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Yamagata A, Ito K, Suzuki T, Dohmae N, Terada T, Shirouzu M. Structural basis for antiepileptic drugs and botulinum neurotoxin recognition of SV2A. Nat Commun 2024; 15:3027. [PMID: 38637505 PMCID: PMC11026379 DOI: 10.1038/s41467-024-47322-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 03/26/2024] [Indexed: 04/20/2024] Open
Abstract
More than one percent of people have epilepsy worldwide. Levetiracetam (LEV) is a successful new-generation antiepileptic drug (AED), and its derivative, brivaracetam (BRV), shows improved efficacy. Synaptic vesicle glycoprotein 2a (SV2A), a putative membrane transporter in the synaptic vesicles (SVs), has been identified as a target of LEV and BRV. SV2A also serves as a receptor for botulinum neurotoxin (BoNT), which is the most toxic protein and has paradoxically emerged as a potent reagent for therapeutic and cosmetic applications. Nevertheless, no structural analysis on AEDs and BoNT recognition by full-length SV2A has been available. Here we describe the cryo-electron microscopy structures of the full-length SV2A in complex with the BoNT receptor-binding domain, BoNT/A2 HC, and either LEV or BRV. The large fourth luminal domain of SV2A binds to BoNT/A2 HC through protein-protein and protein-glycan interactions. LEV and BRV occupy the putative substrate-binding site in an outward-open conformation. A propyl group in BRV creates additional contacts with SV2A, explaining its higher binding affinity than that of LEV, which was further supported by label-free spectral shift assay. Numerous LEV derivatives have been developed as AEDs and positron emission tomography (PET) tracers for neuroimaging. Our work provides a structural framework for AEDs and BoNT recognition of SV2A and a blueprint for the rational design of additional AEDs and PET tracers.
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Affiliation(s)
- Atsushi Yamagata
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, Japan.
| | - Kaori Ito
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, Japan
| | - Takehiro Suzuki
- Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, Japan
| | - Naoshi Dohmae
- Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, Japan
| | - Tohru Terada
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, Japan
| | - Mikako Shirouzu
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, Japan
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Liu Z, Lee PG, Krez N, Lam KH, Liu H, Przykopanski A, Chen P, Yao G, Zhang S, Tremblay JM, Perry K, Shoemaker CB, Rummel A, Dong M, Jin R. Structural basis for botulinum neurotoxin E recognition of synaptic vesicle protein 2. Nat Commun 2023; 14:2338. [PMID: 37095076 PMCID: PMC10125960 DOI: 10.1038/s41467-023-37860-8] [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: 09/15/2021] [Accepted: 04/03/2023] [Indexed: 04/26/2023] Open
Abstract
Botulinum neurotoxin E (BoNT/E) is one of the major causes of human botulism and paradoxically also a promising therapeutic agent. Here we determined the co-crystal structures of the receptor-binding domain of BoNT/E (HCE) in complex with its neuronal receptor synaptic vesicle glycoprotein 2A (SV2A) and a nanobody that serves as a ganglioside surrogate. These structures reveal that the protein-protein interactions between HCE and SV2 provide the crucial location and specificity information for HCE to recognize SV2A and SV2B, but not the closely related SV2C. At the same time, HCE exploits a separated sialic acid-binding pocket to mediate recognition of an N-glycan of SV2. Structure-based mutagenesis and functional studies demonstrate that both the protein-protein and protein-glycan associations are essential for SV2A-mediated cell entry of BoNT/E and for its potent neurotoxicity. Our studies establish the structural basis to understand the receptor-specificity of BoNT/E and to engineer BoNT/E variants for new clinical applications.
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Affiliation(s)
- Zheng Liu
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA, 92697, USA
| | - Pyung-Gang Lee
- Department of Urology, Boston Children's Hospital, Boston, MA, 02115, USA
- Department of Microbiology and Department of Surgery, Harvard Medical School, Boston, MA, 02115, USA
| | - Nadja Krez
- Institute of Toxicology, Hannover Medical School, Hannover, 30623, Germany
| | - Kwok-Ho Lam
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA, 92697, USA
| | - Hao Liu
- Department of Urology, Boston Children's Hospital, Boston, MA, 02115, USA
- Department of Microbiology and Department of Surgery, Harvard Medical School, Boston, MA, 02115, USA
| | - Adina Przykopanski
- Institute of Toxicology, Hannover Medical School, Hannover, 30623, Germany
| | - Peng Chen
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA, 92697, USA
| | - Guorui Yao
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA, 92697, USA
| | - Sicai Zhang
- Department of Urology, Boston Children's Hospital, Boston, MA, 02115, USA
- Department of Microbiology and Department of Surgery, Harvard Medical School, Boston, MA, 02115, USA
| | | | - Kay Perry
- NE-CAT and Department of Chemistry and Chemical Biology, Cornell University, Argonne National Laboratory, Argonne, IL, 60439, USA
| | | | - Andreas Rummel
- Institute of Toxicology, Hannover Medical School, Hannover, 30623, Germany
| | - Min Dong
- Department of Urology, Boston Children's Hospital, Boston, MA, 02115, USA.
- Department of Microbiology and Department of Surgery, Harvard Medical School, Boston, MA, 02115, USA.
| | - Rongsheng Jin
- Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA, 92697, USA.
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Advances in Clostridial and Related Neurotoxins. Int J Mol Sci 2022; 23:ijms232214076. [PMID: 36430554 PMCID: PMC9697359 DOI: 10.3390/ijms232214076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 11/10/2022] [Indexed: 11/18/2022] Open
Abstract
The huge advances in genomics and molecular biology in the past two decades have made now an exciting time to study bacterial toxins, in particular, the most potent bacterial toxin known to humankind, botulinum neurotoxins (BoNTs) [...].
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Cottone G, Chiodo L, Maragliano L, Popoff MR, Rasetti-Escargueil C, Lemichez E, Malliavin TE. In Silico Conformational Features of Botulinum Toxins A1 and E1 According to Intraluminal Acidification. Toxins (Basel) 2022; 14:toxins14090644. [PMID: 36136581 PMCID: PMC9500700 DOI: 10.3390/toxins14090644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 08/13/2022] [Accepted: 09/10/2022] [Indexed: 11/16/2022] Open
Abstract
Although botulinum neurotoxins (BoNTs) are among the most toxic compounds found in nature, their molecular mechanism of action is far from being elucidated. A key event is the conformational transition due to acidification of the interior of synaptic vesicles, leading to translocation of the BoNT catalytic domain into the neuronal cytosol. To investigate these conformational variations, homology modeling and atomistic simulations are combined to explore the internal dynamics of the sub-types BoNT/A1 (the most-used sub-type in medical applications) and BoNT/E1 (the most kinetically efficient sub-type). This first simulation study of di-chain BoNTs in closed and open states considers the effects of both neutral and acidic pH. The conformational mobility is driven by domain displacements of the ganglioside-binding site in the receptor binding domain, the translocation domain (HCNT) switch, and the belt α-helix, which present multiple conformations, depending on the primary sequence and the pH. Fluctuations of the belt α-helix are observed for closed conformations of the toxins and at acidic pH, while patches of more solvent-accessible residues appear under the same conditions in the core translocation domain HCNT. These findings suggest that, during translocation, the higher mobility of the belt could be transmitted to HCNT, leading to the favorable interaction of HCNT residues with the non-polar membrane environment.
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Affiliation(s)
- Grazia Cottone
- Department of Physics and Chemistry Emilio Segré, University of Palermo, Viale delle Scienze, 90128 Palermo, Italy
| | - Letizia Chiodo
- Department of Engineering, University Campus Bio-Medico of Rome, Via Á. del Portillo 21, 00128 Rome, Italy
| | - Luca Maragliano
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131 Ancona, Italy
- Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Largo Rosanna Benzi 10, 16132 Genova, Italy
| | - Michel-Robert Popoff
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Inserm U1306, Unité des Toxines Bactériennes, 75015 Paris, France
| | - Christine Rasetti-Escargueil
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Inserm U1306, Unité des Toxines Bactériennes, 75015 Paris, France
| | - Emmanuel Lemichez
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Inserm U1306, Unité des Toxines Bactériennes, 75015 Paris, France
- Correspondence: (E.L.); (T.E.M.)
| | - Thérèse E. Malliavin
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Unité de Bioinformatique Structurale, 75015 Paris, France
- Laboratoire de Physique et Chimie Théoriques (LPCT), CNRS UMR7019, University of Lorraine, 54506 Vandoeuvre-lès-Nancy, France
- Laboratoire International Associé, CNRS and University of Illinois at Urbana-Champaign, 54506 Vandoeuvre-lès-Nancy, France
- Correspondence: (E.L.); (T.E.M.)
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Structural Analysis of Botulinum Neurotoxins Type B and E by Cryo-EM. Toxins (Basel) 2021; 14:toxins14010014. [PMID: 35050991 PMCID: PMC8781748 DOI: 10.3390/toxins14010014] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 12/20/2021] [Accepted: 12/21/2021] [Indexed: 11/17/2022] Open
Abstract
Botulinum neurotoxins (BoNTs) are the causative agents of a potentially lethal paralytic disease targeting cholinergic nerve terminals. Multiple BoNT serotypes exist, with types A, B and E being the main cause of human botulism. Their extreme toxicity has been exploited for cosmetic and therapeutic uses to treat a wide range of neuromuscular disorders. Although naturally occurring BoNT types share a common end effect, their activity varies significantly based on the neuronal cell-surface receptors and intracellular SNARE substrates they target. These properties are the result of structural variations that have traditionally been studied using biophysical methods such as X-ray crystallography. Here, we determined the first structures of botulinum neurotoxins using single-particle cryogenic electron microscopy. The maps obtained at 3.6 and 3.7 Å for BoNT/B and /E, respectively, highlight the subtle structural dynamism between domains, and of the binding domain in particular. This study demonstrates how the recent advances made in the field of single-particle electron microscopy can be applied to bacterial toxins of clinical relevance and the botulinum neurotoxin family in particular.
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