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Gopal N, Leitz J, Wang C, Esquivies L, Pfuetzner RA, Brunger AT. A new method for isolation and purification of fusion-competent inhibitory synaptic vesicles. Curr Res Physiol 2024; 7:100121. [PMID: 38572021 PMCID: PMC10990708 DOI: 10.1016/j.crphys.2024.100121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 01/18/2024] [Accepted: 02/16/2024] [Indexed: 04/05/2024] Open
Abstract
Synaptic vesicles specific to inhibitory GABA-releasing neurons are critical for regulating neuronal excitability. To study the specific molecular composition, architecture, and function of inhibitory synaptic vesicles, we have developed a new method to isolate and purify GABA synaptic vesicles from mouse brains. GABA synaptic vesicles were immunoisolated from mouse brain tissue using an engineered fragment antigen-binding region (Fab) against the vesicular GABA transporter (vGAT) and purified. Western blot analysis confirmed that the GABA synaptic vesicles were specifically enriched for vGAT and largely depleted of contaminants from other synaptic vesicle types, such as vesicular glutamate transporter (vGLUT1), and other cellular organelles. This degree of purity was achieved despite the relatively low abundance of vGAT vesicles compared to the total synaptic vesicle pool in mammalian brains. Cryo-electron microscopy images of these isolated GABA synaptic vesicles revealed intact morphology with circular shape and protruding proteinaceous densities. The GABA synaptic vesicles are functional, as assessed by a hybrid (ex vivo/in vitro) vesicle fusion assay, and they undergo synchronized fusion with synthetic plasma membrane mimic vesicles in response to Ca2+-triggering, but, as a negative control, not to Mg2+-triggering. Our immunoisolation method could also be applied to other types of vesicles.
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Affiliation(s)
- Nisha Gopal
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, USA
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, USA
- Department of Structural Biology, Stanford University, Stanford, USA
- Department of Photon Science, Stanford University, Stanford, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, USA
| | - Jeremy Leitz
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, USA
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, USA
- Department of Structural Biology, Stanford University, Stanford, USA
- Department of Photon Science, Stanford University, Stanford, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, USA
| | - Chuchu Wang
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, USA
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, USA
- Department of Structural Biology, Stanford University, Stanford, USA
- Department of Photon Science, Stanford University, Stanford, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, USA
| | - Luis Esquivies
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, USA
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, USA
- Department of Structural Biology, Stanford University, Stanford, USA
- Department of Photon Science, Stanford University, Stanford, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, USA
| | - Richard A. Pfuetzner
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, USA
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, USA
- Department of Structural Biology, Stanford University, Stanford, USA
- Department of Photon Science, Stanford University, Stanford, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, USA
| | - Axel T. Brunger
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, USA
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, USA
- Department of Structural Biology, Stanford University, Stanford, USA
- Department of Photon Science, Stanford University, Stanford, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, USA
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Yang K, Wang C, Kreutzberger AJB, White KI, Pfuetzner RA, Esquivies L, Kirchhausen T, Brunger AT. Structure-based design of a SARS-CoV-2 Omicron-specific inhibitor. Proc Natl Acad Sci U S A 2023; 120:e2300360120. [PMID: 36940324 PMCID: PMC10068829 DOI: 10.1073/pnas.2300360120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 02/13/2023] [Indexed: 03/22/2023] Open
Abstract
The Omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) introduced a relatively large number of mutations, including three mutations in the highly conserved heptad repeat 1 (HR1) region of the spike glycoprotein (S) critical for its membrane fusion activity. We show that one of these mutations, N969K induces a substantial displacement in the structure of the heptad repeat 2 (HR2) backbone in the HR1HR2 postfusion bundle. Due to this mutation, fusion-entry peptide inhibitors based on the Wuhan strain sequence are less efficacious. Here, we report an Omicron-specific peptide inhibitor designed based on the structure of the Omicron HR1HR2 postfusion bundle. Specifically, we inserted an additional residue in HR2 near the Omicron HR1 K969 residue to better accommodate the N969K mutation and relieve the distortion in the structure of the HR1HR2 postfusion bundle it introduced. The designed inhibitor recovers the loss of inhibition activity of the original longHR2_42 peptide with the Wuhan strain sequence against the Omicron variant in both a cell-cell fusion assay and a vesicular stomatitis virus (VSV)-SARS-CoV-2 chimera infection assay, suggesting that a similar approach could be used to combat future variants. From a mechanistic perspective, our work suggests the interactions in the extended region of HR2 may mediate the initial landing of HR2 onto HR1 during the transition of the S protein from the prehairpin intermediate to the postfusion state.
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Affiliation(s)
- Kailu Yang
- HHMI, Stanford University, Stanford, CA94305
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA94305
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA94305
- Department of Structural Biology, Stanford University, Stanford, CA94305
- Department of Photon Science, Stanford University, Stanford, CA94305
| | - Chuchu Wang
- HHMI, Stanford University, Stanford, CA94305
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA94305
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA94305
- Department of Structural Biology, Stanford University, Stanford, CA94305
- Department of Photon Science, Stanford University, Stanford, CA94305
| | - Alex J. B. Kreutzberger
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA02115
- Department of Pediatrics, Harvard Medical School, Boston, MA02115
| | - K. Ian White
- HHMI, Stanford University, Stanford, CA94305
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA94305
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA94305
- Department of Structural Biology, Stanford University, Stanford, CA94305
- Department of Photon Science, Stanford University, Stanford, CA94305
| | - Richard A. Pfuetzner
- HHMI, Stanford University, Stanford, CA94305
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA94305
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA94305
- Department of Structural Biology, Stanford University, Stanford, CA94305
- Department of Photon Science, Stanford University, Stanford, CA94305
| | - Luis Esquivies
- HHMI, Stanford University, Stanford, CA94305
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA94305
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA94305
- Department of Structural Biology, Stanford University, Stanford, CA94305
- Department of Photon Science, Stanford University, Stanford, CA94305
| | - Tomas Kirchhausen
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA02115
- Department of Pediatrics, Harvard Medical School, Boston, MA02115
- Department of Cell Biology, Harvard Medical School, Boston, MA02115
| | - Axel T. Brunger
- HHMI, Stanford University, Stanford, CA94305
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA94305
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA94305
- Department of Structural Biology, Stanford University, Stanford, CA94305
- Department of Photon Science, Stanford University, Stanford, CA94305
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3
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Jaczynska K, Esquivies L, Pfuetzner RA, Alten B, Brewer KD, Zhou Q, Kavalali ET, Brunger AT, Rizo J. Analysis of tripartite Synaptotagmin-1-SNARE-complexin-1 complexes in solution. FEBS Open Bio 2023; 13:26-50. [PMID: 36305864 PMCID: PMC9811660 DOI: 10.1002/2211-5463.13503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/19/2022] [Accepted: 10/27/2022] [Indexed: 01/07/2023] Open
Abstract
Characterizing interactions of Synaptotagmin-1 with the SNARE complex is crucial to understand the mechanism of neurotransmitter release. X-ray crystallography revealed how the Synaptotagmin-1 C2 B domain binds to the SNARE complex through a so-called primary interface and to a complexin-1-SNARE complex through a so-called tripartite interface. Mutagenesis and electrophysiology supported the functional relevance of both interfaces, and extensive additional data validated the primary interface. However, ITC evidence suggesting that binding via the tripartite interface occurs in solution was called into question by subsequent NMR data. Here, we describe joint efforts to address this apparent contradiction. Using the same ITC approach with the same C2 B domain mutant used previously (C2 BKA-Q ) but including ion exchange chromatography to purify it, which is crucial to remove polyacidic contaminants, we were unable to observe the substantial endothermic ITC signal that was previously attributed to binding of this mutant to the complexin-1-SNARE complex through the tripartite interface. We were also unable to detect substantial populations of the tripartite interface in NMR analyses of the ITC samples or in measurements of paramagnetic relaxation effects, despite the high sensitivity of this method to detect weak protein complexes. However, these experiments do not rule out the possibility of very low affinity (KD > 1 mm) binding through this interface. These results emphasize the need to develop methods to characterize the structure of synaptotagmin-1-SNARE complexes between two membranes and to perform further structure-function analyses to establish the physiological relevance of the tripartite interface.
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Affiliation(s)
- Klaudia Jaczynska
- Department of BiophysicsUniversity of Texas Southwestern Medical CenterDallasTXUSA
- Department of BiochemistryUniversity of Texas Southwestern Medical CenterDallasTXUSA
- Department of PharmacologyUniversity of Texas Southwestern Medical CenterDallasTXUSA
| | - Luis Esquivies
- Department of Molecular and Cellular PhysiologyStanford UniversityCAUSA
- Department of Neurology and Neurological SciencesStanford UniversityCAUSA
- Department of Structural BiologyStanford UniversityCAUSA
- Department of Photon ScienceStanford UniversityCAUSA
- Howard Hughes Medical InstituteStanford UniversityCAUSA
| | - Richard A. Pfuetzner
- Department of Molecular and Cellular PhysiologyStanford UniversityCAUSA
- Department of Neurology and Neurological SciencesStanford UniversityCAUSA
- Department of Structural BiologyStanford UniversityCAUSA
- Department of Photon ScienceStanford UniversityCAUSA
- Howard Hughes Medical InstituteStanford UniversityCAUSA
| | - Baris Alten
- Department of PharmacologyVanderbilt UniversityNashvilleTNUSA
- Vanderbilt Brain InstituteVanderbilt UniversityNashvilleTNUSA
- Present address:
Department of NeurologyMassachusetts General HospitalBostonMAUSA
- Present address:
Department of NeurologyBrigham and Women's HospitalBostonMAUSA
- Present address:
Harvard Medical SchoolBostonMAUSA
| | - Kyle D. Brewer
- Department of BiophysicsUniversity of Texas Southwestern Medical CenterDallasTXUSA
- Department of BiochemistryUniversity of Texas Southwestern Medical CenterDallasTXUSA
- Department of PharmacologyUniversity of Texas Southwestern Medical CenterDallasTXUSA
- Present address:
ETTA BiotechnologyPalo AltoCAUSA
| | - Qiangjun Zhou
- Vanderbilt Brain InstituteVanderbilt UniversityNashvilleTNUSA
- Department of Cell and Developmental BiologyVanderbilt UniversityNashvilleTNUSA
| | - Ege T. Kavalali
- Department of PharmacologyVanderbilt UniversityNashvilleTNUSA
- Vanderbilt Brain InstituteVanderbilt UniversityNashvilleTNUSA
| | - Axel T. Brunger
- Department of Molecular and Cellular PhysiologyStanford UniversityCAUSA
- Department of Neurology and Neurological SciencesStanford UniversityCAUSA
- Department of Structural BiologyStanford UniversityCAUSA
- Department of Photon ScienceStanford UniversityCAUSA
- Howard Hughes Medical InstituteStanford UniversityCAUSA
| | - Josep Rizo
- Department of BiophysicsUniversity of Texas Southwestern Medical CenterDallasTXUSA
- Department of BiochemistryUniversity of Texas Southwestern Medical CenterDallasTXUSA
- Department of PharmacologyUniversity of Texas Southwestern Medical CenterDallasTXUSA
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4
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Yang K, Wang C, Kreutzberger AJB, Ojha R, Kuivanen S, Couoh-Cardel S, Muratcioglu S, Eisen TJ, White KI, Held RG, Subramanian S, Marcus K, Pfuetzner RA, Esquivies L, Doyle CA, Kuriyan J, Vapalahti O, Balistreri G, Kirchhausen T, Brunger AT. Nanomolar inhibition of SARS-CoV-2 infection by an unmodified peptide targeting the prehairpin intermediate of the spike protein. Proc Natl Acad Sci U S A 2022; 119:e2210990119. [PMID: 36122200 PMCID: PMC9546559 DOI: 10.1073/pnas.2210990119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 08/16/2022] [Indexed: 12/02/2022] Open
Abstract
Variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) challenge currently available coronavirus disease 2019 vaccines and monoclonal antibody therapies through epitope change on the receptor binding domain of the viral spike glycoprotein. Hence, there is a specific urgent need for alternative antivirals that target processes less likely to be affected by mutation, such as the membrane fusion step of viral entry into the host cell. One such antiviral class includes peptide inhibitors, which block formation of the so-called heptad repeat 1 and 2 (HR1HR2) six-helix bundle of the SARS-CoV-2 spike (S) protein and thus interfere with viral membrane fusion. We performed structural studies of the HR1HR2 bundle, revealing an extended, well-folded N-terminal region of HR2 that interacts with the HR1 triple helix. Based on this structure, we designed an extended HR2 peptide that achieves single-digit nanomolar inhibition of SARS-CoV-2 in cell-based and virus-based assays without the need for modifications such as lipidation or chemical stapling. The peptide also strongly inhibits all major SARS-CoV-2 variants to date. This extended peptide is ∼100-fold more potent than all previously published short, unmodified HR2 peptides, and it has a very long inhibition lifetime after washout in virus infection assays, suggesting that it targets a prehairpin intermediate of the SARS-CoV-2 S protein. Together, these results suggest that regions outside the HR2 helical region may offer new opportunities for potent peptide-derived therapeutics for SARS-CoV-2 and its variants, and even more distantly related viruses, and provide further support for the prehairpin intermediate of the S protein.
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Affiliation(s)
- Kailu Yang
- HHMI, Stanford University, Stanford, CA 94305
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305
- Department of Structural Biology, Stanford University, Stanford, CA 94305
- Department of Photon Science, Stanford University, Stanford, CA 94305
| | - Chuchu Wang
- HHMI, Stanford University, Stanford, CA 94305
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305
- Department of Structural Biology, Stanford University, Stanford, CA 94305
- Department of Photon Science, Stanford University, Stanford, CA 94305
| | - Alex J. B. Kreutzberger
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115
| | - Ravi Ojha
- Department of Virology, University of Helsinki, Helsinki 00290, Finland
| | - Suvi Kuivanen
- Department of Virology, University of Helsinki, Helsinki 00290, Finland
| | - Sergio Couoh-Cardel
- HHMI, Stanford University, Stanford, CA 94305
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305
- Department of Structural Biology, Stanford University, Stanford, CA 94305
- Department of Photon Science, Stanford University, Stanford, CA 94305
| | - Serena Muratcioglu
- HHMI, University of California, Berkeley, Berkeley, CA 94720
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
| | - Timothy J. Eisen
- HHMI, University of California, Berkeley, Berkeley, CA 94720
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
| | - K. Ian White
- HHMI, Stanford University, Stanford, CA 94305
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305
- Department of Structural Biology, Stanford University, Stanford, CA 94305
- Department of Photon Science, Stanford University, Stanford, CA 94305
| | - Richard G. Held
- HHMI, Stanford University, Stanford, CA 94305
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305
- Department of Structural Biology, Stanford University, Stanford, CA 94305
- Department of Photon Science, Stanford University, Stanford, CA 94305
| | - Subu Subramanian
- HHMI, University of California, Berkeley, Berkeley, CA 94720
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
| | - Kendra Marcus
- HHMI, University of California, Berkeley, Berkeley, CA 94720
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
| | - Richard A. Pfuetzner
- HHMI, Stanford University, Stanford, CA 94305
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305
- Department of Structural Biology, Stanford University, Stanford, CA 94305
- Department of Photon Science, Stanford University, Stanford, CA 94305
| | - Luis Esquivies
- HHMI, Stanford University, Stanford, CA 94305
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305
- Department of Structural Biology, Stanford University, Stanford, CA 94305
- Department of Photon Science, Stanford University, Stanford, CA 94305
| | - Catherine A. Doyle
- Department of Pharmacology, University of Virginia, Charlottesville, VA 22903
| | - John Kuriyan
- HHMI, University of California, Berkeley, Berkeley, CA 94720
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
| | - Olli Vapalahti
- Department of Virology, University of Helsinki, Helsinki 00290, Finland
- Department of Veterinary Biosciences, University of Helsinki, Helsinki 00290, Finland
- Helsinki University Hospital Diagnostic Center, Clinical Microbiology, University of Helsinki, Helsinki 00290, Finland
| | | | - Tom Kirchhausen
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115
- Program in Cellular and Molecular Medicine, Boston Children’s Hospital, Boston, MA 02115
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115
| | - Axel T. Brunger
- HHMI, Stanford University, Stanford, CA 94305
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305
- Department of Structural Biology, Stanford University, Stanford, CA 94305
- Department of Photon Science, Stanford University, Stanford, CA 94305
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5
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Yang K, Wang C, Kreutzberger AJB, Ojha R, Kuivanen S, Couoh-Cardel S, Muratcioglu S, Eisen TJ, White KI, Held RG, Subramanian S, Marcus K, Pfuetzner RA, Esquivies L, Doyle CA, Kuriyan J, Vapalahti O, Balistreri G, Kirchhausen T, Brunger AT. Nanomolar inhibition of SARS-CoV-2 infection by an unmodified peptide targeting the pre-hairpin intermediate of the spike protein. bioRxiv 2022:2022.08.11.503553. [PMID: 35982670 PMCID: PMC9387137 DOI: 10.1101/2022.08.11.503553] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) challenge currently available COVID-19 vaccines and monoclonal antibody therapies through epitope change on the receptor binding domain of the viral spike glycoprotein. Hence, there is a specific urgent need for alternative antivirals that target processes less likely to be affected by mutation, such as the membrane fusion step of viral entry into the host cell. One such antiviral class includes peptide inhibitors which block formation of the so-called HR1HR2 six-helix bundle of the SARS-CoV-2 spike (S) protein and thus interfere with viral membrane fusion. Here we performed structural studies of the HR1HR2 bundle, revealing an extended, well-folded N-terminal region of HR2 that interacts with the HR1 triple helix. Based on this structure, we designed an extended HR2 peptide that achieves single-digit nanomolar inhibition of SARS-CoV-2 in cell-based fusion, VSV-SARS-CoV-2 chimera, and authentic SARS-CoV-2 infection assays without the need for modifications such as lipidation or chemical stapling. The peptide also strongly inhibits all major SARS-CoV-2 variants to date. This extended peptide is ~100-fold more potent than all previously published short, unmodified HR2 peptides, and it has a very long inhibition lifetime after washout in virus infection assays, suggesting that it targets a pre-hairpin intermediate of the SARS-CoV-2 S protein. Together, these results suggest that regions outside the HR2 helical region may offer new opportunities for potent peptide-derived therapeutics for SARS-CoV-2 and its variants, and even more distantly related viruses, and provide further support for the pre-hairpin intermediate of the S protein. Significance Statement SARS-CoV-2 infection requires fusion of viral and host membranes, mediated by the viral spike glycoprotein (S). Due to the importance of viral membrane fusion, S has been a popular target for developing vaccines and therapeutics. We discovered a simple peptide that inhibits infection by all major variants of SARS-CoV-2 with nanomolar efficacies. In marked contrast, widely used shorter peptides that lack a key N-terminal extension are about 100 x less potent than this peptide. Our results suggest that a simple peptide with a suitable sequence can be a potent and cost-effective therapeutic against COVID-19 and they provide new insights at the virus entry mechanism.
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Lai Y, Tuvim MJ, Leitz J, Peters J, Pfuetzner RA, Esquivies L, Zhou Q, Czako B, Cross JB, Jones P, Dickey BF, Brunger AT. Screening of Hydrocarbon-Stapled Peptides for Inhibition of Calcium-Triggered Exocytosis. Front Pharmacol 2022; 13:891041. [PMID: 35814209 PMCID: PMC9258623 DOI: 10.3389/fphar.2022.891041] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 04/14/2022] [Indexed: 11/13/2022] Open
Abstract
The so-called primary interface between the SNARE complex and synaptotagmin-1 (Syt1) is essential for Ca2+-triggered neurotransmitter release in neuronal synapses. The interacting residues of the primary interface are conserved across different species for synaptotagmins (Syt1, Syt2, Syt9), SNAP-25, and syntaxin-1A homologs involved in fast synchronous release. This Ca2+-independent interface forms prior to Ca2+-triggering and plays a role in synaptic vesicle priming. This primary interface is also conserved in the fusion machinery that is responsible for mucin granule membrane fusion. Ca2+-stimulated mucin secretion is mediated by the SNAREs syntaxin-3, SNAP-23, VAMP8, Syt2, and other proteins. Here, we designed and screened a series of hydrocarbon-stapled peptides consisting of SNAP-25 fragments that included some of the key residues involved in the primary interface as observed in high-resolution crystal structures. We selected a subset of four stapled peptides that were highly α-helical as assessed by circular dichroism and that inhibited both Ca2+-independent and Ca2+-triggered ensemble lipid-mixing with neuronal SNAREs and Syt1. In a single-vesicle content-mixing assay with reconstituted neuronal SNAREs and Syt1 or with reconstituted airway SNAREs and Syt2, the selected peptides also suppressed Ca2+-triggered fusion. Taken together, hydrocarbon-stapled peptides that interfere with the primary interface consequently inhibit Ca2+-triggered exocytosis. Our inhibitor screen suggests that these compounds may be useful to combat mucus hypersecretion, which is a major cause of airway obstruction in the pathophysiology of COPD, asthma, and cystic fibrosis.
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Affiliation(s)
- Ying Lai
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, United States,*Correspondence: Axel T. Brunger, ; Ying Lai, ; Burton F. Dickey,
| | - Michael J. Tuvim
- Department of Pulmonary Medicine, MD Anderson Cancer Center, University of Texas, Houston, TX, United States
| | - Jeremy Leitz
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, United States
| | - John Peters
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, United States
| | - Richard A. Pfuetzner
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, United States,Howard Hughes Medical Institute, Stanford University, Stanford, CA, United States
| | - Luis Esquivies
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, United States,Howard Hughes Medical Institute, Stanford University, Stanford, CA, United States
| | - Qiangjun Zhou
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, United States
| | - Barbara Czako
- Institute for Applied Cancer Science, MD Anderson Cancer Center, University of Texas, Houston, TX, United States
| | - Jason B. Cross
- Institute for Applied Cancer Science, MD Anderson Cancer Center, University of Texas, Houston, TX, United States
| | - Philip Jones
- Institute for Applied Cancer Science, MD Anderson Cancer Center, University of Texas, Houston, TX, United States
| | - Burton F. Dickey
- Department of Pulmonary Medicine, MD Anderson Cancer Center, University of Texas, Houston, TX, United States,*Correspondence: Axel T. Brunger, ; Ying Lai, ; Burton F. Dickey,
| | - Axel T. Brunger
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, United States,Howard Hughes Medical Institute, Stanford University, Stanford, CA, United States,*Correspondence: Axel T. Brunger, ; Ying Lai, ; Burton F. Dickey,
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7
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Yang K, Wang C, White KI, Pfuetzner RA, Esquivies L, Brunger AT. Structural conservation among variants of the SARS-CoV-2 spike postfusion bundle. Proc Natl Acad Sci U S A 2022; 119:e2119467119. [PMID: 35363556 PMCID: PMC9169775 DOI: 10.1073/pnas.2119467119] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Accepted: 02/22/2022] [Indexed: 01/10/2023] Open
Abstract
Variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) challenge currently available COVID-19 vaccines and monoclonal antibody therapies due to structural and dynamic changes of the viral spike glycoprotein (S). The heptad repeat 1 (HR1) and heptad repeat 2 (HR2) domains of S drive virus–host membrane fusion by assembly into a six-helix bundle, resulting in delivery of viral RNA into the host cell. We surveyed mutations of currently reported SARS-CoV-2 variants and selected eight mutations, including Q954H, N969K, and L981F from the Omicron variant, in the postfusion HR1HR2 bundle for functional and structural studies. We designed a molecular scaffold to determine cryogenic electron microscopy (cryo-EM) structures of HR1HR2 at 2.2–3.8 Å resolution by linking the trimeric N termini of four HR1 fragments to four trimeric C termini of the Dps4 dodecamer from Nostoc punctiforme. This molecular scaffold enables efficient sample preparation and structure determination of the HR1HR2 bundle and its mutants by single-particle cryo-EM. Our structure of the wild-type HR1HR2 bundle resolves uncertainties in previously determined structures. The mutant structures reveal side-chain positions of the mutations and their primarily local effects on the interactions between HR1 and HR2. These mutations do not alter the global architecture of the postfusion HR1HR2 bundle, suggesting that the interfaces between HR1 and HR2 are good targets for developing antiviral inhibitors that should be efficacious against all known variants of SARS-CoV-2 to date. We also note that this work paves the way for similar studies in more distantly related viruses.
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Affiliation(s)
- Kailu Yang
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305
- Department of Structural Biology, Stanford University, Stanford, CA 94305
- Department of Photon Science, Stanford University, Stanford, CA 94305
- HHMI, Stanford University, Stanford, CA 94305
| | - Chuchu Wang
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305
- Department of Structural Biology, Stanford University, Stanford, CA 94305
- Department of Photon Science, Stanford University, Stanford, CA 94305
- HHMI, Stanford University, Stanford, CA 94305
| | - K. Ian White
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305
- Department of Structural Biology, Stanford University, Stanford, CA 94305
- Department of Photon Science, Stanford University, Stanford, CA 94305
- HHMI, Stanford University, Stanford, CA 94305
| | - Richard A. Pfuetzner
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305
- Department of Structural Biology, Stanford University, Stanford, CA 94305
- Department of Photon Science, Stanford University, Stanford, CA 94305
- HHMI, Stanford University, Stanford, CA 94305
| | - Luis Esquivies
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305
- Department of Structural Biology, Stanford University, Stanford, CA 94305
- Department of Photon Science, Stanford University, Stanford, CA 94305
- HHMI, Stanford University, Stanford, CA 94305
| | - Axel T. Brunger
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305
- Department of Structural Biology, Stanford University, Stanford, CA 94305
- Department of Photon Science, Stanford University, Stanford, CA 94305
- HHMI, Stanford University, Stanford, CA 94305
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Dunleavy K, Matlock H, Pfuetzner R, Esquivies L, Howells G, Misra B, Gething C, Brunger A, Choi U. Conformational Dynamics of SNARE Proteins during NSF‐Mediated Disassembly. FASEB J 2021. [DOI: 10.1096/fasebj.2021.35.s1.03481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | | | - Richard Pfuetzner
- Molecular and Cellular PhysiologyStanford UniversityStanfordCA
- Howard Hughes Medical InstituteStanford UniversityStanfordCA
| | - Luis Esquivies
- Molecular and Cellular PhysiologyStanford UniversityStanfordCA
- Howard Hughes Medical InstituteStanford UniversityStanfordCA
| | | | - Bishal Misra
- BiochemistryWest Virginia UniversityMorgantownWV
| | | | - Axel Brunger
- Molecular and Cellular PhysiologyStanford UniversityStanfordCA
- Howard Hughes Medical InstituteStanford UniversityStanfordCA
| | - Ucheor Choi
- BiochemistryWest Virginia UniversityMorgantownWV
- Howard Hughes Medical InstituteStanford UniversityStanfordCA
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Alten B, Zhou Q, Shin OH, Esquivies L, Lin PY, White KI, Sun R, Chung WK, Monteggia LM, Brunger AT, Kavalali ET. Role of Aberrant Spontaneous Neurotransmission in SNAP25-Associated Encephalopathies. Neuron 2020; 109:59-72.e5. [PMID: 33147442 DOI: 10.1016/j.neuron.2020.10.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 09/09/2020] [Accepted: 10/07/2020] [Indexed: 01/19/2023]
Abstract
SNARE (soluble N-ethylmaleimide sensitive factor attachment protein receptor) complex, composed of synaptobrevin, syntaxin, and SNAP25, forms the essential fusion machinery for neurotransmitter release. Recent studies have reported several mutations in the gene encoding SNAP25 as a causative factor for developmental and epileptic encephalopathies of infancy and childhood with diverse clinical manifestations. However, it remains unclear how SNAP25 mutations give rise to these disorders. Here, we show that although structurally clustered mutations in SNAP25 give rise to related synaptic transmission phenotypes, specific alterations in spontaneous neurotransmitter release are a key factor to account for disease heterogeneity. Importantly, we identified a single mutation that augments spontaneous release without altering evoked release, suggesting that aberrant spontaneous release is sufficient to cause disease in humans.
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Affiliation(s)
- Baris Alten
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37240-7933, USA; Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN 37240-7933, USA
| | - Qiangjun Zhou
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37240-7933, USA; Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN 37240-7933, USA; Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37240-7933, USA
| | - Ok-Ho Shin
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37240-7933, USA; Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN 37240-7933, USA
| | - Luis Esquivies
- Department of Molecular and Cellular Physiology, Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Pei-Yi Lin
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37240-7933, USA; Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN 37240-7933, USA
| | - K Ian White
- Department of Molecular and Cellular Physiology, Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Rong Sun
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37240-7933, USA; Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN 37240-7933, USA; Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37240-7933, USA
| | - Wendy K Chung
- Department of Pediatrics (in Medicine), Columbia University Medical Center, New York, NY 10032, USA
| | - Lisa M Monteggia
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37240-7933, USA; Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN 37240-7933, USA
| | - Axel T Brunger
- Department of Molecular and Cellular Physiology, Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Ege T Kavalali
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37240-7933, USA; Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN 37240-7933, USA.
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10
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Choi UB, Zhao M, White KI, Pfuetzner RA, Esquivies L, Zhou Q, Brunger AT. NSF-mediated disassembly of on- and off-pathway SNARE complexes and inhibition by complexin. eLife 2018; 7:36497. [PMID: 29985126 PMCID: PMC6130971 DOI: 10.7554/elife.36497] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 07/06/2018] [Indexed: 12/24/2022] Open
Abstract
SNARE complex disassembly by the ATPase NSF is essential for neurotransmitter release and other membrane trafficking processes. We developed a single-molecule FRET assay to monitor repeated rounds of NSF-mediated disassembly and reassembly of individual SNARE complexes. For ternary neuronal SNARE complexes, disassembly proceeds in a single step within 100 msec. We observed short- (<0.32 s) and long-lived (≥0.32 s) disassembled states. The long-lived states represent fully disassembled SNARE complex, while the short-lived states correspond to failed disassembly or immediate reassembly. Either high ionic strength or decreased αSNAP concentration reduces the disassembly rate while increasing the frequency of short-lived states. NSF is also capable of disassembling anti-parallel ternary SNARE complexes, implicating it in quality control. Finally, complexin-1 competes with αSNAP binding to the SNARE complex; addition of complexin-1 has an effect similar to that of decreasing the αSNAP concentration, possibly differentially regulating cis and trans SNARE complexes disassembly.
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Affiliation(s)
- Ucheor B Choi
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States.,Department of Neurology and Neurological Sciences, Stanford University, Stanford, United States.,Department of Structural Biology, Stanford University, Stanford, United States.,Department of Photon Science, Stanford University, Stanford, United States.,Howard Hughes Medical Institute, Stanford University, Stanford, United States
| | - Minglei Zhao
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, United States
| | - K Ian White
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States.,Department of Neurology and Neurological Sciences, Stanford University, Stanford, United States.,Department of Structural Biology, Stanford University, Stanford, United States.,Department of Photon Science, Stanford University, Stanford, United States.,Howard Hughes Medical Institute, Stanford University, Stanford, United States
| | - Richard A Pfuetzner
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States.,Department of Neurology and Neurological Sciences, Stanford University, Stanford, United States.,Department of Structural Biology, Stanford University, Stanford, United States.,Department of Photon Science, Stanford University, Stanford, United States.,Howard Hughes Medical Institute, Stanford University, Stanford, United States
| | - Luis Esquivies
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States.,Department of Neurology and Neurological Sciences, Stanford University, Stanford, United States.,Department of Structural Biology, Stanford University, Stanford, United States.,Department of Photon Science, Stanford University, Stanford, United States.,Howard Hughes Medical Institute, Stanford University, Stanford, United States
| | - Qiangjun Zhou
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States.,Department of Neurology and Neurological Sciences, Stanford University, Stanford, United States.,Department of Structural Biology, Stanford University, Stanford, United States.,Department of Photon Science, Stanford University, Stanford, United States.,Howard Hughes Medical Institute, Stanford University, Stanford, United States
| | - Axel T Brunger
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States.,Department of Neurology and Neurological Sciences, Stanford University, Stanford, United States.,Department of Structural Biology, Stanford University, Stanford, United States.,Department of Photon Science, Stanford University, Stanford, United States.,Howard Hughes Medical Institute, Stanford University, Stanford, United States
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Yoon BH, Esquivies L, Ahn C, Gray PC, Ye SK, Kwiatkowski W, Choe S. An activin A/BMP2 chimera, AB204, displays bone-healing properties superior to those of BMP2. J Bone Miner Res 2014; 29:1950-9. [PMID: 24692083 PMCID: PMC4276739 DOI: 10.1002/jbmr.2238] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Revised: 03/02/2014] [Accepted: 03/13/2014] [Indexed: 12/27/2022]
Abstract
Recombinant bone morphogenetic protein 2 (rhBMP2) has been used clinically to treat bone fractures in human patients. However, the high doses of rhBMP2 required for a therapeutic response can cause undesirable side effects. Here, we demonstrate that a novel Activin A/BMP2 (AB2) chimera, AB204, promotes osteogenesis and bone healing much more potently and effectively than rhBMP2. Remarkably, 1 month of AB204 treatment completely heals tibial and calvarial defects of critical size in mice at a concentration 10-fold lower than a dose of rhBMP2 that only partially heals the defect. We determine the structure of AB204 to 2.3 Å that reveals a distinct BMP2-like fold in which the Activin A sequence segments confer insensitivity to the BMP2 antagonist Noggin and an affinity for the Activin/BMP type II receptor ActRII that is 100-fold greater than that of BMP2. The structure also led to our identification of a single Activin A-derived amino acid residue, which, when mutated to the corresponding BMP2 residue, resulted in a significant increase in the affinity of AB204 for its type I receptor BMPRIa and a further enhancement in AB204's osteogenic potency. Together, these findings demonstrate that rationally designed AB2 chimeras can provide BMP2 substitutes with enhanced potency for treating non-union bone fractures.
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Affiliation(s)
- Byung-Hak Yoon
- Protein Engineering Laboratory, Joint Center for Biosciences at Songdo Global University Campus, Incheon, Republic of Korea; Department of Pharmacology, Seoul National University College of Medicine, Seoul, Republic of Korea
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12
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Esquivies L, Blackler A, Peran M, Rodriguez-Esteban C, Izpisua Belmonte JC, Booker E, Gray PC, Ahn C, Kwiatkowski W, Choe S. Designer nodal/BMP2 chimeras mimic nodal signaling, promote chondrogenesis, and reveal a BMP2-like structure. J Biol Chem 2013; 289:1788-97. [PMID: 24311780 DOI: 10.1074/jbc.m113.529180] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Nodal, a member of the TGF-β superfamily, plays an important role in vertebrate and invertebrate early development. The biochemical study of Nodal and its signaling pathway has been a challenge, mainly because of difficulties in producing the protein in sufficient quantities. We have developed a library of stable, chemically refoldable Nodal/BMP2 chimeric ligands (NB2 library). Three chimeras, named NB250, NB260, and NB264, show Nodal-like signaling properties including dependence on the co-receptor Cripto and activation of the Smad2 pathway. NB250, like Nodal, alters heart looping during the establishment of embryonic left-right asymmetry, and both NB250 and NB260, as well as Nodal, induce chondrogenic differentiation of human adipose-derived stem cells. This Nodal-induced differentiation is shown to be more efficient than BPM2-induced differentiation. Interestingly, the crystal structure of NB250 shows a backbone scaffold similar to that of BMP2. Our results show that these chimeric ligands may have therapeutic implications in cartilage injuries.
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Kefala G, Ahn C, Krupa M, Esquivies L, Maslennikov I, Kwiatkowski W, Choe S. Structures of the OmpF porin crystallized in the presence of foscholine-12. Protein Sci 2010; 19:1117-25. [PMID: 20196071 DOI: 10.1002/pro.369] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The endogenous Escherichia coli porin OmpF was crystallized as an accidental by-product of our efforts to express, purify, and crystallize the E. coli integral membrane protein KdpD in the presence of foscholine-12 (FC12). FC12 is widely used in membrane protein studies, but no crystal structure of a protein that was both purified and crystallized with this detergent has been reported in the Protein Data Bank. Crystallization screening for KdpD yielded two different crystals of contaminating protein OmpF. Here, we report two OmpF structures, the first membrane protein crystal structures for which extraction, purification, and crystallization were done exclusively with FC12. The first structure was refined in space group P21 with cell parameters a = 136.7 A, b = 210.5 A, c = 137 A, and beta = 100.5 degrees , and the resolution of 3.8 A. The second structure was solved at the resolution of 4.4 A and was refined in the P321 space group, with unit cell parameters a = 215.5 A, b = 215.5 A, c = 137.5 A, and gamma = 120 degrees . Both crystal forms show novel crystal packing, in which the building block is a tetrahedral arrangement of four trimers. Additionally, we discuss the use of FC12 for membrane protein crystallization and structure determination, as well as the problem of the OmpF contamination for membrane proteins overexpressed in E. coli.
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Affiliation(s)
- Georgia Kefala
- Structural Biology Laboratory, The Salk Institute for Biological Studies, 10010 North Torrey Pines Rd., La Jolla, California 92037, USA
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