151
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Khazina E, Weichenrieder O. Human LINE-1 retrotransposition requires a metastable coiled coil and a positively charged N-terminus in L1ORF1p. eLife 2018; 7:34960. [PMID: 29565245 PMCID: PMC5940361 DOI: 10.7554/elife.34960] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 03/21/2018] [Indexed: 12/22/2022] Open
Abstract
LINE-1 (L1) is an autonomous retrotransposon, which acted throughout mammalian evolution and keeps contributing to human genotypic diversity, genetic disease and cancer. L1 encodes two essential proteins: L1ORF1p, a unique RNA-binding protein, and L1ORF2p, an endonuclease and reverse transcriptase. L1ORF1p contains an essential, but rapidly evolving N-terminal portion, homo-trimerizes via a coiled coil and packages L1RNA into large assemblies. Here, we determined crystal structures of the entire coiled coil domain of human L1ORF1p. We show that retrotransposition requires a non-ideal and metastable coiled coil structure, and a strongly basic L1ORF1p amino terminus. Human L1ORF1p therefore emerges as a highly calibrated molecular machine, sensitive to mutation but functional in different hosts. Our analysis rationalizes the locally rapid L1ORF1p sequence evolution and reveals striking mechanistic parallels to coiled coil-containing membrane fusion proteins. It also suggests how trimeric L1ORF1p could form larger meshworks and indicates critical novel steps in L1 retrotransposition. Almost half of the human genome consists of DNA strings that have been copied and pasted from one part of the genome to another many thousands of times. These strings of DNA are called mobile genetic elements. Mobile elements can disrupt important genes, causing disease and cancer, but they can also drive evolution. Presently, only one type of mobile element, called LINE-1, is active in the human genome and able to multiply without help from other mobile elements. LINE-1 DNA is ‘transcribed’ to form molecules of LINE-1 RNA, which can then be ‘translated’ into two distinct proteins. These bind to LINE-1 RNA, which then gets back-transcribed into DNA and inserted as a new LINE-1 element in a new region of the genome. One of the two proteins, called L1ORF1p, forms complexes where three copies of the protein come together. These ‘trimers’ cover and protect LINE-1 RNA and are required for LINE-1 mobility. Different versions of L1ORF1p are found in different animals. Part of the protein is the same across all mammals, and this ‘conserved’ part controls the ability of L1ORF1p to bind to RNA. The non-conserved part of L1ORF1p differs even between humans and their closest animal relatives and little was known about its structure or role. However, this rapidly evolving part of L1ORF1p is essential for LINE-1 mobility. Using X-ray crystallography, Khazina and Weichenrieder obtained a molecular snapshot of the part of L1ORF1p that interacts with other copies of the protein to form trimers. Combined with earlier snapshots of L1ORF1p’s conserved part, this generated a complete structural model of the L1ORF1p trimer. Additional biophysical characterizations suggest that L1ORF1p trimers form a semi-stable structure that can partially open up, indicating how trimers could form larger assemblies of L1ORF1p on LINE-1 RNA. Indeed, the need to maintain a semi-stable structure could explain why L1ORF1p is evolving so rapidly. A second important finding is that the beginning of L1ORF1p needs to be positively charged – a requirement that warrants further exploration. The structural and mechanistic insight into L1ORF1p points to critical new steps in LINE-1 mobilization. It will help to design inhibitor molecules with the goal to halt the mobilization process at various points and to dissect such steps in great detail. Understanding how to control LINE-1 mobility could help to improve stem cell therapies and reproduction assistance techniques, due to the fact that LINE-1 mobility is a potential source of mutation in stem cells, egg and sperm cells, and newly formed embryos.
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Affiliation(s)
- Elena Khazina
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Oliver Weichenrieder
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Tübingen, Germany
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152
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Zhao D, Liu S, Gao Y. Single-molecule manipulation and detection. Acta Biochim Biophys Sin (Shanghai) 2018; 50:231-237. [PMID: 29377975 DOI: 10.1093/abbs/gmx146] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 12/23/2017] [Indexed: 11/13/2022] Open
Abstract
Compared to conventional ensemble methods, studying macromolecules at single-molecule level can reveal extraordinary clear and even surprising views for a biological reaction. In the past 20 years, single-molecule techniques have been undergoing a very rapid development, and these cutting edge technologies have revolutionized the biological research by facilitating single-molecule manipulation and detection. Here we give a brief review about these advanced techniques, including optical tweezers, magnetic tweezers, atomic force microscopy (AFM), hydrodynamic flow-stretching assay, and single-molecule fluorescence resonance energy transfer (smFRET). We are trying to describe their basic principles and provide a few examples of applications for each technique. This review aims to give a rather introductory survey of single-molecule techniques for audiences with biological or biophysical background.
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Affiliation(s)
- Deyu Zhao
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Science Research Center, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 201210, China
| | - Siyun Liu
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Science Research Center, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 201210, China
| | - Ying Gao
- State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Science Research Center, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
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153
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Posporelis S, Coughlin JM, Marsman A, Pradhan S, Tanaka T, Wang H, Varvaris M, Ward R, Higgs C, Edwards JA, Ford CN, Kim PK, Lloyd AM, Edden RAE, Schretlen DJ, Cascella NG, Barker PB, Sawa A. Decoupling of Brain Temperature and Glutamate in Recent Onset of Schizophrenia: A 7T Proton Magnetic Resonance Spectroscopy Study. BIOLOGICAL PSYCHIATRY. COGNITIVE NEUROSCIENCE AND NEUROIMAGING 2018; 3:248-254. [PMID: 29486866 PMCID: PMC5836506 DOI: 10.1016/j.bpsc.2017.04.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Revised: 03/23/2017] [Accepted: 04/10/2017] [Indexed: 01/09/2023]
Abstract
BACKGROUND Converging evidence suggests that cerebral metabolic and cellular homeostasis is altered in patients with recent onset of schizophrenia. As a possible marker of metabolic changes that might link to altered neurotransmission, we used proton magnetic resonance spectroscopy to estimate brain temperature, and we evaluated its relationship to a relevant metabolite, glutamate, within this study population. METHODS Using proton magnetic resonance spectroscopy at 7T, 20 patients with recent onset (≤24 months after first psychotic symptoms) of schizophrenia and 20 healthy control subjects were studied. We measured levels of N-acetylaspartate and glutamate and estimated brain temperature in a noninvasive manner. RESULTS Healthy control subjects showed a significant negative correlation between glutamate and brain temperature in the anterior cingulate cortex. In contrast, the physiological correlation between glutamate and brain temperature was lost in patients with recent onset of schizophrenia. CONCLUSIONS This study supports the hypothesized disrupted relationship between brain metabolism and neurotransmission in patients with recent onset of schizophrenia. The findings include mechanistic implications that are to be followed up in both preclinical and clinical studies.
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Affiliation(s)
- Sotirios Posporelis
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins Medical Institutions, Baltimore, Maryland; South London and Maudsley National Health Service Foundation Trust, London, United Kingdom
| | - Jennifer M Coughlin
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins Medical Institutions, Baltimore, Maryland; Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Anouk Marsman
- Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Subechhya Pradhan
- Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Teppei Tanaka
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Hongxing Wang
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Mark Varvaris
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Rebecca Ward
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Cecilia Higgs
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Jamie A Edwards
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Candice N Ford
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Pearl K Kim
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Ashley M Lloyd
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Richard A E Edden
- Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - David J Schretlen
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Nicola G Cascella
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Peter B Barker
- Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins Medical Institutions, Baltimore, Maryland
| | - Akira Sawa
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins Medical Institutions, Baltimore, Maryland.
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154
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Boonstra S, Blijleven JS, Roos WH, Onck PR, van der Giessen E, van Oijen AM. Hemagglutinin-Mediated Membrane Fusion: A Biophysical Perspective. Annu Rev Biophys 2018; 47:153-173. [PMID: 29494252 DOI: 10.1146/annurev-biophys-070317-033018] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Influenza hemagglutinin (HA) is a viral membrane protein responsible for the initial steps of the entry of influenza virus into the host cell. It mediates binding of the virus particle to the host-cell membrane and catalyzes fusion of the viral membrane with that of the host. HA is therefore a major target in the development of antiviral strategies. The fusion of two membranes involves high activation barriers and proceeds through several intermediate states. Here, we provide a biophysical description of the membrane fusion process, relating its kinetic and thermodynamic properties to the large conformational changes taking place in HA and placing these in the context of multiple HA proteins working together to mediate fusion. Furthermore, we highlight the role of novel single-particle experiments and computational approaches in understanding the fusion process and their complementarity with other biophysical approaches.
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Affiliation(s)
- Sander Boonstra
- Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands; , , , ,
| | - Jelle S Blijleven
- Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands; , , , ,
| | - Wouter H Roos
- Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands; , , , ,
| | - Patrick R Onck
- Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands; , , , ,
| | - Erik van der Giessen
- Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands; , , , ,
| | - Antoine M van Oijen
- School of Chemistry; Faculty of Science, Medicine and Health; University of Wollongong, Wollongong, New South Wales 2522, Australia;
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155
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Singh P, Hui CY. Hydrodynamics govern the pre-fusion docking time of synaptic vesicles. J R Soc Interface 2018; 15:rsif.2017.0818. [PMID: 29386403 DOI: 10.1098/rsif.2017.0818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 01/09/2018] [Indexed: 11/12/2022] Open
Abstract
Synaptic vesicle fusion is a crucial step in the neurotransmission process. Neurotransmitter-filled vesicles are pre-docked at the synapse by the mediation of ribbon structures and SNARE proteins at the ribbon synapses. An electrical impulse triggers the fusion process of pre-docked vesicles, leading to the formation of a fusion pore and subsequently resulting in the release of neurotransmitter into the synaptic cleft. In this study, a continuum model of lipid membrane along with lubrication theory is used to determine the traverse time of the synaptic vesicle under the influence of hydrodynamic forces. We find that the traverse time is strongly dependent on how fast the driving force decays or grows with closure of the gap between the vesicle and the plasma membrane. If the correct behaviour is chosen, the traverse time obtained is of the order of a few hundred milliseconds and lies within the experimentally obtained value of approximately 250 ms (Zenisek D, Steyer JA, Almers W. 2000 Nature406, 849-854 (doi:10.1038/35022500)). We hypothesize that there are two different force behaviours, which complies with the experimental findings of pre-fusion docking of synaptic vesicles at the ribbon synapses. The common theme in the proposed force models is that the driving force has to very rapidly increase or decrease with the amount of clamping.
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Affiliation(s)
- Pankaj Singh
- Department of Theoretical and Applied Mechanics, Cornell University, Ithaca, NY 14853, USA
| | - Chung-Yuen Hui
- Department of Mechanical and Aerospace Engineering, Cornell University, Ithaca, NY 14853, USA
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156
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Walter AM, Böhme MA, Sigrist SJ. Vesicle release site organization at synaptic active zones. Neurosci Res 2017; 127:3-13. [PMID: 29275162 DOI: 10.1016/j.neures.2017.12.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 12/04/2017] [Accepted: 12/06/2017] [Indexed: 11/30/2022]
Abstract
Information transfer between nerve cells (neurons) forms the basis of behavior, emotion, and survival. Signal transduction from one neuron to another occurs at synapses, and relies on both electrical and chemical signal propagation. At chemical synapses, incoming electrical action potentials trigger the release of chemical neurotransmitters that are sensed by the connected cell and here reconverted to an electrical signal. The presynaptic conversion of an electrical to a chemical signal is an energy demanding, highly regulated process that relies on a complex, evolutionarily conserved molecular machinery. Here, we review the biophysical characteristics of this process, the current knowledge of the molecules operating in this reaction and genetic specializations that may have evolved to shape inter-neuronal signaling.
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Affiliation(s)
- Alexander M Walter
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Roessle-Straße 10, Berlin 13125, Germany.
| | - Mathias A Böhme
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Roessle-Straße 10, Berlin 13125, Germany
| | - Stephan J Sigrist
- Freie Universität Berlin, Institute for Biology/Genetics, Takustraße 6, 14195 Berlin, Germany; NeuroCure, Cluster of Excellence, Charité Universitätsmedizin, Charitéplatz 1, 10117 Berlin, Germany.
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157
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Boonstra S, Onck PR, van der Giessen E. Computation of Hemagglutinin Free Energy Difference by the Confinement Method. J Phys Chem B 2017; 121:11292-11303. [PMID: 29151344 PMCID: PMC5742479 DOI: 10.1021/acs.jpcb.7b09699] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 11/15/2017] [Indexed: 11/28/2022]
Abstract
Hemagglutinin (HA) mediates membrane fusion, a crucial step during influenza virus cell entry. How many HAs are needed for this process is still subject to debate. To aid in this discussion, the confinement free energy method was used to calculate the conformational free energy difference between the extended intermediate and postfusion state of HA. Special care was taken to comply with the general guidelines for free energy calculations, thereby obtaining convergence and demonstrating reliability of the results. The energy that one HA trimer contributes to fusion was found to be 34.2 ± 3.4kBT, similar to the known contributions from other fusion proteins. Although computationally expensive, the technique used is a promising tool for the further energetic characterization of fusion protein mechanisms. Knowledge of the energetic contributions per protein, and of conserved residues that are crucial for fusion, aids in the development of fusion inhibitors for antiviral drugs.
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Affiliation(s)
- Sander Boonstra
- Micromechanics of Materials,
Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Patrick R. Onck
- Micromechanics of Materials,
Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Erik van der Giessen
- Micromechanics of Materials,
Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands
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158
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Satnav for cells: Destination membrane fusion. Cell Calcium 2017; 68:14-23. [PMID: 29129204 DOI: 10.1016/j.ceca.2017.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 09/20/2017] [Accepted: 10/07/2017] [Indexed: 11/23/2022]
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159
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The Dual Function of the Polybasic Juxtamembrane Region of Syntaxin 1A in Clamping Spontaneous Release and Stimulating Ca 2+-Triggered Release in Neuroendocrine Cells. J Neurosci 2017; 38:220-231. [PMID: 29133430 DOI: 10.1523/jneurosci.1541-17.2017] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2017] [Revised: 09/07/2017] [Accepted: 10/07/2017] [Indexed: 11/21/2022] Open
Abstract
The exact function of the polybasic juxtamembrane region (5RK) of the plasma membrane neuronal SNARE, syntaxin 1A (Syx), in vesicle exocytosis, although widely studied, is currently not clear. Here, we addressed the role of 5RK in Ca2+-triggered release, using our Syx-based intramolecular fluorescence resonance energy transfer (FRET) probe, which previously allowed us to resolve a depolarization-induced Ca2+-dependent close-to-open transition (CDO) of Syx that occurs concomitant with evoked release, both in PC12 cells and hippocampal neurons and was abolished upon charge neutralization of 5RK. First, using dynamic FRET analysis in PC12 cells, we show that CDO occurs following assembly of SNARE complexes that include the vesicular SNARE, synaptobrevin 2, and that the participation of 5RK in CDO goes beyond its participation in the final zippering of the complex, because mutations of residues adjacent to 5RK, believed to be crucial for final zippering, do not abolish this transition. In addition, we show that CDO is contingent on membrane phosphatidylinositol 4,5-bisphosphate (PIP2), which is fundamental for maintaining regulated exocytosis, as depletion of membranal PIP2 abolishes CDO. Prompted by these results, which underscore a potentially significant role of 5RK in exocytosis, we next amperometrically analyzed catecholamine release from PC12 cells, revealing that charge neutralization of 5RK promotes spontaneous and inhibits Ca2+-triggered release events. Namely, 5RK acts as a fusion clamp, making release dependent on stimulation by Ca2+SIGNIFICANCE STATEMENT Syntaxin 1A (Syx) is a central protein component of the SNARE complex, which underlies neurotransmitter release. Although widely studied in relation to its participation in SNARE complex formation and its interaction with phosphoinositides, the function of Syx's polybasic juxtamembrane region (5RK) remains unclear. Previously, we showed that a conformational transition of Syx, related to calcium-triggered release, reported by a Syx-based FRET probe, is abolished upon charge neutralization of 5RK (5RK/A). Here we show that this conformational transition is dependent on phosphatidylinositol 4,5-bisphosphate (PIP2) and is related to SNARE complex formation. Subsequently, we show that the 5RK/A mutation enhances spontaneous release and inhibits calcium-triggered release in neuroendocrine cells, indicating a previously unrecognized role of 5RK in neurotransmitter release.
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160
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Khounlo R, Kim J, Yin L, Shin YK. Botulinum Toxins A and E Inflict Dynamic Destabilization on t-SNARE to Impair SNARE Assembly and Membrane Fusion. Structure 2017; 25:1679-1686.e5. [PMID: 29033286 PMCID: PMC5685167 DOI: 10.1016/j.str.2017.09.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 08/24/2017] [Accepted: 09/12/2017] [Indexed: 01/08/2023]
Abstract
Botulinum toxins (BoNTs) A and E block neurotransmitter release by specifically cleaving the C- terminal ends of SNAP-25, a plasma membrane SNARE protein. Here, we find that SNAP-25A and E, the cleavage products of BoNT A and E, respectively, terminate membrane fusion via completely different mechanisms. Combined studies of single-molecule FRET and single-vesicle fusion assays reveal that SNAP-25E is incapable of supporting SNARE pairing and thus, vesicle docking. In contrast, SNAP-25A facilitates robust SNARE pairing and vesicle docking with somewhat reduced SNARE zippering, which leads to severe impairment of fusion pore opening. The electron paramagnetic resonance results show that the discrepancy between SNAP-25A and E might stem from the extent of the dynamic destabilization of the t-SNARE core at the N-terminal half, which plays a pivotal role in nucleating SNARE complex formation. Thus, the results provide insights into the structure/dynamics-based mechanism by which BoNT A and E impair membrane fusion.
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Affiliation(s)
- Ryan Khounlo
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Jaewook Kim
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Linxiang Yin
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Yeon-Kyun Shin
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA 50011, USA.
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161
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D'Agostino M, Risselada HJ, Lürick A, Ungermann C, Mayer A. A tethering complex drives the terminal stage of SNARE-dependent membrane fusion. Nature 2017; 551:634-638. [PMID: 29088698 DOI: 10.1038/nature24469] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 10/03/2017] [Indexed: 11/09/2022]
Abstract
Membrane fusion in eukaryotic cells mediates the biogenesis of organelles, vesicular traffic between them, and exo- and endocytosis of important signalling molecules, such as hormones and neurotransmitters. Distinct tasks in intracellular membrane fusion have been assigned to conserved protein systems. Tethering proteins mediate the initial recognition and attachment of membranes, whereas SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) protein complexes are considered as the core fusion engine. SNARE complexes provide mechanical energy to distort membranes and drive them through a hemifusion intermediate towards the formation of a fusion pore. This last step is highly energy-demanding. Here we combine the in vivo and in vitro fusion of yeast vacuoles with molecular simulations to show that tethering proteins are critical for overcoming the final energy barrier to fusion pore formation. SNAREs alone drive vacuoles only into the hemifused state. Tethering proteins greatly increase the volume of SNARE complexes and deform the site of hemifusion, which lowers the energy barrier for pore opening and provides the driving force. Thereby, tethering proteins assume a crucial mechanical role in the terminal stage of membrane fusion that is likely to be conserved at multiple steps of vesicular traffic. We therefore propose that SNAREs and tethering proteins should be considered as a single, non-dissociable device that drives fusion. The core fusion machinery may then be larger and more complex than previously thought.
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Affiliation(s)
- Massimo D'Agostino
- Département de Biochimie, Université de Lausanne, Chemin des Boveresses 155, CH-1066 Epalinges, Switzerland
| | - Herre Jelger Risselada
- Georg-August University, Department of Theoretical Physics, Göttingen, Friedrich-Hund-Platz 1, D-37077 Göttingen, Germany.,Leibniz Institute of Surface Modification, Chemical Department, Permoserstrasse 15, D-04318, Leipzig, Germany
| | - Anna Lürick
- University of Osnabrück, Department of Biology/Chemistry, Barbarastrasse 13, D-49076 Osnabrück, Germany
| | - Christian Ungermann
- University of Osnabrück, Department of Biology/Chemistry, Barbarastrasse 13, D-49076 Osnabrück, Germany
| | - Andreas Mayer
- Département de Biochimie, Université de Lausanne, Chemin des Boveresses 155, CH-1066 Epalinges, Switzerland
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162
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Yu H, Siewny MGW, Edwards DT, Sanders AW, Perkins TT. Hidden dynamics in the unfolding of individual bacteriorhodopsin proteins. Science 2017; 355:945-950. [PMID: 28254940 DOI: 10.1126/science.aah7124] [Citation(s) in RCA: 151] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 02/06/2017] [Indexed: 12/27/2022]
Abstract
Protein folding occurs as a set of transitions between structural states within an energy landscape. An oversimplified view of the folding process emerges when transiently populated states are undetected because of limited instrumental resolution. Using force spectroscopy optimized for 1-microsecond resolution, we reexamined the unfolding of individual bacteriorhodopsin molecules in native lipid bilayers. The experimental data reveal the unfolding pathway in unprecedented detail. Numerous newly detected intermediates-many separated by as few as two or three amino acids-exhibited complex dynamics, including frequent refolding and state occupancies of <10 μs. Equilibrium measurements between such states enabled the folding free-energy landscape to be deduced. These results sharpen the picture of the mechanical unfolding of membrane proteins and, more broadly, enable experimental access to previously obscured protein dynamics.
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Affiliation(s)
- Hao Yu
- JILA, National Institute of Standards and Technology and University of Colorado, Boulder, CO 80309, USA
| | - Matthew G W Siewny
- JILA, National Institute of Standards and Technology and University of Colorado, Boulder, CO 80309, USA.,Department of Physics, University of Colorado, Boulder, CO 80309, USA
| | - Devin T Edwards
- JILA, National Institute of Standards and Technology and University of Colorado, Boulder, CO 80309, USA
| | - Aric W Sanders
- Radio Frequency Technology Division, National Institute of Standards and Technology, Boulder, CO 80305, USA
| | - Thomas T Perkins
- JILA, National Institute of Standards and Technology and University of Colorado, Boulder, CO 80309, USA. .,Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
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163
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Rothman JE, Krishnakumar SS, Grushin K, Pincet F. Hypothesis - buttressed rings assemble, clamp, and release SNAREpins for synaptic transmission. FEBS Lett 2017; 591:3459-3480. [PMID: 28983915 PMCID: PMC5698743 DOI: 10.1002/1873-3468.12874] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 10/02/2017] [Accepted: 10/02/2017] [Indexed: 11/21/2022]
Abstract
Neural networks are optimized to detect temporal coincidence on the millisecond timescale. Here, we offer a synthetic hypothesis based on recent structural insights into SNAREs and the C2 domain proteins to explain how synaptic transmission can keep this pace. We suggest that an outer ring of up to six curved Munc13 ‘MUN’ domains transiently anchored to the plasma membrane via its flanking domains surrounds a stable inner ring comprised of synaptotagmin C2 domains to serve as a work‐bench on which SNAREpins are templated. This ‘buttressed‐ring hypothesis’ affords straightforward answers to many principal and long‐standing questions concerning how SNAREpins can be assembled, clamped, and then released synchronously with an action potential.
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Affiliation(s)
- James E Rothman
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Shyam S Krishnakumar
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Kirill Grushin
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Frederic Pincet
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA.,Laboratoire de Physique Statistique, Ecole Normale Supérieure, PSL Research University, Université Paris Diderot Sorbonne Paris Cité, Sorbonne Universités UPMC Univ, CNRS, Paris, France
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164
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Ma L, Cai Y, Li Y, Jiao J, Wu Z, O'Shaughnessy B, De Camilli P, Karatekin E, Zhang Y. Single-molecule force spectroscopy of protein-membrane interactions. eLife 2017; 6:30493. [PMID: 29083305 PMCID: PMC5690283 DOI: 10.7554/elife.30493] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 10/29/2017] [Indexed: 12/17/2022] Open
Abstract
Many biological processes rely on protein–membrane interactions in the presence of mechanical forces, yet high resolution methods to quantify such interactions are lacking. Here, we describe a single-molecule force spectroscopy approach to quantify membrane binding of C2 domains in Synaptotagmin-1 (Syt1) and Extended Synaptotagmin-2 (E-Syt2). Syts and E-Syts bind the plasma membrane via multiple C2 domains, bridging the plasma membrane with synaptic vesicles or endoplasmic reticulum to regulate membrane fusion or lipid exchange, respectively. In our approach, single proteins attached to membranes supported on silica beads are pulled by optical tweezers, allowing membrane binding and unbinding transitions to be measured with unprecedented spatiotemporal resolution. C2 domains from either protein resisted unbinding forces of 2–7 pN and had binding energies of 4–14 kBT per C2 domain. Regulation by bilayer composition or Ca2+ recapitulated known properties of both proteins. The method can be widely applied to study protein–membrane interactions.
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Affiliation(s)
- Lu Ma
- Department of Cell Biology, Yale University School of Medicine, New Haven, United States.,CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China.,Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China
| | - Yiying Cai
- Department of Cell Biology, Yale University School of Medicine, New Haven, United States.,Department of Neuroscience, Yale University School of Medicine, New Haven, United States.,Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, United States.,Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, United States
| | - Yanghui Li
- Department of Cell Biology, Yale University School of Medicine, New Haven, United States.,College of Optical and Electronic Technology, China Jiliang University, Hangzhou, China
| | - Junyi Jiao
- Department of Cell Biology, Yale University School of Medicine, New Haven, United States.,Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, United States
| | - Zhenyong Wu
- Department of Cellular and Molecular Physiology, Yale University School of Medicine, New Haven, United States.,Nanobiology Institute, Yale University, West Haven, United States
| | - Ben O'Shaughnessy
- Department of Chemical Engineering, Columbia University, New York, United States
| | - Pietro De Camilli
- Department of Cell Biology, Yale University School of Medicine, New Haven, United States.,Department of Neuroscience, Yale University School of Medicine, New Haven, United States.,Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, United States.,Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, United States.,Kavli Institute for Neuroscience, Yale University School of Medicine, New Haven, United States
| | - Erdem Karatekin
- Department of Cellular and Molecular Physiology, Yale University School of Medicine, New Haven, United States.,Nanobiology Institute, Yale University, West Haven, United States.,Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, United States.,Laboratoire de Neurophotonique, Faculté des Sciences Fondamentales et Biomédicales, Centre National de la Recherche Scientifique (CNRS) UMR 8250, Université Paris Descartes, Paris, France
| | - Yongli Zhang
- Department of Cell Biology, Yale University School of Medicine, New Haven, United States
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165
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Two Disease-Causing SNAP-25B Mutations Selectively Impair SNARE C-terminal Assembly. J Mol Biol 2017; 430:479-490. [PMID: 29056461 DOI: 10.1016/j.jmb.2017.10.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 10/09/2017] [Accepted: 10/10/2017] [Indexed: 12/17/2022]
Abstract
Synaptic exocytosis relies on assembly of three soluble N-ethylmaleimide-sensitive factor attachment receptor (SNARE) proteins into a parallel four-helix bundle to drive membrane fusion. SNARE assembly occurs by stepwise zippering of the vesicle-associated SNARE (v-SNARE) onto a binary SNARE complex on the target plasma membrane (t-SNARE). Zippering begins with slow N-terminal association followed by rapid C-terminal zippering, which serves as a power stroke to drive membrane fusion. SNARE mutations have been associated with numerous diseases, especially neurological disorders. It remains unclear how these mutations affect SNARE zippering, partly due to difficulties to quantify the energetics and kinetics of SNARE assembly. Here, we used single-molecule optical tweezers to measure the assembly energy and kinetics of SNARE complexes containing single mutations I67T/N in neuronal SNARE synaptosomal-associated protein of 25kDa (SNAP-25B), which disrupt neurotransmitter release and have been implicated in neurological disorders. We found that both mutations significantly reduced the energy of C-terminal zippering by ~10 kBT, but did not affect N-terminal assembly. In addition, we observed that both mutations lead to unfolding of the C-terminal region in the t-SNARE complex. Our findings suggest that both SNAP-25B mutations impair synaptic exocytosis by destabilizing SNARE assembly, rather than stabilizing SNARE assembly as previously proposed. Therefore, our measurements provide insights into the molecular mechanism of the disease caused by SNARE mutations.
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166
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Wang T, Li L, Hong W. SNARE proteins in membrane trafficking. Traffic 2017; 18:767-775. [PMID: 28857378 DOI: 10.1111/tra.12524] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 08/25/2017] [Accepted: 08/25/2017] [Indexed: 12/25/2022]
Abstract
SNAREs are the core machinery mediating membrane fusion. In this review, we provide an update on the recent progress on SNAREs regulating membrane fusion events, especially the more detailed fusion processes dissected by well-developed biophysical methods and in vitro single molecule analysis approaches. We also briefly summarize the relevant research from Chinese laboratories and highlight the significant contributions on our understanding of SNARE-mediated membrane trafficking from scientists in China.
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Affiliation(s)
- Tuanlao Wang
- School of Pharmaceutical Sciences, State Key Laboratory of Cellular Stress Biology, Xiamen University, Xiamen, China
| | - Liangcheng Li
- School of Pharmaceutical Sciences, State Key Laboratory of Cellular Stress Biology, Xiamen University, Xiamen, China
| | - Wanjin Hong
- School of Pharmaceutical Sciences, State Key Laboratory of Cellular Stress Biology, Xiamen University, Xiamen, China.,Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Singapore, Singapore
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167
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Wu Z, Thiyagarajan S, O'Shaughnessy B, Karatekin E. Regulation of Exocytotic Fusion Pores by SNARE Protein Transmembrane Domains. Front Mol Neurosci 2017; 10:315. [PMID: 29066949 PMCID: PMC5641348 DOI: 10.3389/fnmol.2017.00315] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 09/19/2017] [Indexed: 12/26/2022] Open
Abstract
Calcium-triggered exocytotic release of neurotransmitters and hormones from neurons and neuroendocrine cells underlies neuronal communication, motor activity and endocrine functions. The core of the neuronal exocytotic machinery is composed of soluble N-ethyl maleimide sensitive factor attachment protein receptors (SNAREs). Formation of complexes between vesicle-attached v- and plasma-membrane anchored t-SNAREs in a highly regulated fashion brings the membranes into close apposition. Small, soluble proteins called Complexins (Cpx) and calcium-sensing Synaptotagmins cooperate to block fusion at low resting calcium concentrations, but trigger release upon calcium increase. A growing body of evidence suggests that the transmembrane domains (TMDs) of SNARE proteins play important roles in regulating the processes of fusion and release, but the mechanisms involved are only starting to be uncovered. Here we review recent evidence that SNARE TMDs exert influence by regulating the dynamics of the fusion pore, the initial aqueous connection between the vesicular lumen and the extracellular space. Even after the fusion pore is established, hormone release by neuroendocrine cells is tightly controlled, and the same may be true of neurotransmitter release by neurons. The dynamics of the fusion pore can regulate the kinetics of cargo release and the net amount released, and can determine the mode of vesicle recycling. Manipulations of SNARE TMDs were found to affect fusion pore properties profoundly, both during exocytosis and in biochemical reconstitutions. To explain these effects, TMD flexibility, and interactions among TMDs or between TMDs and lipids have been invoked. Exocytosis has provided the best setting in which to unravel the underlying mechanisms, being unique among membrane fusion reactions in that single fusion pores can be probed using high-resolution methods. An important role will likely be played by methods that can probe single fusion pores in a biochemically defined setting which have recently become available. Finally, computer simulations are valuable mechanistic tools because they have the power to access small length scales and very short times that are experimentally inaccessible.
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Affiliation(s)
- Zhenyong Wu
- Department of Cellular and Molecular Physiology, School of Medicine, Yale University, New Haven, CT, United States.,Nanobiology Institute, Yale University, West Haven, CT, United States
| | | | - Ben O'Shaughnessy
- Department of Chemical Engineering, Columbia University, New York, NY, United States
| | - Erdem Karatekin
- Department of Cellular and Molecular Physiology, School of Medicine, Yale University, New Haven, CT, United States.,Nanobiology Institute, Yale University, West Haven, CT, United States.,Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States.,Laboratoire de Neurophotonique, Université Paris Descartes, Faculté des Sciences Fondamentales et Biomédicales, Centre National de la Recherche Scientifique (CNRS), Paris, France
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168
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Praschberger R, Lowe SA, Malintan NT, Giachello CNG, Patel N, Houlden H, Kullmann DM, Baines RA, Usowicz MM, Krishnakumar SS, Hodge JJL, Rothman JE, Jepson JEC. Mutations in Membrin/GOSR2 Reveal Stringent Secretory Pathway Demands of Dendritic Growth and Synaptic Integrity. Cell Rep 2017; 21:97-109. [PMID: 28978487 PMCID: PMC5640804 DOI: 10.1016/j.celrep.2017.09.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 08/17/2017] [Accepted: 09/01/2017] [Indexed: 11/16/2022] Open
Abstract
Mutations in the Golgi SNARE (SNAP [soluble NSF attachment protein] receptor) protein Membrin (encoded by the GOSR2 gene) cause progressive myoclonus epilepsy (PME). Membrin is a ubiquitous and essential protein mediating ER-to-Golgi membrane fusion. Thus, it is unclear how mutations in Membrin result in a disorder restricted to the nervous system. Here, we use a multi-layered strategy to elucidate the consequences of Membrin mutations from protein to neuron. We show that the pathogenic mutations cause partial reductions in SNARE-mediated membrane fusion. Importantly, these alterations were sufficient to profoundly impair dendritic growth in Drosophila models of GOSR2-PME. Furthermore, we show that Membrin mutations cause fragmentation of the presynaptic cytoskeleton coupled with transsynaptic instability and hyperactive neurotransmission. Our study highlights how dendritic growth is vulnerable even to subtle secretory pathway deficits, uncovers a role for Membrin in synaptic function, and provides a comprehensive explanatory basis for genotype-phenotype relationships in GOSR2-PME.
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Affiliation(s)
- Roman Praschberger
- Department of Clinical and Experimental Epilepsy, UCL Institute of Neurology, London, UK
| | - Simon A Lowe
- School of Physiology, Pharmacology, and Neuroscience, University of Bristol, Bristol, UK
| | - Nancy T Malintan
- Department of Clinical and Experimental Epilepsy, UCL Institute of Neurology, London, UK
| | - Carlo N G Giachello
- Faculty of Biology, Medicine, and Health, Division of Neuroscience & Experimental Psychology, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Nian Patel
- Department of Clinical and Experimental Epilepsy, UCL Institute of Neurology, London, UK
| | - Henry Houlden
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | - Dimitri M Kullmann
- Department of Clinical and Experimental Epilepsy, UCL Institute of Neurology, London, UK
| | - Richard A Baines
- Faculty of Biology, Medicine, and Health, Division of Neuroscience & Experimental Psychology, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Maria M Usowicz
- School of Physiology, Pharmacology, and Neuroscience, University of Bristol, Bristol, UK
| | - Shyam S Krishnakumar
- Department of Clinical and Experimental Epilepsy, UCL Institute of Neurology, London, UK; Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA
| | - James J L Hodge
- School of Physiology, Pharmacology, and Neuroscience, University of Bristol, Bristol, UK
| | - James E Rothman
- Department of Clinical and Experimental Epilepsy, UCL Institute of Neurology, London, UK; Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA
| | - James E C Jepson
- Department of Clinical and Experimental Epilepsy, UCL Institute of Neurology, London, UK.
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169
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Dhara M, Mohrmann R, Bruns D. v-SNARE function in chromaffin cells. Pflugers Arch 2017; 470:169-180. [PMID: 28887593 PMCID: PMC5748422 DOI: 10.1007/s00424-017-2066-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 08/28/2017] [Accepted: 08/29/2017] [Indexed: 01/04/2023]
Abstract
Vesicle fusion is elementary for intracellular trafficking and release of signal molecules, thus providing the basis for diverse forms of intercellular communication like hormonal regulation or synaptic transmission. A detailed characterization of the mechanisms underlying exocytosis is key to understand how the nervous system integrates information and generates appropriate responses to stimuli. The machinery for vesicular release employs common molecular players in different model systems including neuronal and neuroendocrine cells, in particular members of the SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptors) protein family, Sec1/Munc18-like proteins, and other accessory factors. To achieve temporal precision and speed, excitable cells utilize specialized regulatory proteins like synaptotagmin and complexin, whose interplay putatively synchronizes vesicle fusion and enhances stimulus-secretion coupling. In this review, we aim to highlight recent progress and emerging views on the molecular mechanisms, by which constitutively forming SNAREpins are organized in functional, tightly regulated units for synchronized release. Specifically, we will focus on the role of vesicle associated membrane proteins, also referred to as vesicular SNAREs, in fusion and rapid cargo discharge. We will further discuss the functions of SNARE regulators during exocytosis and focus on chromaffin cell as a model system of choice that allows for detailed structure-function analyses and direct measurements of vesicle fusion under precise control of intracellular [Ca]i.
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Affiliation(s)
- Madhurima Dhara
- Molecular Neurophysiology, CIPMM, Medical Faculty, Saarland University, 66421, Homburg/Saar, Germany
| | - Ralf Mohrmann
- Zentrum für Human- und Molekularbiologie, Saarland University, 66421, Homburg/Saar, Germany
| | - Dieter Bruns
- Molecular Neurophysiology, CIPMM, Medical Faculty, Saarland University, 66421, Homburg/Saar, Germany.
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170
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Hao Y, Canavan C, Taylor SS, Maillard RA. Integrated Method to Attach DNA Handles and Functionally Select Proteins to Study Folding and Protein-Ligand Interactions with Optical Tweezers. Sci Rep 2017; 7:10843. [PMID: 28883488 PMCID: PMC5589850 DOI: 10.1038/s41598-017-11214-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 08/21/2017] [Indexed: 12/15/2022] Open
Abstract
Optical tweezers has emerged as a powerful tool to study folding, ligand binding, and motor enzymes. The manipulation of proteins with optical tweezers requires attaching molecular handles to the protein of interest. Here, we describe a novel method that integrates the covalent attachment of DNA handles to target proteins with a selection step for functional and properly folded molecules. In addition, this method enables obtaining protein molecules in different liganded states and can be used with handles of different lengths. We apply this method to study the cAMP binding domain A (CBD-A) of Protein kinase A. We find that the functional selection step drastically improves the reproducibility and homogeneity of the single molecule data. In contrast, without a functional selection step, proteins often display misfolded conformations. cAMP binding stabilizes the CBD-A against a denaturing force, and increases the folded state lifetime. Data obtained with handles of 370 and 70 base pairs are indistinguishable, but at low forces short handles provide a higher spatial resolution. Altogether, this method is flexible, selects for properly folded molecules in different liganded states, and can be readily applicable to study protein folding or protein-ligand interactions with force spectroscopy that require molecular handles.
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Affiliation(s)
- Yuxin Hao
- Department of Chemistry, Georgetown University, Washington, DC 20057, USA
| | - Clare Canavan
- Department of Chemistry, Georgetown University, Washington, DC 20057, USA
| | - Susan S Taylor
- Department of Pharmacology & Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Rodrigo A Maillard
- Department of Chemistry, Georgetown University, Washington, DC 20057, USA.
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171
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Ritchie DB, Cappellano TR, Tittle C, Rezajooei N, Rouleau L, Sikkema WKA, Woodside MT. Conformational dynamics of the frameshift stimulatory structure in HIV-1. RNA (NEW YORK, N.Y.) 2017; 23:1376-1384. [PMID: 28522581 PMCID: PMC5558907 DOI: 10.1261/rna.061655.117] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 05/12/2017] [Indexed: 05/02/2023]
Abstract
Programmed ribosomal frameshifting (PRF) in HIV-1 is thought to be stimulated by a hairpin in the mRNA, although a pseudoknot-like triplex has also been proposed. Because the conformational dynamics of the stimulatory structure under tension applied by the ribosomal helicase during translation may play an important role in PRF, we used optical tweezers to apply tension to the HIV stimulatory structure and monitor its unfolding and refolding dynamics. The folding and unfolding kinetics and energy landscape of the hairpin were measured by ramping the force on the hairpin up and down, providing a detailed biophysical characterization. Unexpectedly, whereas unfolding reflected the simple two-state behavior typical of many hairpins, refolding was more complex, displaying significant heterogeneity. Evidence was found for multiple refolding pathways as well as previously unsuspected, partially folded intermediates. Measuring a variant mRNA containing only the sequence required to form the proposed triplex, it behaved largely in the same way. Nonetheless, very rarely, high-force unfolding events characteristic of pseudoknot-like structures were observed. The rare occurrence of the triplex suggests that the hairpin is the functional stimulatory structure. The unusual heterogeneity of the hairpin dynamics under tension suggests a possible functional role in PRF similar to the dynamics of other stimulatory structures.
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Affiliation(s)
- Dustin B Ritchie
- Department of Physics, University of Alberta, Edmonton AB T6G 2E1, Canada
| | - Tonia R Cappellano
- Department of Physics, University of Alberta, Edmonton AB T6G 2E1, Canada
| | - Collin Tittle
- Department of Physics, University of Alberta, Edmonton AB T6G 2E1, Canada
| | - Negar Rezajooei
- Department of Physics, University of Alberta, Edmonton AB T6G 2E1, Canada
| | - Logan Rouleau
- Department of Physics, University of Alberta, Edmonton AB T6G 2E1, Canada
| | | | - Michael T Woodside
- Department of Physics, University of Alberta, Edmonton AB T6G 2E1, Canada
- National Institute for Nanotechnology, National Research Council, Edmonton AB T6G 2M9, Canada
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172
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Rehman A, Hu SH, Tnimov Z, Whitten AE, King GJ, Jarrott RJ, Norwood SJ, Alexandrov K, Collins BM, Christie MP, Martin JL. The nature of the Syntaxin4 C-terminus affects Munc18c-supported SNARE assembly. PLoS One 2017; 12:e0183366. [PMID: 28841669 PMCID: PMC5571939 DOI: 10.1371/journal.pone.0183366] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 08/02/2017] [Indexed: 11/18/2022] Open
Abstract
Vesicular transport of cellular cargo requires targeted membrane fusion and formation of a SNARE protein complex that draws the two apposing fusing membranes together. Insulin-regulated delivery and fusion of glucose transporter-4 storage vesicles at the cell surface is dependent on two key proteins: the SNARE integral membrane protein Syntaxin4 (Sx4) and the soluble regulatory protein Munc18c. Many reported in vitro studies of Munc18c:Sx4 interactions and of SNARE complex formation have used soluble Sx4 constructs lacking the native transmembrane domain. As a consequence, the importance of the Sx4 C-terminal anchor remains poorly understood. Here we show that soluble C-terminally truncated Sx4 dissociates more rapidly from Munc18c than Sx4 where the C-terminal transmembrane domain is replaced with a T4-lysozyme fusion. We also show that Munc18c appears to inhibit SNARE complex formation when soluble C-terminally truncated Sx4 is used but does not inhibit SNARE complex formation when Sx4 is C-terminally anchored (by a C-terminal His-tag bound to resin, by a C-terminal T4L fusion or by the native C-terminal transmembrane domain in detergent micelles). We conclude that the C-terminus of Sx4 is critical for its interaction with Munc18c, and that the reported inhibitory role of Munc18c may be an artifact of experimental design. These results support the notion that a primary role of Munc18c is to support SNARE complex formation and membrane fusion.
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Affiliation(s)
- Asma Rehman
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, QLD, Australia
| | - Shu-Hong Hu
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, QLD, Australia
| | - Zakir Tnimov
- Division of Cell Biology and Molecular Medicine, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, QLD, Australia
| | - Andrew E. Whitten
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, QLD, Australia
| | - Gordon J. King
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, QLD, Australia
| | - Russell J. Jarrott
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, QLD, Australia
| | - Suzanne J. Norwood
- Division of Cell Biology and Molecular Medicine, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, QLD, Australia
| | - Kirill Alexandrov
- Division of Cell Biology and Molecular Medicine, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, QLD, Australia
| | - Brett M. Collins
- Division of Cell Biology and Molecular Medicine, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, QLD, Australia
| | - Michelle P. Christie
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, QLD, Australia
- * E-mail: (MPC); (JLM)
| | - Jennifer L. Martin
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, QLD, Australia
- * E-mail: (MPC); (JLM)
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173
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Gipson P, Fukuda Y, Danev R, Lai Y, Chen DH, Baumeister W, Brunger AT. Morphologies of synaptic protein membrane fusion interfaces. Proc Natl Acad Sci U S A 2017; 114:9110-9115. [PMID: 28739947 PMCID: PMC5576828 DOI: 10.1073/pnas.1708492114] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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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174
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175
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A Membrane-Fusion Model That Exploits a β-to-α Transition in the Hydrophobic Domains of Syntaxin 1A and Synaptobrevin 2. Int J Mol Sci 2017; 18:ijms18071582. [PMID: 28753981 PMCID: PMC5536069 DOI: 10.3390/ijms18071582] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2017] [Revised: 07/14/2017] [Accepted: 07/18/2017] [Indexed: 11/16/2022] Open
Abstract
Parallel zippering of the SNARE domains of syntaxin 1A/B, SNAP-25, and VAMP/synaptobrevin 2 is widely regarded as supplying the driving force for exocytotic events at nerve terminals and elsewhere. However, in spite of intensive research, no consensus has been reached concerning the molecular mechanism by which these SNARE proteins catalyze membrane fusion. As an alternative to SNARE-based models, a scenario was developed in which synaptotagmin 1 (or, 2) can serve as a template to guide lipid movements that underlie fast, synchronous exocytosis at nerve terminals. This “dyad model” advanced a novel proposal concerning the membrane disposition of the palmitoylated, cysteine-rich region of these synaptotagmins. Unexpectedly, it now emerges that a similar principle can be exploited to reveal how the hydrophobic, carboxyl-terminal domains of syntaxin 1A and synaptobrevin 2 can perturb membrane structure at the interface between a docked synaptic vesicle and the plasma membrane. These “β-to-α transition” models will be compared and contrasted with other proposals for how macromolecules are thought to intervene to drive membrane fusion.
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176
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Extension of Helix 12 in Munc18-1 Induces Vesicle Priming. J Neurosci 2017; 36:6881-91. [PMID: 27358447 DOI: 10.1523/jneurosci.0007-16.2016] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2016] [Accepted: 05/14/2016] [Indexed: 11/21/2022] Open
Abstract
UNLABELLED Munc18-1 is essential for vesicle fusion and participates in the docking of large dense-core vesicles to the plasma membrane. Recent structural data suggest that conformational changes in the 12th helix of the Munc18-1 domain 3a within the Munc18-1:syntaxin complex result in an additional interaction with synaptobrevin-2/VAMP2 (vesicle-associated membrane protein 2), leading to SNARE complex formation. To test this hypothesis in living cells, we examined secretion from Munc18-1-null mouse adrenal chromaffin cells expressing Munc18-1 mutants designed to either perturb the extension of helix 12 (Δ324-339), block its interaction with synaptobrevin-2 (L348R), or extend the helix to promote coil-coil interactions with other proteins (P335A). The mutants rescued vesicle docking and syntaxin-1 targeting to the plasma membrane, with the exception of P335A that only supported partial syntaxin-1 targeting. Disruptive mutations (L348R or Δ324-339) lowered the secretory amplitude by decreasing vesicle priming, whereas P335A markedly increased priming and secretory amplitude. The mutants displayed unchanged kinetics and Ca(2+) dependence of fusion, indicating that the mutations specifically affect the vesicle priming step. Mutation of a nearby tyrosine (Y337A), which interacts with closed syntaxin-1, mildly increased secretory amplitude. This correlated with results from an in vitro fusion assay probing the functions of Munc18-1, indicating an easier transition to the extended state in the mutant. Our findings support the notion that a conformational transition within the Munc18-1 domain 3a helix 12 leads to opening of a closed Munc18-1:syntaxin complex, followed by productive SNARE complex assembly and vesicle priming. SIGNIFICANCE STATEMENT The essential postdocking role of Munc18-1 in vesicular exocytosis has remained elusive, but recent data led to the hypothesis that the extension of helix 12 in Munc18 within domain 3a leads to synaptobrevin-2/VAMP2 interaction and SNARE complex formation. Using both lack-of-function and gain-of-function mutants, we here report that the conformation of helix 12 predicts vesicle priming and secretory amplitude in living chromaffin cells. The effects of mutants on secretion could not be explained by differences in syntaxin-1 chaperoning/localization or vesicle docking, and the fusion kinetics and calcium dependence were unchanged, indicating that the effect of helix 12 extension is specific for the vesicle-priming step. We conclude that a conformational change within helix 12 is responsible for the essential postdocking role of Munc18-1 in neurosecretion.
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177
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Distinct Functions of Syntaxin-1 in Neuronal Maintenance, Synaptic Vesicle Docking, and Fusion in Mouse Neurons. J Neurosci 2017; 36:7911-24. [PMID: 27466336 DOI: 10.1523/jneurosci.1314-16.2016] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 06/09/2016] [Indexed: 01/08/2023] Open
Abstract
UNLABELLED Neurotransmitter release requires the formation of soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) complexes by SNARE proteins syntaxin-1 (Stx1), synaptosomal-associated protein 25 (SNAP-25), and synaptobrevin-2 (Syb2). In mammalian systems, loss of SNAP-25 or Syb2 severely impairs neurotransmitter release; however, complete loss of function studies for Stx1 have been elusive due to the functional redundancy between Stx1 isoforms Stx1A and Stx1B and the embryonic lethality of Stx1A/1B double knock-out (DKO) mice. Here, we studied the roles of Stx1 in neuronal maintenance and neurotransmitter release in mice with constitutive or conditional deletion of Stx1B on an Stx1A-null background. Both constitutive and postnatal loss of Stx1 severely compromised neuronal viability in vivo and in vitro, indicating an obligatory role of Stx1 for maintenance of developing and mature neurons. Loss of Munc18-1, a high-affinity binding partner of Stx1, also showed severely impaired neuronal viability, but with a slower time course compared with Stx1A/1B DKO neurons, and exogenous Stx1A or Stx1B expression significantly delayed Munc18-1-dependent lethality. In addition, loss of Stx1 completely abolished fusion-competent vesicles and severely impaired vesicle docking, demonstrating its essential roles in neurotransmission. Putative partial SNARE complex assembly with the SNARE motif mutant Stx1A(AV) (A240V, V244A) was not sufficient to rescue neurotransmission despite full recovery of vesicle docking and neuronal survival. Together, these data suggest that Stx1 has independent functions in neuronal maintenance and neurotransmitter release and complete SNARE complex formation is required for vesicle fusion and priming, whereas partial SNARE complex formation is sufficient for vesicle docking and neuronal maintenance. SIGNIFICANCE STATEMENT Syntaxin-1 (Stx1) is a component of the synaptic vesicle soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) complex and is essential for neurotransmission. We present the first detailed loss-of-function characterization of the two Stx1 isoforms in central mammalian neurons. We show that Stx1 is fundamental for maintenance of developing and mature neurons and also for vesicle docking and neurotransmission. We also demonstrate that neuronal maintenance and neurotransmitter release are regulated by Stx1 through independent functions. Furthermore, we show that SNARE complex formation is required for vesicle fusion, whereas partial SNARE complex formation is sufficient for vesicle docking and neuronal maintenance. Therefore, our work provides insights into differential functions of Stx1 in neuronal maintenance and neurotransmission, with the latter explored further into its functions in vesicle docking and fusion.
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178
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Zhang Y. Energetics, kinetics, and pathway of SNARE folding and assembly revealed by optical tweezers. Protein Sci 2017; 26:1252-1265. [PMID: 28097727 PMCID: PMC5477538 DOI: 10.1002/pro.3116] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 01/03/2017] [Indexed: 01/17/2023]
Abstract
Soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs) are universal molecular engines that drive membrane fusion. Particularly, synaptic SNAREs mediate fast calcium-triggered fusion of neurotransmitter-containing vesicles with plasma membranes for synaptic transmission, the basis of all thought and action. During membrane fusion, complementary SNAREs located on two apposed membranes (often called t- and v-SNAREs) join together to assemble into a parallel four-helix bundle, releasing the energy to overcome the energy barrier for fusion. A long-standing hypothesis suggests that SNAREs act like a zipper to draw the two membranes into proximity and thereby force them to fuse. However, a quantitative test of this SNARE zippering hypothesis was hindered by difficulties to determine the energetics and kinetics of SNARE assembly and to identify the relevant folding intermediates. Here, we first review different approaches that have been applied to study SNARE assembly and then focus on high-resolution optical tweezers. We summarize the folding energies, kinetics, and pathways of both wild-type and mutant SNARE complexes derived from this new approach. These results show that synaptic SNAREs assemble in four distinct stages with different functions: slow N-terminal domain association initiates SNARE assembly; a middle domain suspends and controls SNARE assembly; and rapid sequential zippering of the C-terminal domain and the linker domain directly drive membrane fusion. In addition, the kinetics and pathway of the stagewise assembly are shared by other SNARE complexes. These measurements prove the SNARE zippering hypothesis and suggest new mechanisms for SNARE assembly regulated by other proteins.
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Affiliation(s)
- Yongli Zhang
- Department of Cell Biology, Yale School of MedicineYale UniversityNew HavenConnecticut06511
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179
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Suppressor Analysis of the Fusogenic Lambda Spanins. J Virol 2017; 91:JVI.00413-17. [PMID: 28468876 DOI: 10.1128/jvi.00413-17] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2017] [Accepted: 04/19/2017] [Indexed: 01/07/2023] Open
Abstract
The final step of lysis in phage λ infections of Escherichia coli is mediated by the spanins Rz and Rz1. These proteins form a complex that bridges the cell envelope and that has been proposed to cause fusion of the inner and outer membranes. Accordingly, mutations that block spanin function are found within coiled-coil domains and the proline-rich region, motifs essential in other fusion systems. To gain insight into spanin function, pseudorevertant alleles that restored plaque formation for lysis-defective mutants of Rz and Rz1 were selected. Most second-site suppressors clustered within a coiled-coil domain of Rz near the outer leaflet of the cytoplasmic membrane and were not allele specific. Suppressors largely encoded polar insertions within the hydrophobic core of the coiled-coil interface. Such suppressor changes resulted in decreased proteolytic stability of the Rz double mutants in vivo Unlike the wild type, in which lysis occurs while the cells retain a rod shape, revertant alleles with second-site suppressor mutations supported lysis events that were preceded by spherical cell formation. This suggests that destabilization of the membrane-proximal coiled coil restores function for defective spanin alleles by increasing the conformational freedom of the complex at the cost of its normal, all-or-nothing functionality.IMPORTANCECaudovirales encode cell envelope-spanning proteins called spanins, which are thought to fuse the inner and outer membranes during phage lysis. Recent genetic analysis identified the functional domains of the lambda spanins, which are similar to class I viral fusion proteins. While the pre- and postfusion structures of model fusion systems have been well characterized, the intermediate structure(s) formed during the fusion reaction remains elusive. Genetic analysis would be expected to identify functional connections between intermediates. Since most membrane fusion systems are not genetically tractable, only few such investigations have been reported. Here, we report a suppressor analysis of lambda spanin function. To our knowledge this is the first suppression analysis of a class I-like complex and also the first such analysis of a prokaryote membrane fusion system.
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180
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Zhang Y, Jiao J, Rebane AA. Hidden Markov Modeling with Detailed Balance and Its Application to Single Protein Folding. Biophys J 2017; 111:2110-2124. [PMID: 27851936 DOI: 10.1016/j.bpj.2016.09.045] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Revised: 08/26/2016] [Accepted: 09/27/2016] [Indexed: 12/26/2022] Open
Abstract
Hidden Markov modeling (HMM) has revolutionized kinetic studies of macromolecules. However, results from HMM often violate detailed balance when applied to the transitions under thermodynamic equilibrium, and the consequence of such violation has not been well understood. Here, to our knowledge, we developed a new HMM method that satisfies detailed balance (HMM-DB) and optimizes model parameters by gradient search. We used free energy of stable and transition states as independent fitting parameters and considered both normal and skew normal distributions of the measurement noise. We validated our method by analyzing simulated extension trajectories that mimicked experimental data of single protein folding from optical tweezers. We then applied HMM-DB to elucidate kinetics of regulated SNARE zippering containing degenerate states. For both simulated and measured trajectories, we found that HMM-DB significantly reduced overfitting of short trajectories compared to the standard HMM based on an expectation-maximization algorithm, leading to more accurate and reliable model fitting by HMM-DB. We revealed how HMM-DB could be conveniently used to derive a simplified energy landscape of protein folding. Finally, we extended HMM-DB to correct the baseline drift in single-molecule trajectories. Together, we demonstrated an efficient, versatile, and reliable method of HMM for kinetics studies of macromolecules under thermodynamic equilibrium.
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Affiliation(s)
- Yongli Zhang
- Department of Cell Biology, School of Medicine, Yale University, New Haven, Connecticut.
| | - Junyi Jiao
- Department of Cell Biology, School of Medicine, Yale University, New Haven, Connecticut; Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut
| | - Aleksander A Rebane
- Department of Cell Biology, School of Medicine, Yale University, New Haven, Connecticut; Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut; Department of Physics, Yale University, New Haven, Connecticut; Nanobiology Institute, Yale University, West Haven, Connecticut
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181
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Yang Z, Gou L, Chen S, Li N, Zhang S, Zhang L. Membrane Fusion Involved in Neurotransmission: Glimpse from Electron Microscope and Molecular Simulation. Front Mol Neurosci 2017. [PMID: 28638320 PMCID: PMC5461332 DOI: 10.3389/fnmol.2017.00168] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Membrane fusion is one of the most fundamental physiological processes in eukaryotes for triggering the fusion of lipid and content, as well as the neurotransmission. However, the architecture features of neurotransmitter release machinery and interdependent mechanism of synaptic membrane fusion have not been extensively studied. This review article expounds the neuronal membrane fusion processes, discusses the fundamental steps in all fusion reactions (membrane aggregation, membrane association, lipid rearrangement and lipid and content mixing) and the probable mechanism coupling to the delivery of neurotransmitters. Subsequently, this work summarizes the research on the fusion process in synaptic transmission, using electron microscopy (EM) and molecular simulation approaches. Finally, we propose the future outlook for more exciting applications of membrane fusion involved in synaptic transmission, with the aid of stochastic optical reconstruction microscopy (STORM), cryo-EM (cryo-EM), and molecular simulations.
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Affiliation(s)
- Zhiwei Yang
- Department of Applied Physics, Xi'an Jiaotong UniversityXi'an, China.,Department of Applied Chemistry, Xi'an Jiaotong UniversityXi'an, China.,School of Life Science and Technology, Xi'an Jiaotong UniversityXi'an, China
| | - Lu Gou
- Department of Applied Physics, Xi'an Jiaotong UniversityXi'an, China
| | - Shuyu Chen
- Department of Applied Physics, Xi'an Jiaotong UniversityXi'an, China
| | - Na Li
- Department of Applied Physics, Xi'an Jiaotong UniversityXi'an, China
| | - Shengli Zhang
- Department of Applied Physics, Xi'an Jiaotong UniversityXi'an, China
| | - Lei Zhang
- Department of Applied Physics, Xi'an Jiaotong UniversityXi'an, China
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182
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Entropic forces drive self-organization and membrane fusion by SNARE proteins. Proc Natl Acad Sci U S A 2017; 114:5455-5460. [PMID: 28490503 DOI: 10.1073/pnas.1611506114] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
SNARE proteins are the core of the cell's fusion machinery and mediate virtually all known intracellular membrane fusion reactions on which exocytosis and trafficking depend. Fusion is catalyzed when vesicle-associated v-SNAREs form trans-SNARE complexes ("SNAREpins") with target membrane-associated t-SNAREs, a zippering-like process releasing ∼65 kT per SNAREpin. Fusion requires several SNAREpins, but how they cooperate is unknown and reports of the number required vary widely. To capture the collective behavior on the long timescales of fusion, we developed a highly coarse-grained model that retains key biophysical SNARE properties such as the zippering energy landscape and the surface charge distribution. In simulations the ∼65-kT zippering energy was almost entirely dissipated, with fully assembled SNARE motifs but uncomplexed linker domains. The SNAREpins self-organized into a circular cluster at the fusion site, driven by entropic forces that originate in steric-electrostatic interactions among SNAREpins and membranes. Cooperative entropic forces expanded the cluster and pulled the membranes together at the center point with high force. We find that there is no critical number of SNAREs required for fusion, but instead the fusion rate increases rapidly with the number of SNAREpins due to increasing entropic forces. We hypothesize that this principle finds physiological use to boost fusion rates to meet the demanding timescales of neurotransmission, exploiting the large number of v-SNAREs available in synaptic vesicles. Once in an unfettered cluster, we estimate ≥15 SNAREpins are required for fusion within the ∼1-ms timescale of neurotransmitter release.
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183
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Shi Y, Zhang Y, Lou J. The influence of cell membrane and SNAP25 linker loop on the dynamics and unzipping of SNARE complex. PLoS One 2017; 12:e0176235. [PMID: 28426820 PMCID: PMC5398687 DOI: 10.1371/journal.pone.0176235] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 04/08/2017] [Indexed: 11/29/2022] Open
Abstract
The soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) complex is composed of three neuronal proteins VAMP2, Syntaxin and SNAP25, which plays a core role during the process of membrane fusion. The zipping assembly of the SNARE complex releases energies and drives the vesicle and cell membrane into close proximity. In this study, we use all-atom molecular dynamics simulations to probe the dynamics of SNARE and its unzipping process in the context of membrane at the atomistic details. Our results indicated that the NTD of SNARE core domain is relatively more stable than CTD, which is in agreement with previous experiments. More importantly, possible interactions between the linker loop (LL) region of SNAP25 and VAMP2 are observed, suggests that the LL region may facilitate VAMP2 binding and SNARE initiation. The forced unzipping of SNARE in the presence of membrane and LL of SNAP25 reveals the possible pathway for energy generation of SNARE zipping, provides information to understand how force may regulate the cooperativity between the membrane and the SNARE complex.
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Affiliation(s)
- Yi Shi
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Yong Zhang
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Jizhong Lou
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- * E-mail:
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184
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Zhu D, Xie L, Kang Y, Dolai S, Bondo Hansen J, Qin T, Xie H, Liang T, Rubin DC, Osborne L, Gaisano HY. Syntaxin 2 Acts as Inhibitory SNARE for Insulin Granule Exocytosis. Diabetes 2017; 66:948-959. [PMID: 28115395 PMCID: PMC5860373 DOI: 10.2337/db16-0636] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 12/24/2016] [Indexed: 01/03/2023]
Abstract
Of the four syntaxins specialized for exocytosis, syntaxin (Syn)-2 is the least understood. In this study, we used Syn-2/epimorphin knockout mice to examine the role of Syn-2 in insulin secretory granule (SG) exocytosis. Unexpectedly, Syn-2 knockout mice exhibited paradoxical superior glucose homeostasis resulting from an enhanced insulin secretion. This was confirmed in vitro by pancreatic islet perifusion showing an amplified biphasic glucose-stimulated insulin secretion arising from an increase in size of the readily releasable pool of insulin SGs and enhanced SG pool refilling. The increase in insulin exocytosis was attributed mainly to an enhanced recruitment of the larger pool of newcomer SGs that undergoes no residence time on plasma membrane before fusion and, to a lesser extent, also the predocked SGs. Consistently, Syn-2 depletion resulted in a stimulation-induced increase in abundance of exocytotic complexes we previously demonstrated as mediating the fusion of newcomer SGs (Syn-3/VAMP8/SNAP25/Munc18b) and predocked SGs (Syn-1A/VAMP2/SNAP25/Muncn18a). This work is the first to show in mammals that Syn-2 could function as an inhibitory SNARE protein that, when relieved, could promote exocytosis in pancreatic islet β-cells. Thus, Syn-2 may serve as a potential target to treat diabetes.
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Affiliation(s)
- Dan Zhu
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Li Xie
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Youhou Kang
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Subhankar Dolai
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | | | - Tairan Qin
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Huanli Xie
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Tao Liang
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Deborah C Rubin
- Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, MO
- Department of Developmental Biology, Washington University School of Medicine in St. Louis, St. Louis, MO
| | - Lucy Osborne
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Herbert Y Gaisano
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
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185
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Heo P, Park JB, Shin YK, Kweon DH. Visualization of SNARE-Mediated Hemifusion between Giant Unilamellar Vesicles Arrested by Myricetin. Front Mol Neurosci 2017; 10:93. [PMID: 28408867 PMCID: PMC5374201 DOI: 10.3389/fnmol.2017.00093] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 03/20/2017] [Indexed: 11/13/2022] Open
Abstract
Neurotransmitters are released within a millisecond after Ca2+ arrives at an active zone. However, the vesicle fusion pathway underlying this synchronous release is yet to be understood. At the center of controversy is whether hemifusion, in which outer leaflets are merged while inner leaflets are still separated, is an on-pathway or off-pathway product of Ca2+-triggered exocytosis. Using the single vesicle fusion assay, we recently demonstrated that hemifusion is an on-pathway intermediate that immediately proceeds to full fusion upon Ca2+ triggering. It has been shown that the flavonoid myricetin arrests soluble N-ethylmaleimide-sensitive factor (NSF) attachment protein receptor (SNARE)-mediated vesicle fusion at hemifusion, but that the hemifused vesicles spontaneously convert to full fusion when the myricetin clamp is removed by the enzyme laccase. In the present study, we visualized SNARE-mediated hemifusion between two SNARE-reconstituted giant unilamellar vesicles (GUVs) arrested by myricetin. The large size of the GUVs enabled us to directly image the hemifusion between them. When two merging GUVs were labeled with different fluorescent dyes, GUV pairs showed asymmetric fluorescence intensities depending on the position on the GUV pair consistent with what is expected for hemifusion. The flow of lipids from one vesicle to the other was revealed with fluorescence recovery after photobleaching (FRAP), indicating that the two membranes had hemifused. These results support the hypothesis that hemifusion may be the molecular status that primes Ca2+-triggered millisecond exocytosis. This study represents the first imaging of SNARE-driven hemifusion between GUVs.
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Affiliation(s)
- Paul Heo
- Department of Genetic Engineering, College of Biotechnology and Bioengineering, Sungkyunkwan UniversitySuwon, South Korea
| | - Joon-Bum Park
- Department of Genetic Engineering, College of Biotechnology and Bioengineering, Sungkyunkwan UniversitySuwon, South Korea
| | - Yeon-Kyun Shin
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State UniversityAmes, IA, USA
| | - Dae-Hyuk Kweon
- Department of Genetic Engineering, College of Biotechnology and Bioengineering, Sungkyunkwan UniversitySuwon, South Korea
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186
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Winsor J, Hackney DD, Lee TH. The crossover conformational shift of the GTPase atlastin provides the energy driving ER fusion. J Cell Biol 2017; 216:1321-1335. [PMID: 28356327 PMCID: PMC5412568 DOI: 10.1083/jcb.201609071] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 01/17/2017] [Accepted: 02/17/2017] [Indexed: 01/04/2023] Open
Abstract
The GTPase atlastin mediates homotypic membrane ER fusion through trans-dimerization between GTPase heads. Winsor et al. use a mutagenesis approach to show that, upon contact between atlastin heads, the proteins concurrently display GTP hydrolysis-catalyzed head-to-head dimerization and a crossover conformational shift, and these changes energize fusion. The homotypic fusion of endoplasmic reticulum membranes is catalyzed by the atlastin GTPase. The mechanism involves trans-dimerization between GTPase heads and a favorable crossover conformational shift, catalyzed by GTP hydrolysis, that converts the dimer from a “prefusion” to “postfusion” state. However, whether crossover formation actually energizes fusion remains unclear, as do the sequence of events surrounding it. Here, we made mutations in atlastin to selectively destabilize the crossover conformation and used fluorescence-based kinetic assays to analyze the variants. All variants underwent dimerization and crossover concurrently, and at wild-type rates. However, certain variants were unstable once in the crossover dimer conformation, and crossover dimer stability closely paralleled lipid-mixing activity. Tethering, however, appeared to be unimpaired in all mutant variants. The results suggest that tethering and lipid mixing are catalyzed concurrently by GTP hydrolysis but that the energy requirement for lipid mixing exceeds that for tethering, and the full energy released through crossover formation is necessary for fusion.
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Affiliation(s)
- James Winsor
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213
| | - David D Hackney
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213
| | - Tina H Lee
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213
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187
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Wu Z, Bello OD, Thiyagarajan S, Auclair SM, Vennekate W, Krishnakumar SS, O'Shaughnessy B, Karatekin E. Dilation of fusion pores by crowding of SNARE proteins. eLife 2017; 6. [PMID: 28346138 PMCID: PMC5404929 DOI: 10.7554/elife.22964] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 03/26/2017] [Indexed: 01/29/2023] Open
Abstract
Hormones and neurotransmitters are released through fluctuating exocytotic fusion pores that can flicker open and shut multiple times. Cargo release and vesicle recycling depend on the fate of the pore, which may reseal or dilate irreversibly. Pore nucleation requires zippering between vesicle-associated v-SNAREs and target membrane t-SNAREs, but the mechanisms governing the subsequent pore dilation are not understood. Here, we probed the dilation of single fusion pores using v-SNARE-reconstituted ~23-nm-diameter discoidal nanolipoprotein particles (vNLPs) as fusion partners with cells ectopically expressing cognate, 'flipped' t-SNAREs. Pore nucleation required a minimum of two v-SNAREs per NLP face, and further increases in v-SNARE copy numbers did not affect nucleation rate. By contrast, the probability of pore dilation increased with increasing v-SNARE copies and was far from saturating at 15 v-SNARE copies per face, the NLP capacity. Our experimental and computational results suggest that SNARE availability may be pivotal in determining whether neurotransmitters or hormones are released through a transient ('kiss and run') or an irreversibly dilating pore (full fusion).
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Affiliation(s)
- Zhenyong Wu
- Department of Cellular and Molecular Physiology, School of Medicine, Yale University, New Haven, United States.,Nanobiology Institute, Yale University, West Haven, United States
| | - Oscar D Bello
- Nanobiology Institute, Yale University, West Haven, United States.,Department of Cell Biology, School of Medicine, Yale University, New Haven, United States
| | | | - Sarah Marie Auclair
- Nanobiology Institute, Yale University, West Haven, United States.,Department of Cell Biology, School of Medicine, Yale University, New Haven, United States
| | - Wensi Vennekate
- Department of Cellular and Molecular Physiology, School of Medicine, Yale University, New Haven, United States.,Nanobiology Institute, Yale University, West Haven, United States
| | - Shyam S Krishnakumar
- Nanobiology Institute, Yale University, West Haven, United States.,Department of Cell Biology, School of Medicine, Yale University, New Haven, United States
| | - Ben O'Shaughnessy
- Department of Chemical Engineering, Columbia University, New York, United States
| | - Erdem Karatekin
- Department of Cellular and Molecular Physiology, School of Medicine, Yale University, New Haven, United States.,Nanobiology Institute, Yale University, West Haven, United States.,Molecular Biophysics and Biochemistry, Yale University, New Haven, United States.,Laboratoire de Neurophotonique, Université Paris Descartes, Faculté des Sciences Fondamentales et Biomédicales, Centre National de la Recherche Scientifique, Paris, France
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188
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Harris MC, Cislo D, Lenz JS, Umbach C, Lindau M. AFM/TIRF force clamp measurements of neurosecretory vesicle tethers reveal characteristic unfolding steps. PLoS One 2017; 12:e0173993. [PMID: 28323853 PMCID: PMC5360256 DOI: 10.1371/journal.pone.0173993] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 03/01/2017] [Indexed: 12/31/2022] Open
Abstract
Although several proteins have been implicated in secretory vesicle tethering, the identity and mechanical properties of the components forming the physical vesicle-plasma membrane link remain unknown. Here we present the first experimental measurements of nanomechanical properties of secretory vesicle-plasma membrane tethers using combined AFM force clamp and TIRF microscopy on membrane sheets from PC12 cells expressing the vesicle marker ANF-eGFP. Application of pulling forces generated tether extensions composed of multiple steps with variable length. The frequency of short (<10 nm) tether extension events was markedly higher when a fluorescent vesicle was present at the cantilever tip and increased in the presence of GTPγS, indicating that these events reflect specifically the properties of vesicle-plasma membrane tethers. The magnitude of the short tether extension events is consistent with extension lengths expected from progressive unfolding of individual helices of the exocyst complex, supporting its direct role in forming the physical vesicle-plasma membrane link.
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Affiliation(s)
- Mark C. Harris
- School of Applied and Engineering Physics, Engineering, Cornell University, Ithaca, NY, United States of America
| | - Dillon Cislo
- School of Applied and Engineering Physics, Engineering, Cornell University, Ithaca, NY, United States of America
| | - Joan S. Lenz
- School of Applied and Engineering Physics, Engineering, Cornell University, Ithaca, NY, United States of America
| | - Christopher Umbach
- Department of Materials Science and Engineering, Cornell University, Ithaca, NY, United States of America
| | - Manfred Lindau
- School of Applied and Engineering Physics, Engineering, Cornell University, Ithaca, NY, United States of America
- Laboratory for Nanoscale Cell Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
- * E-mail:
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189
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A stochastic model of active zone material mediated synaptic vesicle docking and priming at resting active zones. Sci Rep 2017; 7:278. [PMID: 28325932 PMCID: PMC5428245 DOI: 10.1038/s41598-017-00360-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 02/21/2017] [Indexed: 11/09/2022] Open
Abstract
Synaptic vesicles (SVs) fuse with the presynaptic membrane (PM) at specialized regions called active zones for synaptic transmission. SVs are associated with dense aggregates of macromolecules called active zone material (AZM) that has been thought to be involved in SV release. However, its role has recently begun to be elucidated. Several morphological studies proposed distinctively different AZM mediated SV docking and priming models: sequential and concurrent SV docking/priming. To explore ways to reconcile the contradictory models we develop a stochastic AZM mediated SV docking and priming model. We assume that the position of each connection site of the AZM macromolecules on their SV, directly linking the SV with the PM, varies by random shortening and lengthening of the macromolecules at resting active zones. We also perform computer simulations of SVs near the PM at resting active zones, and the results show that the distribution of the AZM connection sites can significantly affect the SV's docking efficiency and distribution of its contact area with the PM, thus priming and that the area correlates with the shape of the SVs providing a way to account for seemingly irreconcilable observations reported about the spatial relationship of SVs with the PM at active zones.
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190
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Kweon DH, Kong B, Shin YK. Hemifusion in Synaptic Vesicle Cycle. Front Mol Neurosci 2017; 10:65. [PMID: 28360835 PMCID: PMC5352705 DOI: 10.3389/fnmol.2017.00065] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Accepted: 02/27/2017] [Indexed: 01/04/2023] Open
Abstract
In the neuron, early neurotransmitters are released through the fusion pore prior to the complete vesicle fusion. It has been thought that the fusion pore is a gap junction-like structure made of transmembrane domains (TMDs) of soluble N-ethylmaleimide-sensitive-factor attachment protein receptor (SNARE) proteins. However, evidence has accumulated that lipid mixing occurs prior to the neurotransmitter release through the fusion pore lined predominantly with lipids. To explain these observations, the hemifusion, a membrane structure in which two bilayers are partially merged, has emerged as a key step preceding the formation of the fusion pore. Furthermore, the hemifusion appears to be the bona fide intermediate step not only for the synaptic vesicle cycle, but for a wide range of membrane remodeling processes, such as viral membrane fusion and endocytotic membrane fission.
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Affiliation(s)
- Dae-Hyuk Kweon
- Department of Genetic Engineering, College of Biotechnology and Bioengineering, Sungkyunkwan University Suwon, South Korea
| | - Byoungjae Kong
- Department of Genetic Engineering, College of Biotechnology and Bioengineering, Sungkyunkwan University Suwon, South Korea
| | - Yeon-Kyun Shin
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University Ames, IA, USA
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191
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Ryu JK, Jahn R, Yoon TY. Review: Progresses in understanding N-ethylmaleimide sensitive factor (NSF) mediated disassembly of SNARE complexes. Biopolymers 2017; 105:518-31. [PMID: 27062050 DOI: 10.1002/bip.22854] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 03/19/2016] [Accepted: 04/06/2016] [Indexed: 11/09/2022]
Abstract
N-ethylmaleimide sensitive factor (NSF) is a key protein of intracellular membrane traffic. NSF is a highly conserved protein belonging to the ATPases associated with other activities (AAA+ proteins). AAA+ share common domains and all transduce ATP hydrolysis into major conformational movements that are used to carry out conformational work on client proteins. Together with its cofactor SNAP, NSF is specialized on disassembling highly stable SNARE complexes that form after each membrane fusion event. Although essential for all eukaryotic cells, however, the details of this reaction have long been enigmatic. Recently, major progress has been made in both elucidating the structure of NSF/SNARE complexes and in understanding the reaction mechanism. Advances in both cryo EM and single molecule measurements suggest that NSF, together with its cofactor SNAP, imposes a tight grip on the SNARE complex. After ATP hydrolysis and phosphate release, it then builds up mechanical tension that is ultimately used to rip apart the SNAREs in a single burst. Because the AAA domains are extremely well-conserved, the molecular mechanism elucidated for NSF is presumably shared by many other AAA+ ATPases. © 2016 Wiley Periodicals, Inc. Biopolymers 105: 518-531, 2016.
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Affiliation(s)
- Je-Kyung Ryu
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, CJ, 2628, the Netherlands
| | - Reinhard Jahn
- Department of Neurobiology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, 37077, Germany
| | - Tae-Young Yoon
- Center for Nanomedicine, Institute for Basic Science (IBS) and Y-IBS Institute, Yonsei University, Seoul, 03722, South Korea
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192
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Han J, Pluhackova K, Böckmann RA. The Multifaceted Role of SNARE Proteins in Membrane Fusion. Front Physiol 2017; 8:5. [PMID: 28163686 PMCID: PMC5247469 DOI: 10.3389/fphys.2017.00005] [Citation(s) in RCA: 178] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 01/04/2017] [Indexed: 12/28/2022] Open
Abstract
Membrane fusion is a key process in all living organisms that contributes to a variety of biological processes including viral infection, cell fertilization, as well as intracellular transport, and neurotransmitter release. In particular, the various membrane-enclosed compartments in eukaryotic cells need to exchange their contents and communicate across membranes. Efficient and controllable fusion of biological membranes is known to be driven by cooperative action of SNARE proteins, which constitute the central components of the eukaryotic fusion machinery responsible for fusion of synaptic vesicles with the plasma membrane. During exocytosis, vesicle-associated v-SNARE (synaptobrevin) and target cell-associated t-SNAREs (syntaxin and SNAP-25) assemble into a core trans-SNARE complex. This complex plays a versatile role at various stages of exocytosis ranging from the priming to fusion pore formation and expansion, finally resulting in the release or exchange of the vesicle content. This review summarizes current knowledge on the intricate molecular mechanisms underlying exocytosis triggered and catalyzed by SNARE proteins. Particular attention is given to the function of the peptidic SNARE membrane anchors and the role of SNARE-lipid interactions in fusion. Moreover, the regulatory mechanisms by synaptic auxiliary proteins in SNARE-driven membrane fusion are briefly outlined.
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Affiliation(s)
- Jing Han
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science CenterXi'an, China; Computational Biology, Department of Biology, Friedrich-Alexander Universität Erlangen-NürnbergErlangen, Germany
| | - Kristyna Pluhackova
- Computational Biology, Department of Biology, Friedrich-Alexander Universität Erlangen-Nürnberg Erlangen, Germany
| | - Rainer A Böckmann
- Computational Biology, Department of Biology, Friedrich-Alexander Universität Erlangen-Nürnberg Erlangen, Germany
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193
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Jiao J, Rebane AA, Ma L, Zhang Y. Single-Molecule Protein Folding Experiments Using High-Precision Optical Tweezers. Methods Mol Biol 2017; 1486:357-390. [PMID: 27844436 DOI: 10.1007/978-1-4939-6421-5_14] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
How proteins fold from linear chains of amino acids to delicate three-dimensional structures remains a fundamental biological problem. Single-molecule manipulation based on high-resolution optical tweezers (OT) provides a powerful approach to study protein folding with unprecedented spatiotemporal resolution. In this method, a single protein or protein complex is tethered between two beads confined in optical traps and pulled. Protein unfolding induced by the mechanical force is counteracted by the spontaneous folding of the protein, reaching a dynamic equilibrium at a characteristic force and rate. The transition is monitored by the accompanying extension change of the protein and used to derive conformations and energies of folding intermediates and their associated transition kinetics. Here, we provide general strategies and detailed protocols to study folding of proteins and protein complexes using optical tweezers, including sample preparation, DNA-protein conjugation and methods of data analysis to extract folding energies and rates from the single-molecule measurements.
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Affiliation(s)
- Junyi Jiao
- Department of Cell Biology, School of Medicine and Integrated Graduate Program in Physical and Engineering Biology, Yale University, 333 Cedar Street, New Haven, CT, 06520, USA
| | - Aleksander A Rebane
- Department of Cell Biology, School of Medicine and Integrated Graduate Program in Physical and Engineering Biology, Yale University, 333 Cedar Street, New Haven, CT, 06520, USA
| | - Lu Ma
- Department of Cell Biology, School of Medicine, Yale University, 333 Cedar Street, New Haven, CT, 06520, USA
| | - Yongli Zhang
- Department of Cell Biology, School of Medicine, Yale University, 333 Cedar Street, New Haven, CT, 06520, USA.
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194
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Liang T, Qin T, Xie L, Dolai S, Zhu D, Prentice KJ, Wheeler M, Kang Y, Osborne L, Gaisano HY. New Roles of Syntaxin-1A in Insulin Granule Exocytosis and Replenishment. J Biol Chem 2016; 292:2203-2216. [PMID: 28031464 DOI: 10.1074/jbc.m116.769885] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2016] [Indexed: 01/14/2023] Open
Abstract
In type-2 diabetes (T2D), severely reduced islet syntaxin-1A (Syn-1A) levels contribute to insulin secretory deficiency. We generated β-cell-specific Syn-1A-KO (Syn-1A-βKO) mice to mimic β-cell Syn-1A deficiency in T2D. Glucose tolerance tests showed that Syn-1A-βKO mice exhibited blood glucose elevation corresponding to reduced blood insulin levels. Perifusion of Syn-1A-βKO islets showed impaired first- and second-phase glucose-stimulated insulin secretion (GSIS) resulting from reduction in readily releasable pool and granule pool refilling. To unequivocally determine the β-cell exocytotic defects caused by Syn-1A deletion, EM and total internal reflection fluorescence microscopy showed that Syn-1A-KO β-cells had a severe reduction in the number of secretory granules (SGs) docked onto the plasma membrane (PM) at rest and reduced SG recruitment to the PM after glucose stimulation, the latter indicating defects in replenishment of releasable pools required to sustain second-phase GSIS. Whereas reduced predocked SG fusion accounted for reduced first-phase GSIS, selective reduction of exocytosis of short-dock (but not no-dock) newcomer SGs accounted for the reduced second-phase GSIS. These Syn-1A actions on newcomer SGs were partly mediated by Syn-1A interactions with newcomer SG VAMP8.
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Affiliation(s)
- Tao Liang
- From the Departments of Medicine.,Physiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Tairan Qin
- From the Departments of Medicine.,Physiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Li Xie
- From the Departments of Medicine.,Physiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Subhankar Dolai
- From the Departments of Medicine.,Physiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Dan Zhu
- From the Departments of Medicine.,Physiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Kacey J Prentice
- Physiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Michael Wheeler
- Physiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Youhou Kang
- From the Departments of Medicine.,Physiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Lucy Osborne
- From the Departments of Medicine.,Molecular Genetics, and
| | - Herbert Y Gaisano
- From the Departments of Medicine, .,Physiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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195
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Single-Molecule Chemo-Mechanical Spectroscopy Provides Structural Identity of Folding Intermediates. Biophys J 2016; 110:1280-90. [PMID: 27028638 DOI: 10.1016/j.bpj.2015.12.042] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 12/08/2015] [Accepted: 12/31/2015] [Indexed: 12/19/2022] Open
Abstract
Single-molecule force spectroscopy has emerged as a powerful tool for studying the folding of biological macromolecules. Mechanical manipulation has revealed a wealth of mechanistic information on transient and intermediate states. To date, the majority of state assignment of intermediates has relied on empirical demarcation. However, performing such experiments in the presence of different osmolytes provides an alternative approach that reports on the structural properties of intermediates. Here, we analyze the folding and unfolding of T4 lysozyme with optical tweezers under a chemo-mechanical perturbation by adding osmolytes. We find that two unrelated protective osmolytes, sorbitol and trimethylamine-n-oxide, function by marginally decelerating unfolding rates and specifically modulating early events in the folding process, stabilizing formation of an on-pathway intermediate. The chemo-mechanical perturbation provides access to two independent metrics of the relevant states during folding trajectories, the contour length, and the solvent-accessible surface area. We demonstrate that the dependence of the population of the intermediate in different osmolytes, in conjunction with its measured contour length, provides the ability to discriminate between potential structural models of intermediate states. Our study represents a general strategy that may be employed in the structural modeling of equilibrium intermediate states observed in single-molecule experiments.
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196
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Stability, folding dynamics, and long-range conformational transition of the synaptic t-SNARE complex. Proc Natl Acad Sci U S A 2016; 113:E8031-E8040. [PMID: 27911771 DOI: 10.1073/pnas.1605748113] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Synaptic soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs) couple their stepwise folding to fusion of synaptic vesicles with plasma membranes. In this process, three SNAREs assemble into a stable four-helix bundle. Arguably, the first and rate-limiting step of SNARE assembly is the formation of an activated binary target (t)-SNARE complex on the target plasma membrane, which then zippers with the vesicle (v)-SNARE on the vesicle to drive membrane fusion. However, the t-SNARE complex readily misfolds, and its structure, stability, and dynamics are elusive. Using single-molecule force spectroscopy, we modeled the synaptic t-SNARE complex as a parallel three-helix bundle with a small frayed C terminus. The helical bundle sequentially folded in an N-terminal domain (NTD) and a C-terminal domain (CTD) separated by a central ionic layer, with total unfolding energy of ∼17 kBT, where kB is the Boltzmann constant and T is 300 K. Peptide binding to the CTD activated the t-SNARE complex to initiate NTD zippering with the v-SNARE, a mechanism likely shared by the mammalian uncoordinated-18-1 protein (Munc18-1). The NTD zippering then dramatically stabilized the CTD, facilitating further SNARE zippering. The subtle bidirectional t-SNARE conformational switch was mediated by the ionic layer. Thus, the t-SNARE complex acted as a switch to enable fast and controlled SNARE zippering required for synaptic vesicle fusion and neurotransmission.
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197
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Pinheiro PS, Houy S, Sørensen JB. C2-domain containing calcium sensors in neuroendocrine secretion. J Neurochem 2016; 139:943-958. [DOI: 10.1111/jnc.13865] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 09/17/2016] [Accepted: 10/05/2016] [Indexed: 12/11/2022]
Affiliation(s)
- Paulo S. Pinheiro
- Center for Neuroscience and Cell Biology; University of Coimbra; Coimbra Portugal
| | - Sébastien Houy
- Department of Neuroscience and Pharmacology; Faculty of Health and Medical Sciences; University of Copenhagen; Copenhagen Denmark
| | - Jakob B. Sørensen
- Department of Neuroscience and Pharmacology; Faculty of Health and Medical Sciences; University of Copenhagen; Copenhagen Denmark
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198
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SNARE-mediated membrane fusion trajectories derived from force-clamp experiments. Proc Natl Acad Sci U S A 2016; 113:13051-13056. [PMID: 27807132 DOI: 10.1073/pnas.1615885113] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Fusion of lipid bilayers is usually prevented by large energy barriers arising from removal of the hydration shell, formation of highly curved structures, and, eventually, fusion pore widening. Here, we measured the force-dependent lifetime of fusion intermediates using membrane-coated silica spheres attached to cantilevers of an atomic-force microscope. Analysis of time traces obtained from force-clamp experiments allowed us to unequivocally assign steps in deflection of the cantilever to membrane states during the SNARE-mediated fusion with solid-supported lipid bilayers. Force-dependent lifetime distributions of the various intermediate fusion states allowed us to propose the likelihood of different fusion pathways and to assess the main free energy barrier, which was found to be related to passing of the hydration barrier and splaying of lipids to eventually enter either the fully fused state or a long-lived hemifusion intermediate. The results were compared with SNARE mutants that arrest adjacent bilayers in the docked state and membranes in the absence of SNAREs but presence of PEG or calcium. Only with the WT SNARE construct was appreciable merging of both bilayers observed.
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199
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Vasin A, Volfson D, Littleton JT, Bykhovskaia M. Interaction of the Complexin Accessory Helix with Synaptobrevin Regulates Spontaneous Fusion. Biophys J 2016; 111:1954-1964. [PMID: 27806277 PMCID: PMC5102999 DOI: 10.1016/j.bpj.2016.09.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 09/13/2016] [Accepted: 09/15/2016] [Indexed: 11/30/2022] Open
Abstract
Neuronal transmitters are released from nerve terminals via the fusion of synaptic vesicles with the plasma membrane. Vesicles attach to membranes via a specialized protein machinery composed of membrane-attached (t-SNARE) and vesicle-attached (v-SNARE) proteins that zipper together to form a coiled-coil SNARE bundle that brings the two fusing membranes into close proximity. Neurotransmitter release may occur either in response to an action potential or through spontaneous fusion. A cytosolic protein, Complexin (Cpx), binds the SNARE complex and restricts spontaneous exocytosis by acting as a fusion clamp. We previously proposed a model in which the interaction between Cpx and the v-SNARE serves as a spring to prevent premature zippering of the SNARE complex, thereby reducing the likelihood of fusion. To test this model, we combined molecular-dynamics (MD) simulations and site-directed mutagenesis of Cpx and SNAREs in Drosophila. MD simulations of the Drosophila Cpx-SNARE complex demonstrated that Cpx's interaction with the v-SNARE promotes unraveling of the v-SNARE off the core SNARE bundle. We investigated clamping properties in the syx3-69 paralytic mutant, which has a single-point mutation in the t-SNARE and displays enhanced spontaneous release. MD simulations demonstrated an altered interaction of Cpx with the SNARE bundle that hindered v-SNARE unraveling by Cpx, thus compromising clamping. We used our model to predict mutations that should enhance the ability of Cpx to prevent full assembly of the SNARE complex. MD simulations predicted that a weakened interaction between the Cpx accessory helix and the v-SNARE would enhance Cpx flexibility and thus promote separation of SNAREs, reducing spontaneous fusion. We generated transgenic Drosophila with mutations in Cpx and the v-SNARE that disrupted a salt bridge between these two proteins. As predicted, both lines demonstrated a selective inhibition in spontaneous release, suggesting that Cpx acts as a fusion clamp that restricts full SNARE zippering.
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Affiliation(s)
- Alexander Vasin
- Department of Neurology, Wayne State University, Detroit, Michigan
| | - Dina Volfson
- Massachusetts Institute of Technology, Cambridge, Massachusetts
| | | | - Maria Bykhovskaia
- Department of Neurology, Wayne State University, Detroit, Michigan; Department of Anatomy and Cell Biology, Wayne State University, Detroit, Michigan.
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200
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Rebane AA, Ma L, Zhang Y. Structure-Based Derivation of Protein Folding Intermediates and Energies from Optical Tweezers. Biophys J 2016; 110:441-454. [PMID: 26789767 DOI: 10.1016/j.bpj.2015.12.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Revised: 11/17/2015] [Accepted: 12/04/2015] [Indexed: 11/30/2022] Open
Abstract
Optical tweezers (OTs) measure the force-dependent time-resolved extension of a single macromolecule tethered between two trapped beads. From this measurement, it is possible to determine the folding intermediates, energies, and kinetics of the macromolecule. Previous data analysis generally has used the extension as a reaction coordinate to characterize the observed folding transitions. Despite its convenience, the extension poorly describes folding in the absence of force. Here, we chose the contour length of the unfolded polypeptide as a reaction coordinate and modeled the extensions of protein structures along their predicted folding pathways based on high-resolution structures of the proteins in their native states. We included the extension in our model to calculate the total extensions, energies, and transition rates of the proteins as a function of force. We fit these calculations to the corresponding experimental measurements and obtained the best-fit conformations and energies of proteins in different folding states. We applied our method to analyze single-molecule trajectories of two representative protein complexes responsible for membrane fusion, the HIV-1 glycoprotein 41 and the synaptic SNARE proteins, which involved transitions between two and five states, respectively. Nonlinear fitting of the model to the experimental data revealed the structures of folding intermediates and transition states and their associated energies. Our results demonstrate that the contour length is a useful reaction coordinate to characterize protein folding and that intrinsic extensions of protein structures should be taken into account to properly derive the conformations and energies of protein folding intermediates from single-molecule manipulation experiments.
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Affiliation(s)
- Aleksander A Rebane
- Department of Cell Biology, School of Medicine, Yale University, New Haven, Connecticut; Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut; Department of Physics, Yale University, New Haven, Connecticut
| | - Lu Ma
- Department of Cell Biology, School of Medicine, Yale University, New Haven, Connecticut
| | - Yongli Zhang
- Department of Cell Biology, School of Medicine, Yale University, New Haven, Connecticut.
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