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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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2
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Lai Y, Zhao C, Tian Z, Wang C, Fan J, Hu X, Tu J, Li T, Leitz J, Pfuetzner RA, Liu Z, Zhang S, Su Z, Burré J, Li D, Südhof TC, Zhu ZJ, Liu C, Brunger AT, Diao J. Neutral lysophosphatidylcholine mediates α-synuclein-induced synaptic vesicle clustering. Proc Natl Acad Sci U S A 2023; 120:e2310174120. [PMID: 37883437 PMCID: PMC10622907 DOI: 10.1073/pnas.2310174120] [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: 06/21/2023] [Accepted: 09/21/2023] [Indexed: 10/28/2023] Open
Abstract
α-synuclein (α-Syn) is a presynaptic protein that is involved in Parkinson's and other neurodegenerative diseases and binds to negatively charged phospholipids. Previously, we reported that α-Syn clusters synthetic proteoliposomes that mimic synaptic vesicles. This vesicle-clustering activity depends on a specific interaction of α-Syn with anionic phospholipids. Here, we report that α-Syn surprisingly also interacts with the neutral phospholipid lysophosphatidylcholine (lysoPC). Even in the absence of anionic lipids, lysoPC facilitates α-Syn-induced vesicle clustering but has no effect on Ca2+-triggered fusion in a single vesicle-vesicle fusion assay. The A30P mutant of α-Syn that causes familial Parkinson disease has a reduced affinity to lysoPC and does not induce vesicle clustering. Taken together, the α-Syn-lysoPC interaction may play a role in α-Syn function.
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Affiliation(s)
- Ying Lai
- National Clinical Research Center for Geriatrics, West China Hospital, State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu, Sichuan610065, China
- Department of Molecular and Cellular Physiology, Stanford University, Palo Alto, CA94305
| | - Chunyu Zhao
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai200032, China
| | - Zhiqi Tian
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH45267
| | - Chuchu Wang
- Department of Molecular and Cellular Physiology, Stanford University, Palo Alto, CA94305
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai200032, China
| | - Jiaqi Fan
- National Clinical Research Center for Geriatrics, West China Hospital, State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu, Sichuan610065, China
| | - Xiao Hu
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH45267
| | - Jia Tu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai200032, China
| | - Tihui Li
- State Key Laboratory of Biotherapy, West China Cryo-electron Microscopy Center, West China Hospital, Sichuan University, Chengdu, Sichuan610065, China
| | - Jeremy Leitz
- Department of Molecular and Cellular Physiology, Stanford University, Palo Alto, CA94305
| | - Richard A. Pfuetzner
- Department of Molecular and Cellular Physiology, Stanford University, Palo Alto, CA94305
| | - Zhengtao Liu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai200032, China
| | - Shengnan Zhang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai200032, China
| | - Zhaoming Su
- State Key Laboratory of Biotherapy, West China Cryo-electron Microscopy Center, West China Hospital, Sichuan University, Chengdu, Sichuan610065, China
| | - Jacqueline Burré
- Brain and Mind Research Institute and Appel Institute for Alzheimer’s Disease Research, Weill Cornell Medicine, New York, NY10021
| | - Dan Li
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, Shanghai Jiao Tong University, Shanghai200230, China
| | - Thomas C. Südhof
- Department of Molecular and Cellular Physiology, Stanford University, Palo Alto, CA94305
- HHMI, Stanford University, Palo Alto, CA94305
| | - Zheng-Jiang Zhu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai200032, China
| | - Cong Liu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai200032, China
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai200032, China
| | - Axel T. Brunger
- Department of Molecular and Cellular Physiology, Stanford University, Palo Alto, CA94305
- HHMI, Stanford University, Palo Alto, CA94305
| | - Jiajie Diao
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH45267
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3
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Gao Y, Khan YA, Mo W, White KI, Perkins M, Pfuetzner RA, Trapani JG, Brunger AT, Nicolson T. Sensory deficit screen identifies nsf mutation that differentially affects SNARE recycling and quality control. Cell Rep 2023; 42:112345. [PMID: 37027300 PMCID: PMC10524599 DOI: 10.1016/j.celrep.2023.112345] [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: 11/15/2022] [Revised: 02/24/2023] [Accepted: 03/21/2023] [Indexed: 04/08/2023] Open
Abstract
The AAA+ NSF complex is responsible for SNARE complex disassembly both before and after membrane fusion. Loss of NSF function results in pronounced developmental and degenerative defects. In a genetic screen for sensory deficits in zebrafish, we identified a mutation in nsf, I209N, that impairs hearing and balance in a dosage-dependent manner without accompanying defects in motility, myelination, and innervation. In vitro experiments demonstrate that while the I209N NSF protein recognizes SNARE complexes, the effects on disassembly are dependent upon the type of SNARE complex and I209N concentration. Higher levels of I209N protein produce a modest decrease in binary (syntaxin-SNAP-25) SNARE complex disassembly and residual ternary (syntaxin-1A-SNAP-25-synaptobrevin-2) disassembly, whereas at lower concentrations binary disassembly activity is strongly reduced and ternary disassembly activity is absent. Our study suggests that the differential effect on disassembly of SNARE complexes leads to selective effects on NSF-mediated membrane trafficking and auditory/vestibular function.
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Affiliation(s)
- Yan Gao
- Department of Otolaryngology, Head and Neck Surgery, Stanford Medical School, 300 Pasteur Drive, Stanford, CA 94303, USA
| | - Yousuf A Khan
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA; Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA; Department of Structural Biology, Stanford University, Stanford, CA, USA; Department of Photon Science, Stanford University, Stanford, CA, USA; Center for Biomedical Informatics Research, Stanford University, Stanford, CA, USA
| | - Weike Mo
- Graduate Program Biomedical Sciences, Oregon Hearing Research Center and Vollum Institute, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA
| | - K Ian White
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA; Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA; Department of Structural Biology, Stanford University, Stanford, CA, USA; Department of Photon Science, Stanford University, Stanford, CA, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Matthew Perkins
- Department of Biology and Neuroscience Program, Amherst College, Amherst, MA 01002, USA
| | - Richard A Pfuetzner
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA; Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA; Department of Structural Biology, Stanford University, Stanford, CA, USA; Department of Photon Science, Stanford University, Stanford, CA, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Josef G Trapani
- Department of Biology and Neuroscience Program, Amherst College, Amherst, MA 01002, USA
| | - Axel T Brunger
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA; Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA; Department of Structural Biology, Stanford University, Stanford, CA, USA; Department of Photon Science, Stanford University, Stanford, CA, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Teresa Nicolson
- Department of Otolaryngology, Head and Neck Surgery, Stanford Medical School, 300 Pasteur Drive, Stanford, CA 94303, 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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5
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Yang K, Wang C, Kreutzberger AJB, Ojha R, Kuivanen S, Couoh-Cardel S, Muratcioglu S, Eisen TJ, White KI, Pfuetzner R, Kuriyan J, Vapalahti O, Balistreri G, Kirchhausen T, Brunger AT. Drug discovery targeting SARS-CoV-2 membrane fusion. Biophys J 2023; 122:322a. [PMID: 36783625 DOI: 10.1016/j.bpj.2022.11.1802] [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: 02/12/2023] Open
Affiliation(s)
| | | | | | - Ravi Ojha
- University of Helsinki, Helsinki, Finland
| | | | | | | | | | | | | | - John Kuriyan
- University of California Berkeley, Berkeley, CA, USA
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6
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Abstract
Synaptic neurotransmitter release is mediated by an orchestra of presynaptic proteins that precisely control and trigger fusion between synaptic vesicles and the neuron terminal at the active zone upon the arrival of an action potential. Critical to this process are the neuronal SNAREs (Soluble N-ethylmaleimide sensitive factor Attachment protein REceptor), the Ca2+-sensor synaptotagmin, the activator/regulator complexin, and other factors. Here, we review the interactions between the SNARE complex and synaptotagmin, with focus on the so-called primary interface between synaptotagmin and the SNARE complex that has been validated in terms of its physiological relevance. We discuss several other but less validated interfaces as well, including the so-called tripartite interface, and we discuss the pros and cons for these possible alternative interfaces. We also present new molecular dynamics simulations of the tripartite interface and new data of an inhibitor of the primary interface in a reconstituted system of synaptic vesicle fusion.
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Affiliation(s)
- 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.
| | - Jeremy Leitz
- 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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7
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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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8
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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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9
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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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10
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Dickey BF, Lai Y, Frick M, Brunger AT. Discovery of a drug to treat airway mucus hypersecretion. Clin Transl Med 2022; 12:e972. [PMID: 35908252 PMCID: PMC9339237 DOI: 10.1002/ctm2.972] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 06/27/2022] [Indexed: 02/05/2023] Open
Affiliation(s)
- Burton F. Dickey
- Department of Pulmonary Medicine University of Texas MD Anderson Cancer Center Houston Texas USA
| | - Ying Lai
- National Clinical Research Center for Geriatrics, West China Hospital, State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy Sichuan University Chengdu China
| | - Manfred Frick
- Institute of General Physiology Ulm University Ulm Germany
| | - Axel T. Brunger
- Department of Molecular and Cellular Physiology Stanford University Stanford California USA
- Howard Hughes Medical Institute Stanford University Stanford California USA
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11
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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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12
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Peters JJ, Leitz J, Guo Q, Beck F, Baumeister W, Brunger AT. A feature-guided, focused 3D signal permutation method for subtomogram averaging. J Struct Biol 2022; 214:107851. [PMID: 35346811 PMCID: PMC9149098 DOI: 10.1016/j.jsb.2022.107851] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 12/17/2021] [Revised: 03/18/2022] [Accepted: 03/22/2022] [Indexed: 01/27/2023]
Abstract
Advances in electron microscope instrumentation, cryo-electron tomography data collection, and subtomogram averaging have allowed for the in-situ visualization of molecules and their complexes in their native environment. Current data processing pipelines commonly extract subtomograms as a cubic subvolume with the key assumption that the selected object of interest is discrete from its surroundings. However, in instances when the object is in its native environment, surrounding densities may negatively affect the subsequent alignment and refinement processes, leading to loss of information due to misalignment. For example, the strong densities from surrounding membranes may dominate the alignment process for membrane proteins. Here, we developed methods for feature-guided subtomogram alignment and 3D signal permutation for subtomogram averaging. Our 3D signal permutation method randomizes and filters voxels outside a mask of any shape and blurs the boundary of the mask that encapsulates the object of interest. The randomization preserves global statistical properties such as mean density and standard deviation of voxel density values, effectively producing a featureless background surrounding the object of interest. This signal permutation process can be repeatedly applied with intervening alignments of the 3D signal-permuted subvolumes, recentering of the mask, and optional adjustments of the shape of the mask. We have implemented these methods in a new processing pipeline which starts from tomograms, contains feature-guided subtomogram extraction and alignment, 3D signal-permutation, and subtomogram visualization tools. As an example, feature-guided alignment and 3D signal permutation leads to improved subtomogram average maps for a dataset of synaptic protein complexes in their native environment.
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Affiliation(s)
- John Jacob Peters
- 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
| | - Jeremy Leitz
- 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
| | - Qiang Guo
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China; Department of Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Florian Beck
- CryoEM Technology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Wolfgang Baumeister
- Department of Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - 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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13
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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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14
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Affiliation(s)
- Peter B Moore
- Department of Chemistry, Yale University, New Haven, CT 06520, USA
| | - Wayne A Hendrickson
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | | | - Axel T Brunger
- Department of Molecular and Cellular Physiology, Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
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15
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Dunleavy KM, Matlock H, Gething C, Howells G, Misra B, White KI, Brunger AT, Choi UB. Conformational dynamics of SNARE recycling mediated by NSF. Biophys J 2022. [DOI: 10.1016/j.bpj.2021.11.1284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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16
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van Dorp S, Qiu R, Choi UB, Wu MM, Yen M, Kirmiz M, Brunger AT, Lewis RS. Conformational dynamics of auto-inhibition in the ER calcium sensor STIM1. eLife 2021; 10:66194. [PMID: 34730514 PMCID: PMC8651296 DOI: 10.7554/elife.66194] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 01/02/2021] [Accepted: 10/18/2021] [Indexed: 01/19/2023] Open
Abstract
The dimeric ER Ca2+ sensor STIM1 controls store-operated Ca2+ entry (SOCE) through the regulated binding of its CRAC activation domain (CAD) to Orai channels in the plasma membrane. In resting cells, the STIM1 CC1 domain interacts with CAD to suppress SOCE, but the structural basis of this interaction is unclear. Using single-molecule Förster resonance energy transfer (smFRET) and protein crosslinking approaches, we show that CC1 interacts dynamically with CAD in a domain-swapped configuration with an orientation predicted to sequester its Orai-binding region adjacent to the ER membrane. Following ER Ca2+ depletion and release from CAD, cysteine crosslinking indicates that the two CC1 domains become closely paired along their entire length in the active Orai-bound state. These findings provide a structural basis for the dual roles of CC1: sequestering CAD to suppress SOCE in resting cells and propelling it toward the plasma membrane to activate Orai and SOCE after store depletion.
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Affiliation(s)
- Stijn van Dorp
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, United States
| | - Ruoyi Qiu
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, United States
| | - Ucheor B Choi
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, United States
| | - Minnie M Wu
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, United States
| | - Michelle Yen
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, United States
| | - Michael Kirmiz
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, United States
| | - Axel T Brunger
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, United States.,Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, United States
| | - Richard S Lewis
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, United States
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17
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Peters JJ, Leitz J, Oses-Prieto JA, Burlingame AL, Brunger AT. Molecular Characterization of AMPA-Receptor-Containing Vesicles. Front Mol Neurosci 2021; 14:754631. [PMID: 34720876 PMCID: PMC8554035 DOI: 10.3389/fnmol.2021.754631] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 08/06/2021] [Accepted: 09/16/2021] [Indexed: 12/13/2022] Open
Abstract
Regulated delivery of AMPA receptors (AMPARs) to the postsynaptic membrane is an essential step in synaptic strength modification, and in particular, long-term potentiation (LTP). While LTP has been extensively studied using electrophysiology and light microscopy, several questions regarding the molecular mechanisms of AMPAR delivery via trafficking vesicles remain outstanding, including the gross molecular make up of AMPAR trafficking organelles and identification and location of calcium sensors required for SNARE complex-dependent membrane fusion of such trafficking vesicles with the plasma membrane. Here, we isolated AMPA-containing vesicles (ACVs) from whole mouse brains via immunoisolation and characterized them using immunoelectron microscopy, immunoblotting, and liquid chromatography–tandem mass spectrometry (LC–MS/MS). We identified several proteins on ACVs that were previously found to play a role in AMPAR trafficking, including synaptobrevin-2, Rabs, the SM protein Munc18-1, the calcium-sensor synaptotagmin-1, as well as several new candidates, including synaptophysin and synaptogyrin on ACV membranes. Additionally, we identified two populations of ACVs based on size and molecular composition: small-diameter, synaptobrevin-2- and GluA1-containing ACVs, and larger transferrin- receptor-, GluA1-, GluA2-, and GluA3-containing ACVs. The small-diameter population of ACVs may represent a fusion-capable population of vesicles due to the presence of synaptobrevin-2. Because the fusion of ACVs may be a requisite of LTP, this population could represent trafficking vesicles related to LTP.
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Affiliation(s)
- John Jacob Peters
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, United States.,Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, United States.,Department of Structural Biology, Stanford University, Stanford, CA, United States.,Department of Photon Science, Stanford University, Stanford, CA, United States.,Howard Hughes Medical Institute, Stanford University, Stanford, CA, United States
| | - Jeremy Leitz
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, United States.,Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, United States.,Department of Structural Biology, Stanford University, Stanford, CA, United States.,Department of Photon Science, Stanford University, Stanford, CA, United States.,Howard Hughes Medical Institute, Stanford University, Stanford, CA, United States
| | - Juan A Oses-Prieto
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, United States
| | - Alma L Burlingame
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, United States
| | - Axel T Brunger
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, United States.,Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, United States.,Department of Structural Biology, Stanford University, Stanford, CA, United States.,Department of Photon Science, Stanford University, Stanford, CA, United States.,Howard Hughes Medical Institute, Stanford University, Stanford, CA, United States
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18
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Chen Q, Hao M, Wang L, Li L, Chen Y, Shao X, Tian Z, Pfuetzner RA, Zhong Q, Brunger AT, Guan JL, Diao J. Prefused lysosomes cluster on autophagosomes regulated by VAMP8. Cell Death Dis 2021; 12:939. [PMID: 34645799 PMCID: PMC8514493 DOI: 10.1038/s41419-021-04243-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 09/13/2021] [Accepted: 10/04/2021] [Indexed: 11/21/2022]
Abstract
Lysosome–autophagosome fusion is critical to autophagosome maturation. Although several proteins that regulate this fusion process have been identified, the prefusion architecture and its regulation remain unclear. Herein, we show that upon stimulation, multiple lysosomes form clusters around individual autophagosomes, setting the stage for membrane fusion. The soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) protein on lysosomes—vesicle-associated membrane protein 8 (VAMP8)—plays an important role in forming this prefusion state of lysosomal clusters. To study the potential role of phosphorylation on spontaneous fusion, we investigated the effect of phosphorylation of C-terminal residues of VAMP8. Using a phosphorylation mimic, we observed a decrease of fusion in an ensemble lipid mixing assay and an increase of unfused lysosomes associated with autophagosomes. These results suggest that phosphorylation not only reduces spontaneous fusion for minimizing autophagic flux under normal conditions, but also preassembles multiple lysosomes to increase the fusion probability for resuming autophagy upon stimulation. VAMP8 phosphorylation may thus play an important role in chemotherapy drug resistance by influencing autophagosome maturation.
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Affiliation(s)
- Qixin Chen
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
| | - Mingang Hao
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
| | - Lei Wang
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
| | - Linsen Li
- State Key Lab of Animal Nutrition, China Agricultural University, Beijing, 100193, China
| | - Yang Chen
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
| | - Xintian Shao
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
| | - Zhiqi Tian
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
| | - Richard A Pfuetzner
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, 94305, CA, USA.,Howard Hughes Medical Institute, Stanford University, Stanford, 94305, CA, USA
| | - Qing Zhong
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai, 200025, China
| | - Axel T Brunger
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, 94305, CA, USA.,Howard Hughes Medical Institute, Stanford University, Stanford, 94305, CA, USA
| | - Jun-Lin Guan
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA.
| | - Jiajie Diao
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA.
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19
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Abstract
ATPases associated with diverse cellular activities (AAA+ proteins) are a superfamily of proteins found throughout all domains of life. The hallmark of this family is a conserved AAA+ domain responsible for a diverse range of cellular activities. Typically, AAA+ proteins transduce chemical energy from the hydrolysis of ATP into mechanical energy through conformational change, which can drive a variety of biological processes. AAA+ proteins operate in a variety of cellular contexts with diverse functions including disassembly of SNARE proteins, protein quality control, DNA replication, ribosome assembly, and viral replication. This breadth of function illustrates both the importance of AAA+ proteins in health and disease and emphasizes the importance of understanding conserved mechanisms of chemo-mechanical energy transduction. This review is divided into three major portions. First, the core AAA+ fold is presented. Next, the seven different clades of AAA+ proteins and structural details and reclassification pertaining to proteins in each clade are described. Finally, two well-known AAA+ proteins, NSF and its close relative p97, are reviewed in detail.
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Affiliation(s)
- Yousuf A Khan
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA.,Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA.,Department of Structural Biology, Stanford University, Stanford, CA, USA.,Department of Photon Science, Stanford University, Stanford, CA, USA.,Center for Biomedical Informatics Research, Stanford University, Stanford, CA, USA
| | - K Ian White
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA.,Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA.,Department of Structural Biology, Stanford University, Stanford, CA, USA.,Department of Photon Science, Stanford University, Stanford, CA, USA.,Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Axel T Brunger
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA.,Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA.,Department of Structural Biology, Stanford University, Stanford, CA, USA.,Department of Photon Science, Stanford University, Stanford, CA, USA.,Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
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20
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Song H, Torng TL, Orr AS, Brunger AT, Wickner WT. Sec17/Sec18 can support membrane fusion without help from completion of SNARE zippering. eLife 2021; 10:67578. [PMID: 33944780 PMCID: PMC8143792 DOI: 10.7554/elife.67578] [Citation(s) in RCA: 14] [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: 02/16/2021] [Accepted: 04/30/2021] [Indexed: 11/20/2022] Open
Abstract
Membrane fusion requires R-, Qa-, Qb-, and Qc-family SNAREs that zipper into RQaQbQc coiled coils, driven by the sequestration of apolar amino acids. Zippering has been thought to provide all the force driving fusion. Sec17/αSNAP can form an oligomeric assembly with SNAREs with the Sec17 C-terminus bound to Sec18/NSF, the central region bound to SNAREs, and a crucial apolar loop near the N-terminus poised to insert into membranes. We now report that Sec17 and Sec18 can drive robust fusion without requiring zippering completion. Zippering-driven fusion is blocked by deleting the C-terminal quarter of any Q-SNARE domain or by replacing the apolar amino acids of the Qa-SNARE that face the center of the 4-SNARE coiled coils with polar residues. These blocks, singly or combined, are bypassed by Sec17 and Sec18, and SNARE-dependent fusion is restored without help from completing zippering.
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Affiliation(s)
- Hongki Song
- Department of Biochemistry and Cell Biology Geisel School of Medicine at Dartmouth, Hanover, United States
| | - Thomas L Torng
- Department of Biochemistry and Cell Biology Geisel School of Medicine at Dartmouth, Hanover, United States
| | - Amy S Orr
- Department of Biochemistry and Cell Biology Geisel School of Medicine at Dartmouth, Hanover, United States
| | - Axel T Brunger
- Howard Hughes Medical Institute and Department of Molecular and Cellular Physiology Stanford University, Stanford, United States
| | - William T Wickner
- Department of Biochemistry and Cell Biology Geisel School of Medicine at Dartmouth, Hanover, United States
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21
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Khalaj AJ, Sterky FH, Sclip A, Schwenk J, Brunger AT, Fakler B, Südhof TC. Deorphanizing FAM19A proteins as pan-neurexin ligands with an unusual biosynthetic binding mechanism. J Cell Biol 2021; 219:151974. [PMID: 32706374 PMCID: PMC7480106 DOI: 10.1083/jcb.202004164] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 06/01/2020] [Accepted: 06/05/2020] [Indexed: 12/14/2022] Open
Abstract
Neurexins are presynaptic adhesion molecules that organize synapses by binding to diverse trans-synaptic ligands, but how neurexins are regulated is incompletely understood. Here we identify FAM19A/TAFA proteins, “orphan" cytokines, as neurexin regulators that interact with all neurexins, except for neurexin-1γ, via an unusual mechanism. Specifically, we show that FAM19A1-A4 bind to the cysteine-loop domain of neurexins by forming intermolecular disulfide bonds during transport through the secretory pathway. FAM19A-binding required both the cysteines of the cysteine-loop domain and an adjacent sequence of neurexins. Genetic deletion of neurexins suppressed FAM19A1 expression, demonstrating that FAM19As physiologically interact with neurexins. In hippocampal cultures, expression of exogenous FAM19A1 decreased neurexin O-glycosylation and suppressed its heparan sulfate modification, suggesting that FAM19As regulate the post-translational modification of neurexins. Given the selective expression of FAM19As in specific subtypes of neurons and their activity-dependent regulation, these results suggest that FAM19As serve as cell type–specific regulators of neurexin modifications.
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Affiliation(s)
- Anna J Khalaj
- Department of Molecular and Cellular Physiology, Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA
| | - Fredrik H Sterky
- Department of Molecular and Cellular Physiology, Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA
| | - Alessandra Sclip
- Department of Molecular and Cellular Physiology, Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA
| | - Jochen Schwenk
- Institute of Physiology, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Axel T Brunger
- Department of Molecular and Cellular Physiology, Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA
| | - Bernd Fakler
- Institute of Physiology, Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Centres for Biological Signalling Studies (BIOSS) and Integrative Biological Signalling Studies (CIBSS), Freiburg, Germany.,Center for Basics in NeuroModulation, Freiburg, Germany
| | - Thomas C Südhof
- Department of Molecular and Cellular Physiology, Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA
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22
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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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23
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Wilson SC, White KI, Zhou Q, Pfuetzner RA, Choi UB, Südhof TC, Brunger AT. Structures of neurexophilin-neurexin complexes reveal a regulatory mechanism of alternative splicing. EMBO J 2019; 38:e101603. [PMID: 31566781 PMCID: PMC6856630 DOI: 10.15252/embj.2019101603] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [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: 01/21/2019] [Revised: 08/29/2019] [Accepted: 08/30/2019] [Indexed: 01/09/2023] Open
Abstract
Neurexins are presynaptic, cell-adhesion molecules that specify the functional properties of synapses via interactions with trans-synaptic ligands. Neurexins are extensively alternatively spliced at six canonical sites that regulate multifarious ligand interactions, but the structural mechanisms underlying alternative splicing-dependent neurexin regulation are largely unknown. Here, we determined high-resolution structures of the complex of neurexophilin-1 and the second laminin/neurexin/sex-hormone-binding globulin domain (LNS2) of neurexin-1 and examined how alternative splicing at splice site #2 (SS2) regulates the complex. Our data reveal a unique, extensive, neurexophilin-neurexin binding interface that extends the jelly-roll β-sandwich of LNS2 of neurexin-1 into neurexophilin-1. The SS2A insert of LNS2 augments this interface, increasing the binding affinity of LNS2 for neurexophilin-1. Taken together, our data reveal an unexpected architecture of neurexophilin-neurexin complexes that accounts for the modulation of binding by alternative splicing, which in turn regulates the competition of neurexophilin for neurexin binding with other ligands.
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Affiliation(s)
- Steven C Wilson
- Department of Molecular and Cellular PhysiologyStanford UniversityStanfordCAUSA
| | - K Ian White
- Department of Molecular and Cellular PhysiologyStanford UniversityStanfordCAUSA
| | - Qiangjun Zhou
- Department of Molecular and Cellular PhysiologyStanford UniversityStanfordCAUSA
| | - Richard A Pfuetzner
- Department of Molecular and Cellular PhysiologyStanford UniversityStanfordCAUSA
| | - Ucheor B Choi
- Department of Molecular and Cellular PhysiologyStanford UniversityStanfordCAUSA
| | - Thomas C Südhof
- Department of Molecular and Cellular PhysiologyStanford UniversityStanfordCAUSA
- Howard Hughes Medical InstituteStanford UniversityStanfordCAUSA
| | - Axel T Brunger
- Department of Molecular and Cellular PhysiologyStanford UniversityStanfordCAUSA
- Howard Hughes Medical InstituteStanford UniversityStanfordCAUSA
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24
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Abstract
This review summarizes current knowledge of synaptic proteins that are central to synaptic vesicle fusion in presynaptic active zones, including SNAREs (soluble N-ethylmaleimide sensitive factor attachment protein receptors), synaptotagmin, complexin, Munc18 (mammalian uncoordinated-18), and Munc13 (mammalian uncoordinated-13), and highlights recent insights in the cooperation of these proteins for neurotransmitter release. Structural and functional studies of the synaptic fusion machinery suggest new molecular models of synaptic vesicle priming and Ca2+-triggered fusion. These studies will be a stepping-stone toward answering the question of how the synaptic vesicle fusion machinery achieves such high speed and sensitivity.
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Affiliation(s)
- Axel T Brunger
- Department of Molecular and Cellular Physiology, Department of Neurology and Neurological Sciences, Department of Structural Biology, Department of Photon Science, Howard Hughes Medical Institute, Stanford University, Stanford, California 94305, USA;
| | - Ucheor B Choi
- Department of Molecular and Cellular Physiology, Department of Neurology and Neurological Sciences, Department of Structural Biology, Department of Photon Science, Howard Hughes Medical Institute, Stanford University, Stanford, California 94305, USA;
| | - Ying Lai
- Department of Molecular and Cellular Physiology, Department of Neurology and Neurological Sciences, Department of Structural Biology, Department of Photon Science, Howard Hughes Medical Institute, Stanford University, Stanford, California 94305, USA;
| | - Jeremy Leitz
- Department of Molecular and Cellular Physiology, Department of Neurology and Neurological Sciences, Department of Structural Biology, Department of Photon Science, Howard Hughes Medical Institute, Stanford University, Stanford, California 94305, USA;
| | - Qiangjun Zhou
- Department of Molecular and Cellular Physiology, Department of Neurology and Neurological Sciences, Department of Structural Biology, Department of Photon Science, Howard Hughes Medical Institute, Stanford University, Stanford, California 94305, USA;
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25
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Brunger AT, Choi UB, Lai Y, Leitz J, White KI, Zhou Q. The pre-synaptic fusion machinery. Curr Opin Struct Biol 2019; 54:179-188. [PMID: 30986753 PMCID: PMC6939388 DOI: 10.1016/j.sbi.2019.03.007] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Revised: 03/02/2019] [Accepted: 03/06/2019] [Indexed: 11/26/2022]
Abstract
Here, we review recent insights into the neuronal presynaptic fusion machinery that releases neurotransmitter molecules into the synaptic cleft upon stimulation. The structure of the pre-fusion state of the SNARE/complexin-1/synaptotagmin-1 synaptic protein complex suggests a new model for the initiation of fast Ca2+-triggered membrane fusion. Functional studies have revealed roles of the essential factors Munc18 and Munc13, demonstrating that a part of their function involves the proper assembly of synaptic protein complexes. Near-atomic resolution structures of the NSF/αSNAP/SNARE complex provide first glimpses of the molecular machinery that disassembles the SNARE complex during the synaptic vesicle cycle. These structures show how this machinery captures the SNARE substrate and provide clues as to a possible processing mechanism.
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Affiliation(s)
- 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.
| | - Ucheor B Choi
- 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
| | - Ying Lai
- 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
| | - Kristopher Ian White
- 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
| | - Qiangjun Zhou
- 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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26
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Uervirojnangkoorn M, Lyubimov AY, Zhou Q, Weis WI, Brunger AT. Resolving indexing ambiguities in X-ray free-electron laser diffraction patterns. Acta Crystallogr D Struct Biol 2019; 75:234-241. [PMID: 30821711 PMCID: PMC6400252 DOI: 10.1107/s2059798318013177] [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: 05/01/2018] [Accepted: 09/17/2018] [Indexed: 11/23/2022] Open
Abstract
Processing X-ray free-electron laser (XFEL) diffraction images poses challenges, as an XFEL pulse is powerful enough to destroy or damage the diffracting volume and thereby yields only one diffraction image per volume. Moreover, the crystal is stationary during the femtosecond pulse, so reflections are generally only partially recorded. Therefore, each XFEL diffraction image must be scaled individually and, ideally, corrected for partiality prior to merging. An additional complication may arise owing to indexing ambiguities when the symmetry of the Bravais lattice is higher than that of the space group, or when the unit-cell dimensions are similar to each other. Here, an automated method is presented that diagnoses these indexing ambiguities based on the Brehm-Diederichs algorithm [Brehm & Diederichs (2014), Acta Cryst. D70, 101-109] and produces a consistent indexing choice for the large majority of diffraction images. This method was applied to an XFEL diffraction data set measured from crystals of the neuronal SNARE-complexin-1-synaptotagmin-1 complex. After correcting the indexing ambiguities, substantial improvements were observed in the merging statistics and the atomic model refinement R values. This method should be a useful addition to the arsenal of tools for the processing of XFEL diffraction data sets.
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Affiliation(s)
| | - Artem Y. Lyubimov
- Stanford Synchrotron Radiation Laboratory, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Qiangjun Zhou
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA
- Department of Neurology and Neurological Science, Stanford University, Stanford, CA 94305, USA
- Department of Structural Biology, Stanford University, Stanford, CA 94305, USA
- Department of Photon Science, Stanford University, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - William I. Weis
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA
- Department of Structural Biology, Stanford University, Stanford, CA 94305, USA
- Department of Photon Science, Stanford University, Stanford, CA 94305, USA
| | - Axel T. Brunger
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
- Stanford Synchrotron Radiation Laboratory, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA
- Department of Neurology and Neurological Science, Stanford University, Stanford, CA 94305, USA
- Department of Structural Biology, Stanford University, Stanford, CA 94305, USA
- Department of Photon Science, Stanford University, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
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27
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White KI, Zhao M, Choi UB, Pfuetzner RA, Brunger AT. Structural principles of SNARE complex recognition by the AAA+ protein NSF. eLife 2018; 7:38888. [PMID: 30198481 PMCID: PMC6160233 DOI: 10.7554/elife.38888] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 08/26/2018] [Indexed: 12/13/2022] Open
Abstract
The recycling of SNARE proteins following complex formation and membrane fusion is an essential process in eukaryotic trafficking. A highly conserved AAA+ protein, NSF (N-ethylmaleimide sensitive factor) and an adaptor protein, SNAP (soluble NSF attachment protein), disassemble the SNARE complex. We report electron-cryomicroscopy structures of the complex of NSF, αSNAP, and the full-length soluble neuronal SNARE complex (composed of syntaxin-1A, synaptobrevin-2, SNAP-25A) in the presence of ATP under non-hydrolyzing conditions at ~3.9 Å resolution. These structures reveal electrostatic interactions by which two αSNAP molecules interface with a specific surface of the SNARE complex. This interaction positions the SNAREs such that the 15 N-terminal residues of SNAP-25A are loaded into the D1 ring pore of NSF via a spiral pattern of interactions between a conserved tyrosine NSF residue and SNAP-25A backbone atoms. This loading process likely precedes ATP hydrolysis. Subsequent ATP hydrolysis then drives complete disassembly.
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Affiliation(s)
- 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
| | - Minglei Zhao
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, United States
| | - 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
| | - 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
| | - 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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28
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Brunger AT, Leitz J, Zhou Q, Choi UB, Lai Y. Ca 2+-Triggered Synaptic Vesicle Fusion Initiated by Release of Inhibition. Trends Cell Biol 2018; 28:631-645. [PMID: 29706534 PMCID: PMC6056330 DOI: 10.1016/j.tcb.2018.03.004] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [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: 01/09/2018] [Revised: 03/17/2018] [Accepted: 03/26/2018] [Indexed: 12/20/2022]
Abstract
Recent structural and functional studies of the synaptic vesicle fusion machinery suggest an inhibited tripartite complex consisting of neuronal soluble N-ethylmaleimide sensitive factor attachment protein receptors (SNAREs), synaptotagmin, and complexin prior to Ca2+-triggered synaptic vesicle fusion. We speculate that Ca2+-triggered fusion commences with the release of inhibition by Ca2+ binding to synaptotagmin C2 domains. Subsequently, fusion is assisted by SNARE complex zippering and by active membrane remodeling properties of synaptotagmin. This additional, inhibitory role of synaptotagmin may be a general principle since other recent studies suggest that Ca2+ binding to extended synaptotagmin C2 domains enables lipid transport by releasing an inhibited state of the system, and that Munc13 may nominally be in an inhibited state, which is released upon Ca2+ binding to one of its C2 domains.
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Affiliation(s)
- Axel T Brunger
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA; Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA; Department of Structural Biology, Stanford University, Stanford, CA, USA; Department of Photon Science, Stanford University, Stanford, CA, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA.
| | - Jeremy Leitz
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA; Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA; Department of Structural Biology, Stanford University, Stanford, CA, USA; Department of Photon Science, Stanford University, Stanford, CA, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Qiangjun Zhou
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA; Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA; Department of Structural Biology, Stanford University, Stanford, CA, USA; Department of Photon Science, Stanford University, Stanford, CA, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Ucheor B Choi
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA; Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA; Department of Structural Biology, Stanford University, Stanford, CA, USA; Department of Photon Science, Stanford University, Stanford, CA, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Ying Lai
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA; Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA; Department of Structural Biology, Stanford University, Stanford, CA, USA; Department of Photon Science, Stanford University, Stanford, CA, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
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29
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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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30
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31
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Lai Y, Brunger AT. Molecular Mechanisms of Synaptic Vesicle Priming by Munc13 and Munc18. Biophys J 2018. [DOI: 10.1016/j.bpj.2017.11.856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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32
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Lai Y, Choi UB, Leitz J, Rhee HJ, Lee C, Altas B, Zhao M, Pfuetzner RA, Wang AL, Brose N, Rhee J, Brunger AT. Molecular Mechanisms of Synaptic Vesicle Priming by Munc13 and Munc18. Neuron 2017; 95:591-607.e10. [PMID: 28772123 DOI: 10.1016/j.neuron.2017.07.004] [Citation(s) in RCA: 148] [Impact Index Per Article: 21.1] [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: 09/02/2016] [Revised: 05/08/2017] [Accepted: 07/06/2017] [Indexed: 11/18/2022]
Abstract
Munc13 catalyzes the transit of syntaxin from a closed complex with Munc18 into the ternary SNARE complex. Here we report a new function of Munc13, independent of Munc18: it promotes the proper syntaxin/synaptobrevin subconfiguration during assembly of the ternary SNARE complex. In cooperation with Munc18, Munc13 additionally ensures the proper syntaxin/SNAP-25 subconfiguration. In a reconstituted fusion assay with SNAREs, complexin, and synaptotagmin, inclusion of both Munc13 and Munc18 quadruples the Ca2+-triggered amplitude and achieves Ca2+ sensitivity at near-physiological concentrations. In Munc13-1/2 double-knockout neurons, expression of a constitutively open mutant of syntaxin could only minimally restore neurotransmitter release relative to Munc13-1 rescue. Together, the physiological functions of Munc13 may be related to regulation of proper SNARE complex assembly.
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Affiliation(s)
- Ying Lai
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA; Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305, USA; Department of Structural Biology, Stanford University, Stanford, CA 94305, USA; Department of Photon Science, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Ucheor B Choi
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA; Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305, USA; Department of Structural Biology, Stanford University, Stanford, CA 94305, USA; Department of Photon Science, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Jeremy Leitz
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA; Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305, USA; Department of Structural Biology, Stanford University, Stanford, CA 94305, USA; Department of Photon Science, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Hong Jun Rhee
- Department of Molecular Neurobiology, Max Planck Institute for Experimental Medicine, 37075 Göttingen, Germany
| | - Choongku Lee
- Department of Molecular Neurobiology, Max Planck Institute for Experimental Medicine, 37075 Göttingen, Germany
| | - Bekir Altas
- Department of Molecular Neurobiology, Max Planck Institute for Experimental Medicine, 37075 Göttingen, Germany
| | - Minglei Zhao
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA; Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305, USA; Department of Structural Biology, Stanford University, Stanford, CA 94305, USA; Department of Photon Science, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Richard A Pfuetzner
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA; Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305, USA; Department of Structural Biology, Stanford University, Stanford, CA 94305, USA; Department of Photon Science, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Austin L Wang
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA; Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305, USA; Department of Structural Biology, Stanford University, Stanford, CA 94305, USA; Department of Photon Science, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Nils Brose
- Department of Molecular Neurobiology, Max Planck Institute for Experimental Medicine, 37075 Göttingen, Germany
| | - JeongSeop Rhee
- Department of Molecular Neurobiology, Max Planck Institute for Experimental Medicine, 37075 Göttingen, Germany
| | - Axel T Brunger
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA; Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305, USA; Department of Structural Biology, Stanford University, Stanford, CA 94305, USA; Department of Photon Science, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA.
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33
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Mathews II, Allison K, Robbins T, Lyubimov AY, Uervirojnangkoorn M, Brunger AT, Khosla C, DeMirci H, McPhillips SE, Hollenbeck M, Soltis M, Cohen AE. The Conformational Flexibility of the Acyltransferase from the Disorazole Polyketide Synthase Is Revealed by an X-ray Free-Electron Laser Using a Room-Temperature Sample Delivery Method for Serial Crystallography. Biochemistry 2017; 56:4751-4756. [PMID: 28832129 DOI: 10.1021/acs.biochem.7b00711] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The crystal structure of the trans-acyltransferase (AT) from the disorazole polyketide synthase (PKS) was determined at room temperature to a resolution of 2.5 Å using a new method for the direct delivery of the sample into an X-ray free-electron laser. A novel sample extractor efficiently delivered limited quantities of microcrystals directly from the native crystallization solution into the X-ray beam at room temperature. The AT structure revealed important catalytic features of this core PKS enzyme, including the occurrence of conformational changes around the active site. The implications of these conformational changes for polyketide synthase reaction dynamics are discussed.
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Affiliation(s)
- Irimpan I Mathews
- Stanford Synchrotron Radiation Lightsource , 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - Kim Allison
- Stanford Synchrotron Radiation Lightsource , 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | | | - Artem Y Lyubimov
- Stanford Synchrotron Radiation Lightsource , 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | | | | | | | - Hasan DeMirci
- Stanford Synchrotron Radiation Lightsource , 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - Scott E McPhillips
- Stanford Synchrotron Radiation Lightsource , 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - Michael Hollenbeck
- Stanford Synchrotron Radiation Lightsource , 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - Michael Soltis
- Stanford Synchrotron Radiation Lightsource , 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - Aina E Cohen
- Stanford Synchrotron Radiation Lightsource , 2575 Sand Hill Road, Menlo Park, California 94025, United States
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34
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Abstract
Neurotransmitter release is orchestrated by synaptic proteins, such as SNAREs, synaptotagmin, and complexin, but the molecular mechanisms remain unclear. We visualized functionally active synaptic proteins reconstituted into proteoliposomes and their interactions in a native membrane environment by electron cryotomography with a Volta phase plate for improved resolvability. The images revealed individual synaptic proteins and synaptic protein complex densities at prefusion contact sites between membranes. We observed distinct morphologies of individual synaptic proteins and their complexes. The minimal system, consisting of neuronal SNAREs and synaptotagmin-1, produced point and long-contact prefusion states. Morphologies and populations of these states changed as the regulatory factors complexin and Munc13 were added. Complexin increased the membrane separation, along with a higher propensity of point contacts. Further inclusion of the priming factor Munc13 exclusively restricted prefusion states to point contacts, all of which efficiently fused upon Ca2+ triggering. We conclude that synaptic proteins have evolved to limit possible contact site assemblies and morphologies to those that promote fast Ca2+-triggered release.
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Affiliation(s)
- Preeti Gipson
- 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
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305
| | - Yoshiyuki Fukuda
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Radostin Danev
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Ying Lai
- 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
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305
| | - Dong-Hua Chen
- Department of Structural Biology, Stanford University, Stanford, CA 94305
| | - Wolfgang Baumeister
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - 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
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305
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35
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Lyubimov A, Uervirojnangkoorn M, Cohen AE, Brunger AT. Integration optimization, triage and analysis tools for serial crystallography. Acta Crystallogr A Found Adv 2017. [DOI: 10.1107/s0108767317096039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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36
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Wang S, Choi UB, Gong J, Yang X, Li Y, Wang AL, Yang X, Brunger AT, Ma C. Conformational change of syntaxin linker region induced by Munc13s initiates SNARE complex formation in synaptic exocytosis. EMBO J 2017; 36:816-829. [PMID: 28137749 PMCID: PMC5350566 DOI: 10.15252/embj.201695775] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [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: 09/22/2016] [Revised: 01/01/2017] [Accepted: 01/04/2017] [Indexed: 01/04/2023] Open
Abstract
The soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) protein syntaxin-1 adopts a closed conformation when bound to Munc18-1, preventing binding to synaptobrevin-2 and SNAP-25 to form the ternary SNARE complex. Although it is known that the MUN domain of Munc13-1 catalyzes the transition from the Munc18-1/syntaxin-1 complex to the SNARE complex, the molecular mechanism is unclear. Here, we identified two conserved residues (R151, I155) in the syntaxin-1 linker region as key sites for the MUN domain interaction. This interaction is essential for SNARE complex formation in vitro and synaptic vesicle priming in neuronal cultures. Moreover, this interaction is important for a tripartite Munc18-1/syntaxin-1/MUN complex, in which syntaxin-1 still adopts a closed conformation tightly bound to Munc18-1, whereas the syntaxin-1 linker region changes its conformation, similar to that of the LE mutant of syntaxin-1 when bound to Munc18-1. We suggest that the conformational change of the syntaxin-1 linker region induced by Munc13-1 initiates ternary SNARE complex formation in the neuronal system.
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Affiliation(s)
- Shen Wang
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology and the Collaborative Innovation Center for Brain Science, Huazhong University of Science and Technology, Wuhan, China
| | - Ucheor B Choi
- Departments of Molecular and Cellular Physiology, Neurology and Neurological Sciences, Photon Science, and Structural Biology, Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Jihong Gong
- Key Laboratory of Cognitive Science, Hubei Key Laboratory of Medical Information Analysis and Tumor Diagnosis & Treatment, Laboratory of Membrane Ion Channels and Medicine, College of Biomedical Engineering, College of Life Science, South-Central University for Nationalities, Wuhan, China
| | - Xiaoyu Yang
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology and the Collaborative Innovation Center for Brain Science, Huazhong University of Science and Technology, Wuhan, China
| | - Yun Li
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology and the Collaborative Innovation Center for Brain Science, Huazhong University of Science and Technology, Wuhan, China
| | - Austin L Wang
- Departments of Molecular and Cellular Physiology, Neurology and Neurological Sciences, Photon Science, and Structural Biology, Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Xiaofei Yang
- Key Laboratory of Cognitive Science, Hubei Key Laboratory of Medical Information Analysis and Tumor Diagnosis & Treatment, Laboratory of Membrane Ion Channels and Medicine, College of Biomedical Engineering, College of Life Science, South-Central University for Nationalities, Wuhan, China
| | - Axel T Brunger
- Departments of Molecular and Cellular Physiology, Neurology and Neurological Sciences, Photon Science, and Structural Biology, Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Cong Ma
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology and the Collaborative Innovation Center for Brain Science, Huazhong University of Science and Technology, Wuhan, China
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37
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Young ID, Ibrahim M, Chatterjee R, Gul S, Fuller F, Koroidov S, Brewster AS, Tran R, Alonso-Mori R, Kroll T, Michels-Clark T, Laksmono H, Sierra RG, Stan CA, Hussein R, Zhang M, Douthit L, Kubin M, de Lichtenberg C, Long Vo P, Nilsson H, Cheah MH, Shevela D, Saracini C, Bean MA, Seuffert I, Sokaras D, Weng TC, Pastor E, Weninger C, Fransson T, Lassalle L, Bräuer P, Aller P, Docker PT, Andi B, Orville AM, Glownia JM, Nelson S, Sikorski M, Zhu D, Hunter MS, Lane TJ, Aquila A, Koglin JE, Robinson J, Liang M, Boutet S, Lyubimov AY, Uervirojnangkoorn M, Moriarty NW, Liebschner D, Afonine PV, Waterman DG, Evans G, Wernet P, Dobbek H, Weis WI, Brunger AT, Zwart PH, Adams PD, Zouni A, Messinger J, Bergmann U, Sauter NK, Kern J, Yachandra VK, Yano J. Structure of photosystem II and substrate binding at room temperature. Nature 2016; 540:453-457. [PMID: 27871088 DOI: 10.1038/nature20161] [Citation(s) in RCA: 281] [Impact Index Per Article: 35.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 10/14/2016] [Indexed: 12/16/2022]
Abstract
Light-induced oxidation of water by photosystem II (PS II) in plants, algae and cyanobacteria has generated most of the dioxygen in the atmosphere. PS II, a membrane-bound multi-subunit pigment protein complex, couples the one-electron photochemistry at the reaction centre with the four-electron redox chemistry of water oxidation at the Mn4CaO5 cluster in the oxygen-evolving complex (OEC). Under illumination, the OEC cycles through five intermediate S-states (S0 to S4), in which S1 is the dark-stable state and S3 is the last semi-stable state before O-O bond formation and O2 evolution. A detailed understanding of the O-O bond formation mechanism remains a challenge, and will require elucidation of both the structures of the OEC in the different S-states and the binding of the two substrate waters to the catalytic site. Here we report the use of femtosecond pulses from an X-ray free electron laser (XFEL) to obtain damage-free, room temperature structures of dark-adapted (S1), two-flash illuminated (2F; S3-enriched), and ammonia-bound two-flash illuminated (2F-NH3; S3-enriched) PS II. Although the recent 1.95 Å resolution structure of PS II at cryogenic temperature using an XFEL provided a damage-free view of the S1 state, measurements at room temperature are required to study the structural landscape of proteins under functional conditions, and also for in situ advancement of the S-states. To investigate the water-binding site(s), ammonia, a water analogue, has been used as a marker, as it binds to the Mn4CaO5 cluster in the S2 and S3 states. Since the ammonia-bound OEC is active, the ammonia-binding Mn site is not a substrate water site. This approach, together with a comparison of the native dark and 2F states, is used to discriminate between proposed O-O bond formation mechanisms.
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Affiliation(s)
- Iris D Young
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Mohamed Ibrahim
- Institut für Biologie, Humboldt-Universität zu Berlin, D-10099 Berlin, Germany
| | - Ruchira Chatterjee
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Sheraz Gul
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Franklin Fuller
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Sergey Koroidov
- Institutionen för Kemi, Kemiskt Biologiskt Centrum, Umeå Universitet, SE 90187 Umeå, Sweden
| | - Aaron S Brewster
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Rosalie Tran
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | | | - Thomas Kroll
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.,SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Tara Michels-Clark
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Hartawan Laksmono
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Raymond G Sierra
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.,Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Claudiu A Stan
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Rana Hussein
- Institut für Biologie, Humboldt-Universität zu Berlin, D-10099 Berlin, Germany
| | - Miao Zhang
- Institut für Biologie, Humboldt-Universität zu Berlin, D-10099 Berlin, Germany
| | - Lacey Douthit
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Markus Kubin
- Institute for Methods and Instrumentation on Synchrotron Radiation Research, Helmholtz Zentrum, 14109 Berlin, Germany
| | - Casper de Lichtenberg
- Institutionen för Kemi, Kemiskt Biologiskt Centrum, Umeå Universitet, SE 90187 Umeå, Sweden
| | - Pham Long Vo
- Institutionen för Kemi, Kemiskt Biologiskt Centrum, Umeå Universitet, SE 90187 Umeå, Sweden
| | - Håkan Nilsson
- Institutionen för Kemi, Kemiskt Biologiskt Centrum, Umeå Universitet, SE 90187 Umeå, Sweden
| | - Mun Hon Cheah
- Institutionen för Kemi, Kemiskt Biologiskt Centrum, Umeå Universitet, SE 90187 Umeå, Sweden
| | - Dmitriy Shevela
- Institutionen för Kemi, Kemiskt Biologiskt Centrum, Umeå Universitet, SE 90187 Umeå, Sweden
| | - Claudio Saracini
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Mackenzie A Bean
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Ina Seuffert
- Institut für Biologie, Humboldt-Universität zu Berlin, D-10099 Berlin, Germany
| | | | - Tsu-Chien Weng
- SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Ernest Pastor
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Clemens Weninger
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Thomas Fransson
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Louise Lassalle
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Philipp Bräuer
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.,Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Pierre Aller
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Peter T Docker
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Babak Andi
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY, 11973, USA
| | - Allen M Orville
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - James M Glownia
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Silke Nelson
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Marcin Sikorski
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Diling Zhu
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Mark S Hunter
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Thomas J Lane
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Andy Aquila
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Jason E Koglin
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Joseph Robinson
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Mengning Liang
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Sébastien Boutet
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Artem Y Lyubimov
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA
| | | | - Nigel W Moriarty
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Dorothee Liebschner
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Pavel V Afonine
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - David G Waterman
- STFC Rutherford Appleton Laboratory, Didcot, OX11 0QX, UK and CCP4, Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot, OX11 0FA, UK
| | - Gwyndaf Evans
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK
| | - Philippe Wernet
- Institute for Methods and Instrumentation on Synchrotron Radiation Research, Helmholtz Zentrum, 14109 Berlin, Germany
| | - Holger Dobbek
- Institut für Biologie, Humboldt-Universität zu Berlin, D-10099 Berlin, Germany
| | - William I Weis
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA.,Department of Photon Science, Stanford University, Stanford, CA 94305.,Department of Structural Biology, Stanford University, Stanford, CA 94305
| | - Axel T Brunger
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA.,Department of Photon Science, Stanford University, Stanford, CA 94305
| | - Petrus H Zwart
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Paul D Adams
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.,Department of Bioengineering, University of California Berkeley, Berkeley, CA 94720
| | - Athina Zouni
- Institut für Biologie, Humboldt-Universität zu Berlin, D-10099 Berlin, Germany
| | - Johannes Messinger
- Institutionen för Kemi, Kemiskt Biologiskt Centrum, Umeå Universitet, SE 90187 Umeå, Sweden.,Department of Chemistry, Molecular Biomimetics, Ångström Laboratory, Uppsala University, SE 75237 Uppsala, Sweden
| | - Uwe Bergmann
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Nicholas K Sauter
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jan Kern
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.,LCLS, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Vittal K Yachandra
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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38
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Lyubimov AY, Uervirojnangkoorn M, Zeldin OB, Zhou Q, Zhao M, Brewster AS, Michels-Clark T, Holton JM, Sauter NK, Weis WI, Brunger AT. Advances in X-ray free electron laser (XFEL) diffraction data processing applied to the crystal structure of the synaptotagmin-1 / SNARE complex. eLife 2016; 5. [PMID: 27731796 PMCID: PMC5094853 DOI: 10.7554/elife.18740] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [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: 06/12/2016] [Accepted: 10/11/2016] [Indexed: 12/03/2022] Open
Abstract
X-ray free electron lasers (XFELs) reduce the effects of radiation damage on macromolecular diffraction data and thereby extend the limiting resolution. Previously, we adapted classical post-refinement techniques to XFEL diffraction data to produce accurate diffraction data sets from a limited number of diffraction images (Uervirojnangkoorn et al., 2015), and went on to use these techniques to obtain a complete data set from crystals of the synaptotagmin-1 / SNARE complex and to determine the structure at 3.5 Å resolution (Zhou et al., 2015). Here, we describe new advances in our methods and present a reprocessed XFEL data set of the synaptotagmin-1 / SNARE complex. The reprocessing produced small improvements in electron density maps and the refined atomic model. The maps also contained more information than those of a lower resolution (4.1 Å) synchrotron data set. Processing a set of simulated XFEL diffraction images revealed that our methods yield accurate data and atomic models. DOI:http://dx.doi.org/10.7554/eLife.18740.001
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Affiliation(s)
- Artem Y Lyubimov
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States.,Neurology and Neurological Science, Stanford University, Stanford, United States.,Structural Biology, Stanford University, Stanford, United States.,Photon Science, Stanford University, Stanford, United States.,Howard Hughes Medical Institute, Stanford University, Stanford, United States
| | - Monarin Uervirojnangkoorn
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States.,Neurology and Neurological Science, Stanford University, Stanford, United States.,Photon Science, Stanford University, Stanford, United States.,Structural Biology, Stanford University, Stanford, United States.,Howard Hughes Medical Institute, Stanford University, Stanford, United States
| | - Oliver B Zeldin
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States.,Neurology and Neurological Science, Stanford University, Stanford, United States.,Photon Science, Stanford University, Stanford, United States.,Structural Biology, 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.,Neurology and Neurological Science, Stanford University, Stanford, United States.,Photon Science, Stanford University, Stanford, United States.,Structural Biology, Stanford University, Stanford, United States.,Howard Hughes Medical Institute, Stanford University, Stanford, United States
| | - Minglei Zhao
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States.,Neurology and Neurological Science, Stanford University, Stanford, United States.,Photon Science, Stanford University, Stanford, United States.,Structural Biology, Stanford University, Stanford, United States.,Howard Hughes Medical Institute, Stanford University, Stanford, United States
| | - Aaron S Brewster
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Tara Michels-Clark
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - James M Holton
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, United States.,Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, United States.,Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
| | - Nicholas K Sauter
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - William I Weis
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States.,Structural Biology, Stanford University, Stanford, United States.,Photon Science, Stanford University, Stanford, United States
| | - Axel T Brunger
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States.,Neurology and Neurological Science, Stanford University, Stanford, United States.,Photon Science, Stanford University, Stanford, United States.,Structural Biology, Stanford University, Stanford, United States.,Howard Hughes Medical Institute, Stanford University, Stanford, United States
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39
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Colletier JP, Sawaya MR, Gingery M, Rodriguez JA, Cascio D, Brewster AS, Michels-Clark T, Hice RH, Coquelle N, Boutet S, Williams GJ, Messerschmidt M, DePonte DP, Sierra RG, Laksmono H, Koglin JE, Hunter MS, Park HW, Uervirojnangkoorn M, Bideshi DK, Brunger AT, Federici BA, Sauter NK, Eisenberg DS. De novo phasing with X-ray laser reveals mosquito larvicide BinAB structure. Nature 2016; 539:43-47. [PMID: 27680699 PMCID: PMC5161637 DOI: 10.1038/nature19825] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 09/07/2016] [Indexed: 11/30/2022]
Abstract
BinAB is a naturally occurring paracrystalline larvicide distributed worldwide to combat the devastating diseases borne by mosquitoes. These crystals are composed of homologous molecules, BinA and BinB, which play distinct roles in the multi-step intoxication process, transforming from harmless, robust crystals, to soluble protoxin heterodimers, to internalized mature toxin, and finally toxic oligomeric pores. The small size of the crystals, 50 unit cells per edge, on average, has impeded structural characterization by conventional means. Here, we report the structure of BinAB solved de novo by serial-femtosecond crystallography at an X-ray free-electron laser (XFEL). The structure reveals tyrosine and carboxylate-mediated contacts acting as pH switches to release soluble protoxin in the alkaline larval midgut. An enormous heterodimeric interface appears responsible for anchoring BinA to receptor-bound BinB for co-internalization. Remarkably, this interface is largely composed of propeptides, suggesting that proteolytic maturation would trigger dissociation of the heterodimer and progression to pore formation.
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Affiliation(s)
| | - Michael R Sawaya
- UCLA-DOE Institute for Genomics and Proteomics, Department of Biological Chemistry, University of California, Los Angeles, California 90095-1570, USA.,Howard Hughes Medical Institute, University of California, Los Angeles, California 90095-1570, USA
| | - Mari Gingery
- UCLA-DOE Institute for Genomics and Proteomics, Department of Biological Chemistry, University of California, Los Angeles, California 90095-1570, USA
| | - Jose A Rodriguez
- UCLA-DOE Institute for Genomics and Proteomics, Department of Biological Chemistry, University of California, Los Angeles, California 90095-1570, USA
| | - Duilio Cascio
- UCLA-DOE Institute for Genomics and Proteomics, Department of Biological Chemistry, University of California, Los Angeles, California 90095-1570, USA
| | - Aaron S Brewster
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Tara Michels-Clark
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Robert H Hice
- Department of Entomology and Graduate Program in Cell, Molecular and Developmental Biology, University of California, Riverside, California 92521, USA
| | - Nicolas Coquelle
- Institut de Biologie Structurale (IBS), Univ. Grenoble Alpes, CEA, CNRS, 38044 Grenoble, France
| | - Sébastien Boutet
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Garth J Williams
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Marc Messerschmidt
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Daniel P DePonte
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Raymond G Sierra
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Hartawan Laksmono
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Jason E Koglin
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Mark S Hunter
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Hyun-Woo Park
- Department of Entomology and Graduate Program in Cell, Molecular and Developmental Biology, University of California, Riverside, California 92521, USA.,Department of Biological Sciences, California Baptist University, Riverside, California 92504, USA
| | - Monarin Uervirojnangkoorn
- Molecular and Cellular Physiology, and Howard Hughes Medical Institute, Stanford University, Stanford, California 94305, USA
| | - Dennis K Bideshi
- Department of Entomology and Graduate Program in Cell, Molecular and Developmental Biology, University of California, Riverside, California 92521, USA.,Department of Biological Sciences, California Baptist University, Riverside, California 92504, USA
| | - Axel T Brunger
- Molecular and Cellular Physiology, and Howard Hughes Medical Institute, Stanford University, Stanford, California 94305, USA
| | - Brian A Federici
- Department of Entomology and Graduate Program in Cell, Molecular and Developmental Biology, University of California, Riverside, California 92521, USA
| | - Nicholas K Sauter
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - David S Eisenberg
- UCLA-DOE Institute for Genomics and Proteomics, Department of Biological Chemistry, University of California, Los Angeles, California 90095-1570, USA.,Howard Hughes Medical Institute, University of California, Los Angeles, California 90095-1570, USA
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40
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Malmersjö S, Di Palma S, Diao J, Lai Y, Pfuetzner RA, Wang AL, McMahon MA, Hayer A, Porteus M, Bodenmiller B, Brunger AT, Meyer T. Phosphorylation of residues inside the SNARE complex suppresses secretory vesicle fusion. EMBO J 2016; 35:1810-21. [PMID: 27402227 PMCID: PMC5010044 DOI: 10.15252/embj.201694071] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [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: 02/08/2016] [Accepted: 06/09/2016] [Indexed: 12/22/2022] Open
Abstract
Membrane fusion is essential for eukaryotic life, requiring SNARE proteins to zipper up in an α‐helical bundle to pull two membranes together. Here, we show that vesicle fusion can be suppressed by phosphorylation of core conserved residues inside the SNARE domain. We took a proteomics approach using a PKCB knockout mast cell model and found that the key mast cell secretory protein VAMP8 becomes phosphorylated by PKC at multiple residues in the SNARE domain. Our data suggest that VAMP8 phosphorylation reduces vesicle fusion in vitro and suppresses secretion in living cells, allowing vesicles to dock but preventing fusion with the plasma membrane. Markedly, we show that the phosphorylation motif is absent in all eukaryotic neuronal VAMPs, but present in all other VAMPs. Thus, phosphorylation of SNARE domains is a general mechanism to restrict how much cells secrete, opening the door for new therapeutic strategies for suppression of secretion.
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Affiliation(s)
- Seth Malmersjö
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
| | - Serena Di Palma
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland Functional Genomics Center Zurich, ETH Zurich/University of Zurich, Zurich, Switzerland
| | - Jiajie Diao
- Departments of Molecular and Cellular Physiology, Neurology and Neurological Sciences, Photon Science, and Structural Biology, Stanford University, Stanford, CA, USA Howard Hughes Medical Institute, Stanford, CA, USA
| | - Ying Lai
- Departments of Molecular and Cellular Physiology, Neurology and Neurological Sciences, Photon Science, and Structural Biology, Stanford University, Stanford, CA, USA Howard Hughes Medical Institute, Stanford, CA, USA
| | - Richard A Pfuetzner
- Departments of Molecular and Cellular Physiology, Neurology and Neurological Sciences, Photon Science, and Structural Biology, Stanford University, Stanford, CA, USA Howard Hughes Medical Institute, Stanford, CA, USA
| | - Austin L Wang
- Departments of Molecular and Cellular Physiology, Neurology and Neurological Sciences, Photon Science, and Structural Biology, Stanford University, Stanford, CA, USA Howard Hughes Medical Institute, Stanford, CA, USA
| | - Moira A McMahon
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Arnold Hayer
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
| | - Matthew Porteus
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Bernd Bodenmiller
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Axel T Brunger
- Departments of Molecular and Cellular Physiology, Neurology and Neurological Sciences, Photon Science, and Structural Biology, Stanford University, Stanford, CA, USA Howard Hughes Medical Institute, Stanford, CA, USA
| | - Tobias Meyer
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA, USA
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41
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Choi UB, Zhao M, Zhang Y, Lai Y, Brunger AT. Complexin induces a conformational change at the membrane-proximal C-terminal end of the SNARE complex. eLife 2016; 5. [PMID: 27253060 PMCID: PMC4927292 DOI: 10.7554/elife.16886] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [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: 04/13/2016] [Accepted: 06/01/2016] [Indexed: 01/14/2023] Open
Abstract
Complexin regulates spontaneous and activates Ca2+-triggered neurotransmitter release, yet the molecular mechanisms are still unclear. Here we performed single molecule fluorescence resonance energy transfer experiments and uncovered two conformations of complexin-1 bound to the ternary SNARE complex. In the cis conformation, complexin-1 induces a conformational change at the membrane-proximal C-terminal end of the ternary SNARE complex that specifically depends on the N-terminal, accessory, and central domains of complexin-1. The complexin-1 induced conformation of the ternary SNARE complex may be related to a conformation that is juxtaposing the synaptic vesicle and plasma membranes. In the trans conformation, complexin-1 can simultaneously interact with a ternary SNARE complex via the central domain and a binary SNARE complex consisting of syntaxin-1A and SNAP-25A via the accessory domain. The cis conformation may be involved in activation of synchronous neurotransmitter release, whereas both conformations may be involved in regulating spontaneous release. DOI:http://dx.doi.org/10.7554/eLife.16886.001 Nerve cells communicate via electrical signals that travel at high speeds. However, these signals cannot pass across the gaps – called synapses – that separate one nerve cell from the next. Instead, signals pass between nerve cells via molecules called neurotransmitters that are released from the membrane of the first cell and recognized by receptors in the membrane of the next. Prior to being released, neurotransmitters are packaged inside bubble-like structures called vesicles. The synaptic vesicles must fuse with the cell membrane in order to release their contents into the synaptic cleft. Proteins called SNAREs work together with other proteins to allow this membrane fusion to occur rapidly after the electrical signal arrives. Complexin is a synaptic protein that binds tightly to a complex of SNARE proteins to regulate membrane fusion. This protein activates the quick release of neurotransmitters, which is triggered by an increase in calcium ions as the electrical signal reachess the synapse. Complexin also regulates a different type of neurotransmitter release, which is known as “spontaneous release”. The complexin protein is made up of different regions, each of which is required for one or more of the protein’s activities. However, it is not clear how these regions, or domains, interact with SNAREs and other proteins to enable complexin to perform these roles. Choi et al. have now investigated whether the different activities of mammalian complexin are related to the structure that it adopts when it interacts with the SNARE complex. Complexes of SNARE proteins were assembled with one of the SNARE proteins tethered to a surface for imaging. Next, a light-based imaging technique called single molecule Förster resonance energy transfer (or FRET) was used to monitor how complexin interacts with the SNARE complex. This technique allows individual proteins that have been labeled with fluorescent markers to be followed under a microscope and can show how they interact in real-time. Using this approach, Choi et al. showed that complexin could adopt two different shapes or conformations when it binds to the SNARE complex. In one, complexin interacted closely with the SNARE complex so that it made part of the complex change shape. In the other, complexin was able to bridge two SNARE complexes. Complexin can therefore interact with SNARE complexes in different ways by using different regions of the protein. These findings provide insight into how complexin may regulate membrane fusion via the SNARE complex. In the future, single molecule FRET could be used to study other proteins found at synapses and understand the other steps that regulate the release of neurotransmitters. DOI:http://dx.doi.org/10.7554/eLife.16886.002
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Affiliation(s)
- Ucheor B Choi
- Department of Molecular and Cellular Physiology, Howard Hughes Medical Institute, Stanford University, Stanford, United States.,Department of Neurology and Neurological Sciences, Howard Hughes Medical Institute, Stanford University, Stanford, United States.,Department of Photon Science, Howard Hughes Medical Institute, Stanford University, Stanford, United States.,Department of Structural Biology, Howard Hughes Medical Institute, Stanford University, Stanford, United States
| | - Minglei Zhao
- Department of Molecular and Cellular Physiology, Howard Hughes Medical Institute, Stanford University, Stanford, United States.,Department of Neurology and Neurological Sciences, Howard Hughes Medical Institute, Stanford University, Stanford, United States.,Department of Photon Science, Howard Hughes Medical Institute, Stanford University, Stanford, United States.,Department of Structural Biology, Howard Hughes Medical Institute, Stanford University, Stanford, United States
| | - Yunxiang Zhang
- Department of Molecular and Cellular Physiology, Howard Hughes Medical Institute, Stanford University, Stanford, United States.,Department of Neurology and Neurological Sciences, Howard Hughes Medical Institute, Stanford University, Stanford, United States.,Department of Photon Science, Howard Hughes Medical Institute, Stanford University, Stanford, United States.,Department of Structural Biology, Howard Hughes Medical Institute, Stanford University, Stanford, United States
| | - Ying Lai
- Department of Molecular and Cellular Physiology, Howard Hughes Medical Institute, Stanford University, Stanford, United States.,Department of Neurology and Neurological Sciences, Howard Hughes Medical Institute, Stanford University, Stanford, United States.,Department of Photon Science, Howard Hughes Medical Institute, Stanford University, Stanford, United States.,Department of Structural Biology, Howard Hughes Medical Institute, Stanford University, Stanford, United States
| | - Axel T Brunger
- Department of Molecular and Cellular Physiology, Howard Hughes Medical Institute, Stanford University, Stanford, United States.,Department of Neurology and Neurological Sciences, Howard Hughes Medical Institute, Stanford University, Stanford, United States.,Department of Photon Science, Howard Hughes Medical Institute, Stanford University, Stanford, United States.,Department of Structural Biology, Howard Hughes Medical Institute, Stanford University, Stanford, United States
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42
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Lyubimov AY, Uervirojnangkoorn M, Zeldin OB, Brewster AS, Murray TD, Sauter NK, Berger JM, Weis WI, Brunger AT. IOTA: integration optimization, triage and analysis tool for the processing of XFEL diffraction images. J Appl Crystallogr 2016; 49:1057-1064. [PMID: 27275148 PMCID: PMC4886991 DOI: 10.1107/s1600576716006683] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 04/19/2016] [Indexed: 01/25/2023] Open
Abstract
Serial femtosecond crystallography (SFX) uses an X-ray free-electron laser to extract diffraction data from crystals not amenable to conventional X-ray light sources owing to their small size or radiation sensitivity. However, a limitation of SFX is the high variability of the diffraction images that are obtained. As a result, it is often difficult to determine optimal indexing and integration parameters for the individual diffraction images. Presented here is a software package, called IOTA, which uses a grid-search technique to determine optimal spot-finding parameters that can in turn affect the success of indexing and the quality of integration on an image-by-image basis. Integration results can be filtered using a priori information about the Bravais lattice and unit-cell dimensions and analyzed for unit-cell isomorphism, facilitating an improvement in subsequent data-processing steps.
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Affiliation(s)
- Artem Y. Lyubimov
- Department of Molecular and Cellular Physiology, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA
- Department of Neurology and Neurological Science, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA
- Department of Structural Biology, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA
- Department of Photon Science, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Monarin Uervirojnangkoorn
- Department of Molecular and Cellular Physiology, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA
- Department of Neurology and Neurological Science, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA
- Department of Structural Biology, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA
- Department of Photon Science, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Oliver B. Zeldin
- Department of Molecular and Cellular Physiology, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA
- Department of Neurology and Neurological Science, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA
- Department of Structural Biology, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA
- Department of Photon Science, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Aaron S. Brewster
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Thomas D. Murray
- Biophysics Graduate Group, University of California, Berkeley, CA 94720, USA
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Nicholas K. Sauter
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - James M. Berger
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - William I. Weis
- Department of Molecular and Cellular Physiology, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA
- Department of Structural Biology, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA
- Department of Photon Science, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA
| | - Axel T. Brunger
- Department of Molecular and Cellular Physiology, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA
- Department of Neurology and Neurological Science, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA
- Department of Structural Biology, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA
- Department of Photon Science, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
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43
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Lin J, van den Bedem H, Brunger AT, Wilson MA. Atomic resolution experimental phase information reveals extensive disorder and bound 2-methyl-2,4-pentanediol in Ca(2+)-calmodulin. Acta Crystallogr D Struct Biol 2016; 72:83-92. [PMID: 26894537 PMCID: PMC4756614 DOI: 10.1107/s2059798315021609] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [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: 10/08/2015] [Accepted: 11/14/2015] [Indexed: 11/10/2022] Open
Abstract
Calmodulin (CaM) is the primary calcium signaling protein in eukaryotes and has been extensively studied using various biophysical techniques. Prior crystal structures have noted the presence of ambiguous electron density in both hydrophobic binding pockets of Ca(2+)-CaM, but no assignment of these features has been made. In addition, Ca(2+)-CaM samples many conformational substates in the crystal and accurately modeling the full range of this functionally important disorder is challenging. In order to characterize these features in a minimally biased manner, a 1.0 Å resolution single-wavelength anomalous diffraction data set was measured for selenomethionine-substituted Ca(2+)-CaM. Density-modified electron-density maps enabled the accurate assignment of Ca(2+)-CaM main-chain and side-chain disorder. These experimental maps also substantiate complex disorder models that were automatically built using low-contour features of model-phased electron density. Furthermore, experimental electron-density maps reveal that 2-methyl-2,4-pentanediol (MPD) is present in the C-terminal domain, mediates a lattice contact between N-terminal domains and may occupy the N-terminal binding pocket. The majority of the crystal structures of target-free Ca(2+)-CaM have been derived from crystals grown using MPD as a precipitant, and thus MPD is likely to be bound in functionally critical regions of Ca(2+)-CaM in most of these structures. The adventitious binding of MPD helps to explain differences between the Ca(2+)-CaM crystal and solution structures and is likely to favor more open conformations of the EF-hands in the crystal.
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Affiliation(s)
- Jiusheng Lin
- Department of Biochemistry and Redox Biology Center, University of Nebraska, Beadle Center, Lincoln, NE 68588, USA
| | - Henry van den Bedem
- Biosciences Division, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025, USA
| | - Axel T. Brunger
- Departments of Molecular and Cellular Physiology, Neurology and Neurological Sciences, Structural Biology, and Photon Science, Stanford University and Howard Hughes Medical Institute, Stanford, CA 94305, USA
| | - Mark A. Wilson
- Department of Biochemistry and Redox Biology Center, University of Nebraska, Beadle Center, Lincoln, NE 68588, USA
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44
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Baxter EL, Aguila L, Alonso-Mori R, Barnes CO, Bonagura CA, Brehmer W, Brunger AT, Calero G, Caradoc-Davies TT, Chatterjee R, Degrado WF, Fraser JS, Ibrahim M, Kern J, Kobilka BK, Kruse AC, Larsson KM, Lemke HT, Lyubimov AY, Manglik A, McPhillips SE, Norgren E, Pang SS, Soltis SM, Song J, Thomaston J, Tsai Y, Weis WI, Woldeyes RA, Yachandra V, Yano J, Zouni A, Cohen AE. High-density grids for efficient data collection from multiple crystals. Acta Crystallogr D Struct Biol 2016; 72:2-11. [PMID: 26894529 PMCID: PMC4756618 DOI: 10.1107/s2059798315020847] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [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: 07/14/2015] [Accepted: 11/03/2015] [Indexed: 03/01/2023] Open
Abstract
Higher throughput methods to mount and collect data from multiple small and radiation-sensitive crystals are important to support challenging structural investigations using microfocus synchrotron beamlines. Furthermore, efficient sample-delivery methods are essential to carry out productive femtosecond crystallography experiments at X-ray free-electron laser (XFEL) sources such as the Linac Coherent Light Source (LCLS). To address these needs, a high-density sample grid useful as a scaffold for both crystal growth and diffraction data collection has been developed and utilized for efficient goniometer-based sample delivery at synchrotron and XFEL sources. A single grid contains 75 mounting ports and fits inside an SSRL cassette or uni-puck storage container. The use of grids with an SSRL cassette expands the cassette capacity up to 7200 samples. Grids may also be covered with a polymer film or sleeve for efficient room-temperature data collection from multiple samples. New automated routines have been incorporated into the Blu-Ice/DCSS experimental control system to support grids, including semi-automated grid alignment, fully automated positioning of grid ports, rastering and automated data collection. Specialized tools have been developed to support crystallization experiments on grids, including a universal adaptor, which allows grids to be filled by commercial liquid-handling robots, as well as incubation chambers, which support vapor-diffusion and lipidic cubic phase crystallization experiments. Experiments in which crystals were loaded into grids or grown on grids using liquid-handling robots and incubation chambers are described. Crystals were screened at LCLS-XPP and SSRL BL12-2 at room temperature and cryogenic temperatures.
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Affiliation(s)
- Elizabeth L. Baxter
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Laura Aguila
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Roberto Alonso-Mori
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Christopher O. Barnes
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | | | - Winnie Brehmer
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Axel T. Brunger
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Guillermo Calero
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Tom T. Caradoc-Davies
- The ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, Victoria 3800, Australia
- Australian Synchrotron, 800 Blackburn Road, Clayton, Melbourne, Victoria 3168, Australia
| | - Ruchira Chatterjee
- Physical Bioscences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - William F. Degrado
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA
| | - James S. Fraser
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA
| | - Mohamed Ibrahim
- Institut für Biologie, Humboldt-Universität zu Berlin, 10099 Berlin, Germany
| | - Jan Kern
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
- Physical Bioscences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Brian K. Kobilka
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA
| | - Andrew C. Kruse
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA
| | - Karl M. Larsson
- Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Heinrik T. Lemke
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Artem Y. Lyubimov
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Aashish Manglik
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA
| | - Scott E. McPhillips
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Erik Norgren
- Art Robbins Instruments, Sunnyvale, CA 94089, USA
| | - Siew S. Pang
- The ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, Victoria 3800, Australia
| | - S. M. Soltis
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Jinhu Song
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Jessica Thomaston
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA
| | - Yingssu Tsai
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - William I. Weis
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA
- Department of Structural Biology, Stanford University, Stanford, CA 94305, USA
| | - Rahel A. Woldeyes
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA
| | - Vittal Yachandra
- Physical Bioscences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Junko Yano
- Physical Bioscences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Athina Zouni
- Institut für Biologie, Humboldt-Universität zu Berlin, 10099 Berlin, Germany
| | - Aina E. Cohen
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
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Diao J, Grob P, Cipriano DJ, Kyoung M, Zhang Y, Shah S, Nguyen A, Padolina M, Srivastava A, Vrljic M, Shah A, Nogales E, Chu S, Brunger AT. Correction: Synaptic proteins promote calcium-triggered fast transition from point contact to full fusion. eLife 2015; 4:e12289. [PMID: 26486862 PMCID: PMC4610116 DOI: 10.7554/elife.12289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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46
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Murray TD, Lyubimov AY, Ogata CM, Vo H, Uervirojnangkoorn M, Brunger AT, Berger JM. A high-transparency, micro-patternable chip for X-ray diffraction analysis of microcrystals under native growth conditions. Acta Crystallogr D Biol Crystallogr 2015; 71:1987-97. [PMID: 26457423 PMCID: PMC4601365 DOI: 10.1107/s1399004715015011] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [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] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 08/11/2015] [Indexed: 11/14/2022]
Abstract
Microcrystals present a significant impediment to the determination of macromolecular structures by X-ray diffraction methods. Although microfocus synchrotron beamlines and X-ray free-electron lasers (XFELs) can enable the collection of interpretable diffraction data from microcrystals, there is a need for efficient methods of harvesting small volumes (<2 µl) of microcrystals grown under common laboratory formats and delivering them to an X-ray beam source under native growth conditions. One approach that shows promise in overcoming the challenges intrinsic to microcrystal analysis is to pair so-called `fixed-target' sample-delivery devices with microbeam-based X-ray diffraction methods. However, to record weak diffraction patterns it is necessary to fabricate devices from X-ray-transparent materials that minimize background scattering. Presented here is the design of a new micro-diffraction device consisting of three layers fabricated from silicon nitride, photoresist and polyimide film. The chip features low X-ray scattering and X-ray absorption properties, and uses a customizable blend of hydrophobic and hydrophilic surface patterns to help localize microcrystals to defined regions. Microcrystals in their native growth conditions can be loaded into the chips with a standard pipette, allowing data collection at room temperature. Diffraction data collected from hen egg-white lysozyme microcrystals (10-15 µm) loaded into the chips yielded a complete, high-resolution (<1.6 Å) data set sufficient to determine a high-quality structure by molecular replacement. The features of the chip allow the rapid and user-friendly analysis of microcrystals grown under virtually any laboratory format at microfocus synchrotron beamlines and XFELs.
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Affiliation(s)
- Thomas D. Murray
- Biophysics Graduate Group, University of California, Berkeley, CA 94720, USA
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Artem Y. Lyubimov
- Departments of Molecular and Cellular Physiology, Neurology and Neurological Sciences, Structural Biology and Photon Science, and Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Craig M. Ogata
- GM/CA@APS, X-Ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Huy Vo
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Monarin Uervirojnangkoorn
- Departments of Molecular and Cellular Physiology, Neurology and Neurological Sciences, Structural Biology and Photon Science, and Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Axel T. Brunger
- Departments of Molecular and Cellular Physiology, Neurology and Neurological Sciences, Structural Biology and Photon Science, and Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - James M. Berger
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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Keedy DA, Kenner LR, Warkentin M, Woldeyes RA, Hopkins JB, Thompson MC, Brewster AS, Van Benschoten AH, Baxter EL, Uervirojnangkoorn M, McPhillips SE, Song J, Alonso-Mori R, Holton JM, Weis WI, Brunger AT, Soltis SM, Lemke H, Gonzalez A, Sauter NK, Cohen AE, van den Bedem H, Thorne RE, Fraser JS. Mapping the conformational landscape of a dynamic enzyme by multitemperature and XFEL crystallography. eLife 2015; 4. [PMID: 26422513 PMCID: PMC4721965 DOI: 10.7554/elife.07574] [Citation(s) in RCA: 117] [Impact Index Per Article: 13.0] [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: 03/19/2015] [Accepted: 09/29/2015] [Indexed: 12/14/2022] Open
Abstract
Determining the interconverting conformations of dynamic proteins in atomic detail is a major challenge for structural biology. Conformational heterogeneity in the active site of the dynamic enzyme cyclophilin A (CypA) has been previously linked to its catalytic function, but the extent to which the different conformations of these residues are correlated is unclear. Here we compare the conformational ensembles of CypA by multitemperature synchrotron crystallography and fixed-target X-ray free-electron laser (XFEL) crystallography. The diffraction-before-destruction nature of XFEL experiments provides a radiation-damage-free view of the functionally important alternative conformations of CypA, confirming earlier synchrotron-based results. We monitored the temperature dependences of these alternative conformations with eight synchrotron datasets spanning 100-310 K. Multiconformer models show that many alternative conformations in CypA are populated only at 240 K and above, yet others remain populated or become populated at 180 K and below. These results point to a complex evolution of conformational heterogeneity between 180-–240 K that involves both thermal deactivation and solvent-driven arrest of protein motions in the crystal. The lack of a single shared conformational response to temperature within the dynamic active-site network provides evidence for a conformation shuffling model, in which exchange between rotamer states of a large aromatic ring in the middle of the network shifts the conformational ensemble for the other residues in the network. Together, our multitemperature analyses and XFEL data motivate a new generation of temperature- and time-resolved experiments to structurally characterize the dynamic underpinnings of protein function. DOI:http://dx.doi.org/10.7554/eLife.07574.001 Proteins are the workhorses of the cell. The shape that a protein molecule adopts enables it to carry out its role. However, a protein’s shape, or 'conformation', is not static. Instead, a protein can shift between different conformations. This is particularly true for enzymes – the proteins that catalyze chemical reactions. The region of an enzyme where the chemical reaction happens, known as the active site, often has to change its conformation to allow catalysis to proceed. Changes in temperature can also make a protein shift between alternative conformations. Understanding how a protein shifts between conformations gives insight into how it works. A common method for studying protein conformation is X-ray crystallography. This technique uses a beam of X-rays to figure out where the atoms of the protein are inside a crystal made of millions of copies of that protein. At room temperature or biological temperature, X-rays can rapidly damage the protein. Because of this, most crystal structures are determined at very low temperatures to minimize damage. But cooling to low temperatures changes the conformations that the protein adopts, and usually causes fewer conformations to be present. Keedy, Kenner, Warkentin, Woldeyes et al. have used X-ray crystallography from a very low temperature (-173°C or 100 K) to above room temperature (up to 27°C or 300 K) to explore the alternative conformations of an enzyme called cyclophilin A. These alternative conformations include those that have previously been linked to this enzyme’s activity. Starting at a low temperature, parts of the enzyme were seen to shift from having a single conformation to many conformations above a threshold temperature. Unexpectedly, different parts of the enzyme have different threshold temperatures, suggesting that there isn’t a single transition across the whole protein. Instead, it appears the way a protein’s conformation changes in response to temperature is more complex than was previously realized. This result suggests that conformations in different parts of a protein are coupled to each other in complex ways. Keedy, Kenner, Warkentin, Woldeyes et al. then performed X-ray crystallography at room temperature using an X-ray free-electron laser (XFEL). This technique can capture the protein’s structure before radiation damage occurs, and confirmed that the alternative conformations observed were not affected by radiation damage. The combination of X-ray crystallography at multiple temperatures, new analysis methods for identifying and measuring alternative conformations, and XFEL crystallography should help future studies to characterize conformational changes in other proteins. DOI:http://dx.doi.org/10.7554/eLife.07574.002
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Affiliation(s)
- Daniel A Keedy
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States
| | - Lillian R Kenner
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States
| | | | - Rahel A Woldeyes
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States
| | - Jesse B Hopkins
- Department of Physics, Cornell University, Ithaca, United States
| | - Michael C Thompson
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States
| | - Aaron S Brewster
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Andrew H Van Benschoten
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States
| | - Elizabeth L Baxter
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, United States
| | - Monarin Uervirojnangkoorn
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States.,Howard Hughes Medical Institute, Stanford University, Stanford, United States
| | - Scott E McPhillips
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, United States
| | - Jinhu Song
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, United States
| | - Roberto Alonso-Mori
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, United States
| | - James M Holton
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, United States.,Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, United States.,Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
| | - William I Weis
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States.,Department of Structural Biology, Stanford University, Stanford, United States.,Department of Photon Science, SLAC National Accelerator Laboratory, Menlo Park, United States
| | - Axel T Brunger
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States.,Howard Hughes Medical Institute, Stanford University, Stanford, United States.,Department of Structural Biology, Stanford University, Stanford, United States.,Department of Photon Science, SLAC National Accelerator Laboratory, Menlo Park, United States
| | - S Michael Soltis
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, United States
| | - Henrik Lemke
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, United States
| | - Ana Gonzalez
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, United States
| | - Nicholas K Sauter
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Aina E Cohen
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, United States
| | - Henry van den Bedem
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, United States
| | - Robert E Thorne
- Department of Physics, Cornell University, Ithaca, United States
| | - James S Fraser
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States
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Lyubimov AY, Murray TD, Koehl A, Araci IE, Uervirojnangkoorn M, Zeldin OB, Cohen AE, Soltis SM, Baxter EL, Brewster AS, Sauter NK, Brunger AT, Berger JM. Capture and X-ray diffraction studies of protein microcrystals in a microfluidic trap array. Acta Crystallogr D Biol Crystallogr 2015; 71:928-40. [PMID: 25849403 PMCID: PMC4388268 DOI: 10.1107/s1399004715002308] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [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] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 02/03/2015] [Indexed: 11/10/2022]
Abstract
X-ray free-electron lasers (XFELs) promise to enable the collection of interpretable diffraction data from samples that are refractory to data collection at synchrotron sources. At present, however, more efficient sample-delivery methods that minimize the consumption of microcrystalline material are needed to allow the application of XFEL sources to a wide range of challenging structural targets of biological importance. Here, a microfluidic chip is presented in which microcrystals can be captured at fixed, addressable points in a trap array from a small volume (<10 µl) of a pre-existing slurry grown off-chip. The device can be mounted on a standard goniostat for conducting diffraction experiments at room temperature without the need for flash-cooling. Proof-of-principle tests with a model system (hen egg-white lysozyme) demonstrated the high efficiency of the microfluidic approach for crystal harvesting, permitting the collection of sufficient data from only 265 single-crystal still images to permit determination and refinement of the structure of the protein. This work shows that microfluidic capture devices can be readily used to facilitate data collection from protein microcrystals grown in traditional laboratory formats, enabling analysis when cryopreservation is problematic or when only small numbers of crystals are available. Such microfluidic capture devices may also be useful for data collection at synchrotron sources.
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Affiliation(s)
- Artem Y. Lyubimov
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA
- Department of Neurology and Neurological Science, Stanford University, Stanford, CA 94305, USA
- Department of Structural Biology, Stanford University, Stanford, CA 94305, USA
- Department of Photon Science, Stanford University, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Thomas D. Murray
- Biophysics Graduate Group, University of California, Berkeley, CA 94720, USA
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Antoine Koehl
- Department of Structural Biology, Stanford University, Stanford, CA 94305, USA
| | - Ismail Emre Araci
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Monarin Uervirojnangkoorn
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA
- Department of Neurology and Neurological Science, Stanford University, Stanford, CA 94305, USA
- Department of Structural Biology, Stanford University, Stanford, CA 94305, USA
- Department of Photon Science, Stanford University, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Oliver B. Zeldin
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA
- Department of Neurology and Neurological Science, Stanford University, Stanford, CA 94305, USA
- Department of Structural Biology, Stanford University, Stanford, CA 94305, USA
- Department of Photon Science, Stanford University, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Aina E. Cohen
- SLAC National Accelerator Laboratory, Stanford, CA 94305, USA
| | | | | | - Aaron S. Brewster
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Nicholas K. Sauter
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Axel T. Brunger
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA
- Department of Neurology and Neurological Science, Stanford University, Stanford, CA 94305, USA
- Department of Structural Biology, Stanford University, Stanford, CA 94305, USA
- Department of Photon Science, Stanford University, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - James M. Berger
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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Abstract
Proteoliposomes have been widely used for in vitro studies of membrane fusion mediated by synaptic proteins. Initially, such studies were made with large unsynchronized ensembles of vesicles. Such ensemble assays limited the insights into the SNARE-mediated fusion mechanism that could be obtained from them. Single particle microscopy experiments can alleviate many of these limitations but they pose significant technical challenges. Here we summarize various approaches that have enabled studies of fusion mediated by SNAREs and other synaptic proteins at a single-particle level. Currently available methods are described and their advantages and limitations are discussed.
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50
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Uervirojnangkoorn M, Zeldin OB, Lyubimov AY, Hattne J, Brewster AS, Sauter NK, Brunger AT, Weis WI. Enabling X-ray free electron laser crystallography for challenging biological systems from a limited number of crystals. eLife 2015; 4. [PMID: 25781634 PMCID: PMC4397907 DOI: 10.7554/elife.05421] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [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: 10/31/2014] [Accepted: 03/16/2015] [Indexed: 02/02/2023] Open
Abstract
There is considerable potential for X-ray free electron lasers (XFELs) to enable determination of macromolecular crystal structures that are difficult to solve using current synchrotron sources. Prior XFEL studies often involved the collection of thousands to millions of diffraction images, in part due to limitations of data processing methods. We implemented a data processing system based on classical post-refinement techniques, adapted to specific properties of XFEL diffraction data. When applied to XFEL data from three different proteins collected using various sample delivery systems and XFEL beam parameters, our method improved the quality of the diffraction data as well as the resulting refined atomic models and electron density maps. Moreover, the number of observations for a reflection necessary to assemble an accurate data set could be reduced to a few observations. These developments will help expand the applicability of XFEL crystallography to challenging biological systems, including cases where sample is limited.
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Affiliation(s)
| | - Oliver B Zeldin
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States
| | - Artem Y Lyubimov
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States
| | | | - Aaron S Brewster
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Nicholas K Sauter
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Axel T Brunger
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States
| | - William I Weis
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States
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