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Leka O, Wu Y, Zanetti G, Furler S, Reinberg T, Marinho J, Schaefer JV, Plückthun A, Li X, Pirazzini M, Kammerer RA. A DARPin promotes faster onset of botulinum neurotoxin A1 action. Nat Commun 2023; 14:8317. [PMID: 38110403 PMCID: PMC10728214 DOI: 10.1038/s41467-023-44102-4] [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: 12/24/2022] [Accepted: 11/30/2023] [Indexed: 12/20/2023] Open
Abstract
In this study, we characterize Designed Ankyrin Repeat Proteins (DARPins) as investigative tools to probe botulinum neurotoxin A1 (BoNT/A1) structure and function. We identify DARPin-F5 that completely blocks SNAP25 substrate cleavage by BoNT/A1 in vitro. X-ray crystallography reveals that DARPin-F5 inhibits BoNT/A1 activity by interacting with a substrate-binding region between the α- and β-exosite. This DARPin does not block substrate cleavage of BoNT/A3, indicating that DARPin-F5 is a subtype-specific inhibitor. BoNT/A1 Glu-171 plays a critical role in the interaction with DARPin-F5 and its mutation to Asp, the residue found in BoNT/A3, results in a loss of inhibition of substrate cleavage. In contrast to the in vitro results, DARPin-F5 promotes faster substrate cleavage of BoNT/A1 in primary neurons and muscle tissue by increasing toxin translocation. Our findings could have important implications for the application of BoNT/A1 in therapeutic areas requiring faster onset of toxin action combined with long persistence.
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Affiliation(s)
- Oneda Leka
- Laboratory of Biomolecular Research, Division of Biology, Paul Scherrer Institut, 5232, Villigen PSI, Switzerland
| | - Yufan Wu
- Laboratory of Biomolecular Research, Division of Biology, Paul Scherrer Institut, 5232, Villigen PSI, Switzerland
| | - Giulia Zanetti
- Department of Biomedical Sciences, University of Padova, 35121, Padova, Italy
| | - Sven Furler
- Department of Biochemistry, University of Zurich, 8057, Zurich, Switzerland
| | - Thomas Reinberg
- Department of Biochemistry, University of Zurich, 8057, Zurich, Switzerland
| | - Joana Marinho
- Department of Biochemistry, University of Zurich, 8057, Zurich, Switzerland
| | - Jonas V Schaefer
- Department of Biochemistry, University of Zurich, 8057, Zurich, Switzerland
| | - Andreas Plückthun
- Department of Biochemistry, University of Zurich, 8057, Zurich, Switzerland
| | - Xiaodan Li
- Laboratory of Biomolecular Research, Division of Biology, Paul Scherrer Institut, 5232, Villigen PSI, Switzerland
| | - Marco Pirazzini
- Department of Biomedical Sciences, University of Padova, 35121, Padova, Italy
| | - Richard A Kammerer
- Laboratory of Biomolecular Research, Division of Biology, Paul Scherrer Institut, 5232, Villigen PSI, Switzerland.
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Gregory KS, Hall PR, Onuh JP, Mojanaga OO, Liu SM, Acharya KR. Crystal Structure of the Catalytic Domain of a Botulinum Neurotoxin Homologue from Enterococcus faecium: Potential Insights into Substrate Recognition. Int J Mol Sci 2023; 24:12721. [PMID: 37628902 PMCID: PMC10454453 DOI: 10.3390/ijms241612721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 07/25/2023] [Accepted: 08/10/2023] [Indexed: 08/27/2023] Open
Abstract
Clostridium botulinum neurotoxins (BoNTs) are the most potent toxins known, causing the deadly disease botulism. They function through Zn2+-dependent endopeptidase cleavage of SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) proteins, preventing vesicular fusion and subsequent neurotransmitter release from motor neurons. Several serotypes of BoNTs produced by Clostridium botulinum (BoNT/A-/G and/X) have been well-characterised over the years. However, a BoNT-like gene (homologue of BoNT) was recently identified in the non-clostridial species, Enterococcus faecium, which is the leading cause of hospital-acquired multi-drug resistant infections. Here, we report the crystal structure of the catalytic domain of a BoNT homologue from Enterococcus faecium (LC/En) at 2.0 Å resolution. Detailed structural analysis in comparison with the full-length BoNT/En AlphaFold2-predicted structure, LC/A (from BoNT/A), and LC/F (from BoNT/F) revealed putative subsites and exosites (including loops 1-5) involved in recognition of LC/En substrates. LC/En also appears to possess a conserved autoproteolytic cleavage site whose function is yet to be established.
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Affiliation(s)
- Kyle S. Gregory
- Department of Life Sciences, University of Bath, Claverton Down, Bath BA2 7AY, UK; (K.S.G.); (P.-R.H.); (J.P.O.); (O.O.M.)
| | - Peter-Rory Hall
- Department of Life Sciences, University of Bath, Claverton Down, Bath BA2 7AY, UK; (K.S.G.); (P.-R.H.); (J.P.O.); (O.O.M.)
| | - Jude Prince Onuh
- Department of Life Sciences, University of Bath, Claverton Down, Bath BA2 7AY, UK; (K.S.G.); (P.-R.H.); (J.P.O.); (O.O.M.)
| | - Otsile O. Mojanaga
- Department of Life Sciences, University of Bath, Claverton Down, Bath BA2 7AY, UK; (K.S.G.); (P.-R.H.); (J.P.O.); (O.O.M.)
| | - Sai Man Liu
- Protein Sciences Department, Ipsen Bioinnovation Limited, 102 Park Drive, Milton Park, Abingdon OX14 4RY, UK;
| | - K. Ravi Acharya
- Department of Life Sciences, University of Bath, Claverton Down, Bath BA2 7AY, UK; (K.S.G.); (P.-R.H.); (J.P.O.); (O.O.M.)
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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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