL, 32303, USA
- Current Location: Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK
| | - Alex Wei
- New York Structural Biology Center, New York, NY, 10027, USA
| | | | - M. Elizabeth Stroupe
- Department of Biological Science and Institute of Molecular Biophysics, Florida State University, Tallahassee, FL, 32303, USA
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47
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Henze E, Ehrlich JJ, Robertson JL, Kawate T. The C-terminal activating domain promotes Panx1 channel opening. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.13.598903. [PMID: 38915727 PMCID: PMC11195165 DOI: 10.1101/2024.06.13.598903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Pannexin 1 (Panx1) constitutes a large pore channel responsible for the release of ATP from apoptotic cells. Strong evidence indicates that caspase-mediated cleavage of the C-terminus promotes the opening of the Panx1 channel by unplugging the pore. However, this simple pore-plugging mechanism alone cannot account for the observation that a Panx1 construct ending before the caspase cleavage site remains closed. Here, we show that a helical region located immediately before the caspase cleavage site, referred to as the "C-terminal activating domain (CAD)," plays a pivotal role in facilitating Panx1 activation. Electrophysiology and mutagenesis studies uncovered that two conserved leucine residues within the CAD plays a pivotal role. Cryo-EM analysis of the construct ending before reaching the CAD demonstrated that the N-terminus extends into an intracellular pocket. In contrast, the construct including the CAD revealed that this domain occupies the intracellular pocket, causing the N-terminus to flip upward within the pore. Analysis of electrostatic free energy landscape in the closed conformation indicated that the intracellular side of the ion permeation pore may be occupied by anions like ATP, creating an electrostatic barrier for anions attempting to permeate the pore. When the N-terminus flips up, it diminishes the positively charged surface, thereby reducing the drive to accumulate anions inside the pore. This dynamic change in the electrostatic landscape likely contributes to the selection of permeant ions. Collectively, these experiments put forth a novel mechanism in which C-terminal cleavage liberates the CAD, causing the repositioning of the N-terminus to promote Panx1 channel opening.
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Affiliation(s)
- Erik Henze
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA
| | | | - Janice L. Robertson
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Toshimitsu Kawate
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA
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48
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Thach T, Dhanabalan K, Nandekar PP, Stauffer S, Heisler I, Alvarado S, Snyder J, Subramanian R. A Second Drug Binding Site in P2X3. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.10.598171. [PMID: 38915546 PMCID: PMC11195084 DOI: 10.1101/2024.06.10.598171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Purinergic P2X3 receptors form trimeric cation-gated channels, which are activated by extracellular ATP. P2X3 plays a crucial role in chronic cough and affects over 10% of the population. Despite considerable efforts to develop drugs targeting P2X3, the highly conserved structure within the P2X receptor family presents obstacles for achieving selectivity. Camlipixant, a potent and selective P2X3 antagonist, is currently in phase III clinical trials. However, the mechanisms underlying receptor desensitization, ion permeation, principles governing antagonism, and the structure of P2X3 when bound to camlipixant remain elusive. In this study, we established a stable cell line expressing homotrimeric P2X3 and utilized a peptide scaffold to purify the complex and determine its structure using cryo-electron microscopy (cryo-EM). P2X3 binds to camlipixant at a previously unidentified drug-binding site and functions as an allosteric inhibitor. Structure-activity studies combined with modeling and simulations have shed light on the mechanisms underlying the selective targeting and inhibition of P2X3 by camlipixant, distinguishing it from other members of the P2X receptor family.
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Affiliation(s)
- Trung Thach
- Department of Biological Sciences, Purdue University, West Lafayette, IN-47907, USA
| | | | | | - Seth Stauffer
- Elanco Animal Health, 2500 Innovation Way, Greenfield, IN-46140, USA
| | - Iring Heisler
- Elanco Animal Health, 2500 Innovation Way, Greenfield, IN-46140, USA
| | - Sarah Alvarado
- Elanco Animal Health, 2500 Innovation Way, Greenfield, IN-46140, USA
| | - Jonathan Snyder
- Elanco Animal Health, 2500 Innovation Way, Greenfield, IN-46140, USA
| | - Ramaswamy Subramanian
- Department of Biological Sciences, Purdue University, West Lafayette, IN-47907, USA
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN-47907, USA
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49
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Arkinson C, Dong KC, Gee CL, Costello SM, Marqusee S, Martin A. Nub1 traps unfolded FAT10 for ubiquitin-independent degradation by the 26S proteasome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.12.598715. [PMID: 38915702 PMCID: PMC11195292 DOI: 10.1101/2024.06.12.598715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
The ubiquitin-like modifier FAT10 targets hundreds of proteins in the mammalian immune system to the 26S proteasome for degradation. This degradation pathway requires the cofactor Nub1, yet the underlying mechanisms remain unknown. Here, we reconstituted a minimal in vitro system and revealed that Nub1 utilizes FAT10's intrinsic instability to trap its N-terminal ubiquitin-like domain in an unfolded state and deliver it to the 26S proteasome for engagement, allowing the degradation of FAT10-ylated substrates in a ubiquitin- and p97-independent manner. Through hydrogen-deuterium exchange, structural modeling, and site-directed mutagenesis, we identified the formation of a peculiar complex with FAT10 that activates Nub1 for docking to the 26S proteasome, and our cryo-EM studies visualized the highly dynamic Nub1 complex bound to the proteasomal Rpn1 subunit during FAT10 delivery and the early stages of ATP-dependent degradation. These studies thus identified a novel mode of cofactor-mediated, ubiquitin-independent substrate delivery to the 26S proteasome that relies on trapping partially unfolded states for engagement by the proteasomal ATPase motor.
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Affiliation(s)
- Connor Arkinson
- California Institute for Quantitative Biosciences, University of California at Berkeley, Berkeley, CA94720, USA
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA94720, USA
- Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA94720, USA
| | - Ken C. Dong
- Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA94720, USA
| | - Christine L. Gee
- California Institute for Quantitative Biosciences, University of California at Berkeley, Berkeley, CA94720, USA
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA94720, USA
- Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA94720, USA
| | - Shawn M. Costello
- Biophysics Graduate Program, University of California, Berkeley, CA, USA
| | - Susan Marqusee
- California Institute for Quantitative Biosciences, University of California at Berkeley, Berkeley, CA94720, USA
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA94720, USA
- Department of Chemistry, University of California, Berkeley, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Andreas Martin
- California Institute for Quantitative Biosciences, University of California at Berkeley, Berkeley, CA94720, USA
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA94720, USA
- Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA94720, USA
- Lead contact
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50
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Navratna V, Kumar A, Rana JK, Mosalaganti S. Structure of the human systemic RNAi defective transmembrane protein 1 (hSIDT1) reveals the conformational flexibility of its lipid binding domain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.21.572875. [PMID: 38187772 PMCID: PMC10769365 DOI: 10.1101/2023.12.21.572875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
In C. elegans, inter-cellular transport of the small non-coding RNA causing systemic RNA interference (RNAi) is mediated by the transmembrane protein SID1, encoded by the sid1 gene in the systemic RNA interference-defective (sid) loci. SID1 shares structural and sequence similarity with cholesterol uptake protein 1 (CHUP1) and is classified as a member of the cholesterol uptake family (ChUP). Although systemic RNAi is not an evolutionarily conserved process, the sid gene products are found across the animal kingdom, suggesting the existence of other novel gene regulatory mechanisms mediated by small non-coding RNAs. Human homologs of sid gene products - hSIDT1 and hSIDT2 - mediate contact-dependent lipophilic small non-coding dsRNA transport. Here, we report the structure of recombinant human SIDT1. We find that the extra-cytosolic domain (ECD) of hSIDT1 adopts a double jelly roll fold, and the transmembrane domain (TMD) exists as two modules - a flexible lipid binding domain (LBD) and a rigid TMD core. Our structural analyses provide insights into the inherent conformational dynamics within the lipid binding domain in cholesterol uptake (ChUP) family members.
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Affiliation(s)
- Vikas Navratna
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, 48109, United States
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan, 48109, United States
| | - Arvind Kumar
- Thermo Fisher Scientific, Waltham, Massachusetts, 02451, United States
| | - Jaimin K. Rana
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, 48109, United States
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan, 48109, United States
| | - Shyamal Mosalaganti
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, 48109, United States
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan, 48109, United States
- Department of Biophysics, College of Literature, Science and the Arts, University of Michigan, Ann Arbor, Michigan, 48109, United States
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