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Toulmé E, Lázaro AS, Trimbuch T, Rizo J, Rosenmund C. Neurotransmitter release is triggered by a calcium-induced rearrangement in the Synaptotagmin-1/SNARE complex primary interface. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.17.599435. [PMID: 38948868 PMCID: PMC11213007 DOI: 10.1101/2024.06.17.599435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
The Ca2+ sensor synaptotagmin-1 triggers neurotransmitter release together with the neuronal SNARE complex formed by syntaxin-1, SNAP25 and synaptobrevin. Moreover, synaptotagmin-1 increases synaptic vesicle priming and impairs spontaneous vesicle release. The synaptotagmin-1 C2B domain binds to the SNARE complex through a primary interface via two regions (I and II), but how exactly this interface mediates distinct functions of synaptotagmin-1, and the mechanism underlying Ca2+-triggering of release is unknown. Using mutagenesis and electrophysiological experiments, we show that region II is functionally and spatially subdivided: binding of C2B domain arginines to SNAP-25 acidic residues at one face of region II is crucial for Ca2+-evoked release but not for vesicle priming or clamping of spontaneous release, whereas other SNAP-25 and syntaxin-1 acidic residues at the other face mediate priming and clamping of spontaneous release but not evoked release. Mutations that disrupt region I impair the priming and clamping functions of synaptotagmin-1 while, strikingly, mutations that enhance binding through this region increase vesicle priming and clamping of spontaneous release, but strongly inhibit evoked release and vesicle fusogenicity. These results support previous findings that the primary interface mediates the functions of synaptotagmin-1 in vesicle priming and clamping of spontaneous release, and, importantly, show that Ca2+-triggering of release requires a rearrangement of the primary interface involving dissociation of region I, while region II remains bound. Together with modeling and biophysical studies presented in the accompanying paper, our data suggest a model whereby this rearrangement pulls the SNARE complex to facilitate fast synaptic vesicle fusion.
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Affiliation(s)
- Estelle Toulmé
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Neurophysiology, Berlin, Germany
- NeuroCure Cluster of Excellence, Berlin, Germany
| | - Andrea Salazar Lázaro
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Neurophysiology, Berlin, Germany
- NeuroCure Cluster of Excellence, Berlin, Germany
| | - Thorsten Trimbuch
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Neurophysiology, Berlin, Germany
- NeuroCure Cluster of Excellence, Berlin, Germany
| | - Josep Rizo
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Christian Rosenmund
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Neurophysiology, Berlin, Germany
- NeuroCure Cluster of Excellence, Berlin, Germany
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2
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Jaczynska K, Esser V, Xu J, Sari L, Lin MM, Rosenmund C, Rizo J. A lever hypothesis for Synaptotagmin-1 action in neurotransmitter release. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.17.599417. [PMID: 38948826 PMCID: PMC11212951 DOI: 10.1101/2024.06.17.599417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Neurotransmitter release is triggered in microseconds by Ca2+-binding to the Synaptotagmin-1 C2 domains and by SNARE complexes that form four-helix bundles between synaptic vesicles and plasma membranes, but the coupling mechanism between Ca2+-sensing and membrane fusion is unknown. Release requires extension of SNARE helices into juxtamembrane linkers that precede transmembrane regions (linker zippering) and binding of the Synaptotagmin-1 C2B domain to SNARE complexes through a 'primary interface' comprising two regions (I and II). The Synaptotagmin-1 Ca2+-binding loops were believed to accelerate membrane fusion by inducing membrane curvature, perturbing lipid bilayers or helping bridge the membranes, but SNARE complex binding orients the Ca2+-binding loops away from the fusion site, hindering these putative activities. Molecular dynamics simulations now suggest that Synaptotagmin-1 C2 domains near the site of fusion hinder SNARE action, providing an explanation for this paradox and arguing against previous models of Sytnaptotagmin-1 action. NMR experiments reveal that binding of C2B domain arginines to SNARE acidic residues at region II remains after disruption of region I. These results and fluorescence resonance energy transfer assays, together with previous data, suggest that Ca2+ causes reorientation of the C2B domain on the membrane and dissociation from the SNAREs at region I but not region II. Based on these results and molecular modeling, we propose that Synaptotagmin-1 acts as a lever that pulls the SNARE complex when Ca2+ causes reorientation of the C2B domain, facilitating linker zippering and fast membrane fusion. This hypothesis is supported by the electrophysiological data described in the accompanying paper.
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Affiliation(s)
- Klaudia Jaczynska
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Victoria Esser
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Junjie Xu
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Levent Sari
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
- Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Milo M. Lin
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
- Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Christian Rosenmund
- Charité – Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Neurophysiology, Berlin, Germany
- NeuroCure Cluster of Excellence, Berlin, Germany
| | - Josep Rizo
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
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3
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Bykhovskaia M. Dynamic Formation of the Protein-Lipid Pre-fusion Complex. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.17.589983. [PMID: 38659925 PMCID: PMC11042276 DOI: 10.1101/2024.04.17.589983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Synaptic vesicles (SVs) fuse with the presynaptic membrane (PM) to release neuronal transmitters. The SV protein Synaptotagmin 1 (Syt1) serves as a Ca2+ sensor for evoked fusion. Syt1 is thought to trigger fusion by penetrating into PM upon Ca2+ binding, however the mechanistic detail of this process is still debated. Syt1 interacts with the SNARE complex, a coiled-coil four-helical bundle that enables the SV-PM attachment. The SNARE-associated protein Complexin (Cpx) promotes the Ca2+-dependent fusion, possibly interacting with Syt1. We employed all-atom molecular dynamics (MD) to investigate the formation of the Syt1-SNARE-Cpx complex interacting with the lipid bilayers of PM and SV. Our simulations demonstrated that the PM-Syt1-SNARE-Cpx complex can transition to a "dead-end" state, wherein Syt1 attaches tightly to PM but does not immerse into it, as opposed to a pre-fusion state, which has the tips of the Ca2+-bound C2 domains of Syt1 inserted into PM. Our simulations unraveled the sequence of Syt1 conformational transitions, including the simultaneous Syt1 docking to the SNARE-Cpx bundle and PM, followed by the Ca2+ chelation and the penetration of the tips of Syt1 domains into PM, leading to the pre-fusion state of the protein-lipid complex. Importantly, we found that the direct Syt1-Cpx interactions are required to promote these transitions. Thus, we developed the all-atom dynamic model of the conformational transitions that lead to the formation of the pre-fusion PM-Syt1-SNARE-Cpx complex. Our simulations also revealed an alternative "dead-end" state of the protein-lipid complex that can be formed if this pathway is disrupted.
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López-Murcia FJ, Lin KH, Berns MMM, Ranjan M, Lipstein N, Neher E, Brose N, Reim K, Taschenberger H. Complexin has a dual synaptic function as checkpoint protein in vesicle priming and as a promoter of vesicle fusion. Proc Natl Acad Sci U S A 2024; 121:e2320505121. [PMID: 38568977 PMCID: PMC11009659 DOI: 10.1073/pnas.2320505121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Accepted: 03/04/2024] [Indexed: 04/05/2024] Open
Abstract
The presynaptic SNARE-complex regulator complexin (Cplx) enhances the fusogenicity of primed synaptic vesicles (SVs). Consequently, Cplx deletion impairs action potential-evoked transmitter release. Conversely, though, Cplx loss enhances spontaneous and delayed asynchronous release at certain synapse types. Using electrophysiology and kinetic modeling, we show that such seemingly contradictory transmitter release phenotypes seen upon Cplx deletion can be explained by an additional of Cplx in the control of SV priming, where its ablation facilitates the generation of a "faulty" SV fusion apparatus. Supporting this notion, a sequential two-step priming scheme, featuring reduced vesicle fusogenicity and increased transition rates into the faulty primed state, reproduces all aberrations of transmitter release modes and short-term synaptic plasticity seen upon Cplx loss. Accordingly, we propose a dual presynaptic function for the SNARE-complex interactor Cplx, one as a "checkpoint" protein that guarantees the proper assembly of the fusion machinery during vesicle priming, and one in boosting vesicle fusogenicity.
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Affiliation(s)
- Francisco José López-Murcia
- Department of Molecular Neurobiology, Max Planck Institute for Multidisciplinary Sciences, Göttingen37075, Germany
| | - Kun-Han Lin
- Laboratory of Membrane Biophysics, Max Planck Institute for Multidisciplinary Sciences, Göttingen37077, Germany
| | - Manon M. M. Berns
- Department of Molecular Neurobiology, Max Planck Institute for Multidisciplinary Sciences, Göttingen37075, Germany
| | - Mrinalini Ranjan
- Department of Molecular Neurobiology, Max Planck Institute for Multidisciplinary Sciences, Göttingen37075, Germany
- Göttingen Graduate School for Neurosciences, Biophysics, and Molecular Biosciences, Georg August University Göttingen, Göttingen37077, Germany
| | - Noa Lipstein
- Department of Molecular Neurobiology, Max Planck Institute for Multidisciplinary Sciences, Göttingen37075, Germany
| | - Erwin Neher
- Laboratory of Membrane Biophysics, Max Planck Institute for Multidisciplinary Sciences, Göttingen37077, Germany
- Cluster of Excellence ‘Multiscale Bioimaging’, Georg August University Göttingen, Göttingen37073, Germany
| | - Nils Brose
- Department of Molecular Neurobiology, Max Planck Institute for Multidisciplinary Sciences, Göttingen37075, Germany
- Cluster of Excellence ‘Multiscale Bioimaging’, Georg August University Göttingen, Göttingen37073, Germany
| | - Kerstin Reim
- Department of Molecular Neurobiology, Max Planck Institute for Multidisciplinary Sciences, Göttingen37075, Germany
| | - Holger Taschenberger
- Department of Molecular Neurobiology, Max Planck Institute for Multidisciplinary Sciences, Göttingen37075, Germany
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Bolz S, Kaempf N, Puchkov D, Krauss M, Russo G, Soykan T, Schmied C, Lehmann M, Müller R, Schultz C, Perrais D, Maritzen T, Haucke V. Synaptotagmin 1-triggered lipid signaling facilitates coupling of exo- and endocytosis. Neuron 2023; 111:3765-3774.e7. [PMID: 37738980 DOI: 10.1016/j.neuron.2023.08.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 06/16/2023] [Accepted: 08/16/2023] [Indexed: 09/24/2023]
Abstract
Exocytosis and endocytosis are essential physiological processes and are of prime importance for brain function. Neurotransmission depends on the Ca2+-triggered exocytosis of synaptic vesicles (SVs). In neurons, exocytosis is spatiotemporally coupled to the retrieval of an equal amount of membrane and SV proteins by compensatory endocytosis. How exocytosis and endocytosis are balanced to maintain presynaptic membrane homeostasis and, thereby, sustain brain function is essentially unknown. We combine mouse genetics with optical imaging to show that the SV calcium sensor Synaptotagmin 1 couples exocytic SV fusion to the endocytic retrieval of SV membranes by promoting the local activity-dependent formation of the signaling lipid phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2) at presynaptic sites. Interference with these mechanisms impairs PI(4,5)P2-triggered SV membrane retrieval but not exocytic SV fusion. Our findings demonstrate that the coupling of SV exocytosis and endocytosis involves local Synaptotagmin 1-induced lipid signaling to maintain presynaptic membrane homeostasis in central nervous system neurons.
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Affiliation(s)
- Svenja Bolz
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Natalie Kaempf
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Dmytro Puchkov
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Michael Krauss
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Giulia Russo
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Tolga Soykan
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Christopher Schmied
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Martin Lehmann
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Rainer Müller
- European Molecular Biology Laboratory (EMBL), Cell Biology and Biophysics Unit, 69117 Heidelberg, Germany
| | - Carsten Schultz
- European Molecular Biology Laboratory (EMBL), Cell Biology and Biophysics Unit, 69117 Heidelberg, Germany; Department of Chemical Physiology & Biochemistry, Oregon Health & Science University (OHSU), Portland, OR 97239, USA
| | - David Perrais
- University of Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, UMR 5297, 33000 Bordeaux, France
| | - Tanja Maritzen
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, 13125 Berlin, Germany; Department of Nanophysiology, University of Kaiserslautern-Landau, 67663 Kaiserslautern, Germany
| | - Volker Haucke
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, 13125 Berlin, Germany; Faculty of Biology, Chemistry, Pharmacy, Freie Universität Berlin, 14195 Berlin, Germany; NeuroCure Cluster of Excellence, Charité Universitätsmedizin Berlin, 10117 Berlin, Germany.
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6
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Norman CA, Krishnakumar SS, Timofeeva Y, Volynski KE. The release of inhibition model reproduces kinetics and plasticity of neurotransmitter release in central synapses. Commun Biol 2023; 6:1091. [PMID: 37891212 PMCID: PMC10611806 DOI: 10.1038/s42003-023-05445-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023] Open
Abstract
Calcium-evoked release of neurotransmitters from synaptic vesicles (SVs) is catalysed by SNARE proteins. The predominant view is that, at rest, complete assembly of SNARE complexes is inhibited ('clamped') by synaptotagmin and complexin molecules. Calcium binding by synaptotagmins releases this fusion clamp and triggers fast SV exocytosis. However, this model has not been quantitatively tested over physiological timescales. Here we describe an experimentally constrained computational modelling framework to quantitatively assess how the molecular architecture of the fusion clamp affects SV exocytosis. Our results argue that the 'release-of-inhibition' model can indeed account for fast calcium-activated SV fusion, and that dual binding of synaptotagmin-1 and synaptotagmin-7 to the same SNARE complex enables synergistic regulation of the kinetics and plasticity of neurotransmitter release. The developed framework provides a powerful and adaptable tool to link the molecular biochemistry of presynaptic proteins to physiological data and efficiently test the plausibility of calcium-activated neurotransmitter release models.
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Affiliation(s)
- Christopher A Norman
- University College London Institute of Neurology, University College London, London, WC1N 3BG, UK
- Department of Computer Science, University of Warwick, Coventry, CV4 7AL, UK
- Mathematics for Real-World Systems Centre for Doctoral Training, University of Warwick, Coventry, CV4 7AL, UK
| | - Shyam S Krishnakumar
- University College London Institute of Neurology, University College London, London, WC1N 3BG, UK.
- Department of Neurology, Yale Nanobiology Institute, Yale University School of Medicine, New Haven, CT, 06510, USA.
| | - Yulia Timofeeva
- University College London Institute of Neurology, University College London, London, WC1N 3BG, UK.
- Department of Computer Science, University of Warwick, Coventry, CV4 7AL, UK.
| | - Kirill E Volynski
- University College London Institute of Neurology, University College London, London, WC1N 3BG, UK.
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, 06510, USA.
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Geddes JW, Bondada V, Croall DE, Rodgers DW, Gal J. Impaired activity and membrane association of most calpain-5 mutants causal for neovascular inflammatory vitreoretinopathy. Biochim Biophys Acta Mol Basis Dis 2023; 1869:166747. [PMID: 37207905 DOI: 10.1016/j.bbadis.2023.166747] [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: 07/22/2022] [Revised: 03/29/2023] [Accepted: 05/02/2023] [Indexed: 05/21/2023]
Abstract
Neovascular inflammatory vitreoretinopathy (NIV) is a rare eye disease that ultimately leads to complete blindness and is caused by mutations in the gene encoding calpain-5 (CAPN5), with six pathogenic mutations identified. In transfected SH-SY5Y cells, five of the mutations resulted in decreased membrane association, diminished S-acylation, and reduced calcium-induced autoproteolysis of CAPN5. CAPN5 proteolysis of the autoimmune regulator AIRE was impacted by several NIV mutations. R243, L244, K250 and the adjacent V249 are on β-strands in the protease core 2 domain. Conformational changes induced by Ca2+binding result in these β-strands forming a β-sheet and a hydrophobic pocket which docks W286 side chain away from the catalytic cleft, enabling calpain activation based on comparison with the Ca2+-bound CAPN1 protease core. The pathologic variants R243L, L244P, K250N, and R289W are predicted to disrupt the β-strands, β-sheet, and hydrophobic pocket, impairing calpain activation. The mechanism by which these variants impair membrane association is unclear. G376S impacts a conserved residue in the CBSW domain and is predicted to disrupt a loop containing acidic residues which may contribute to membrane binding. G267S did not impair membrane association and resulted in a slight but significant increase in autoproteolytic and proteolytic activity. However, G267S is also identified in individuals without NIV. Combined with the autosomal dominant pattern of NIV inheritance and evidence that CAPN5 may dimerize, the results are consistent with a dominant negative mechanism for the five pathogenic variants which resulted in impaired CAPN5 activity and membrane association and a gain-of-function for the G267S variant.
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Affiliation(s)
- James W Geddes
- Spinal Cord and Brain Injury Research Center (SCoBIRC), University of Kentucky, Lexington, KY 40536, USA; Department of Neuroscience, University of Kentucky, Lexington, KY 40536, USA.
| | - Vimala Bondada
- Spinal Cord and Brain Injury Research Center (SCoBIRC), University of Kentucky, Lexington, KY 40536, USA
| | - Dorothy E Croall
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME 04469, USA.
| | - David W Rodgers
- Department of Molecular and Cellular Biochemistry and Center for Structural Biology, University of Kentucky, Lexington, KY 40536, USA.
| | - Jozsef Gal
- Spinal Cord and Brain Injury Research Center (SCoBIRC), University of Kentucky, Lexington, KY 40536, USA; Department of Neuroscience, University of Kentucky, Lexington, KY 40536, USA.
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8
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Bykhovskaia M. Molecular Dynamics Simulations of the Proteins Regulating Synaptic Vesicle Fusion. MEMBRANES 2023; 13:307. [PMID: 36984694 PMCID: PMC10058449 DOI: 10.3390/membranes13030307] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 02/11/2023] [Accepted: 03/01/2023] [Indexed: 06/18/2023]
Abstract
Neuronal transmitters are packaged in synaptic vesicles (SVs) and released by the fusion of SVs with the presynaptic membrane (PM). An inflow of Ca2+ into the nerve terminal triggers fusion, and the SV-associated protein Synaptotagmin 1 (Syt1) serves as a Ca2+ sensor. In preparation for fusion, SVs become attached to the PM by the SNARE protein complex, a coiled-coil bundle that exerts the force overcoming SV-PM repulsion. A cytosolic protein Complexin (Cpx) attaches to the SNARE complex and differentially regulates the evoked and spontaneous release components. It is still debated how the dynamic interactions of Syt1, SNARE proteins and Cpx lead to fusion. This problem is confounded by heterogeneity in the conformational states of the prefusion protein-lipid complex and by the lack of tools to experimentally monitor the rapid conformational transitions of the complex, which occur at a sub-millisecond scale. However, these complications can be overcome employing molecular dynamics (MDs), a computational approach that enables simulating interactions and conformational transitions of proteins and lipids. This review discusses the use of molecular dynamics for the investigation of the pre-fusion protein-lipid complex. We discuss the dynamics of the SNARE complex between lipid bilayers, as well as the interactions of Syt1 with lipids and SNARE proteins, and Cpx regulating the assembly of the SNARE complex.
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Affiliation(s)
- Maria Bykhovskaia
- Neurology Department, Wayne State University, Detroit, MI 48202, USA
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9
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Xue M, Cao Y, Shen C, Guo W. Computational Advances of Protein/Neurotransmitter-membrane Interactions Involved in Vesicle Fusion and Neurotransmitter Release. J Mol Biol 2023; 435:167818. [PMID: 36089056 DOI: 10.1016/j.jmb.2022.167818] [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: 05/31/2022] [Revised: 08/22/2022] [Accepted: 09/04/2022] [Indexed: 02/04/2023]
Abstract
Vesicle fusion is of crucial importance to neuronal communication at neuron terminals. The exquisite but complex fusion machinery for neurotransmitter release is tightly controlled and regulated by protein/neurotransmitter-membrane interactions. Computational 'microscopies', in particular molecular dynamics simulations and related techniques, have provided notable insight into the physiological process over the past decades, and have made enormous contributions to fields such as neurology, pharmacology and pathophysiology. Here we review the computational advances of protein/neurotransmitter-membrane interactions related to presynaptic vesicle-membrane fusion and neurotransmitter release, and outline the in silico challenges ahead for understanding this important physiological process.
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Affiliation(s)
- Minmin Xue
- Key Laboratory for Intelligent Nano Materials and Devices of Ministry of Education, State Key Laboratory of Mechanics and Control of Mechanical Structures, and Institute for Frontier Science, Nanjing University of Aeronautics and Astronautics, Nanjing 210016, China
| | - Yuwei Cao
- State Key Laboratory of Tribology, Department of Mechanical Engineering, Tsinghua University, Beijing, China
| | - Chun Shen
- Key Laboratory for Intelligent Nano Materials and Devices of Ministry of Education, State Key Laboratory of Mechanics and Control of Mechanical Structures, and Institute for Frontier Science, Nanjing University of Aeronautics and Astronautics, Nanjing 210016, China.
| | - Wanlin Guo
- Key Laboratory for Intelligent Nano Materials and Devices of Ministry of Education, State Key Laboratory of Mechanics and Control of Mechanical Structures, and Institute for Frontier Science, Nanjing University of Aeronautics and Astronautics, Nanjing 210016, China; State Key Laboratory of Tribology, Department of Mechanical Engineering, Tsinghua University, Beijing, China.
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10
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Brunger AT, Leitz J. The Core Complex of the Ca 2+-Triggered Presynaptic Fusion Machinery. J Mol Biol 2023; 435:167853. [PMID: 36243149 PMCID: PMC10578080 DOI: 10.1016/j.jmb.2022.167853] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/30/2022] [Accepted: 10/03/2022] [Indexed: 11/05/2022]
Abstract
Synaptic neurotransmitter release is mediated by an orchestra of presynaptic proteins that precisely control and trigger fusion between synaptic vesicles and the neuron terminal at the active zone upon the arrival of an action potential. Critical to this process are the neuronal SNAREs (Soluble N-ethylmaleimide sensitive factor Attachment protein REceptor), the Ca2+-sensor synaptotagmin, the activator/regulator complexin, and other factors. Here, we review the interactions between the SNARE complex and synaptotagmin, with focus on the so-called primary interface between synaptotagmin and the SNARE complex that has been validated in terms of its physiological relevance. We discuss several other but less validated interfaces as well, including the so-called tripartite interface, and we discuss the pros and cons for these possible alternative interfaces. We also present new molecular dynamics simulations of the tripartite interface and new data of an inhibitor of the primary interface in a reconstituted system of synaptic vesicle fusion.
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Affiliation(s)
- Axel T Brunger
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States; Department of Neurology and Neurological Sciences, Stanford University, Stanford, United States; Department of Structural Biology, Stanford University, Stanford, United States; Department of Photon Science, Stanford University, Stanford, United States; Howard Hughes Medical Institute, Stanford University, Stanford, United States.
| | - Jeremy Leitz
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States; Department of Neurology and Neurological Sciences, Stanford University, Stanford, United States; Department of Structural Biology, Stanford University, Stanford, United States; Department of Photon Science, Stanford University, Stanford, United States; Howard Hughes Medical Institute, Stanford University, Stanford, United States
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11
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Jaczynska K, Esquivies L, Pfuetzner RA, Alten B, Brewer KD, Zhou Q, Kavalali ET, Brunger AT, Rizo J. Analysis of tripartite Synaptotagmin-1-SNARE-complexin-1 complexes in solution. FEBS Open Bio 2023; 13:26-50. [PMID: 36305864 PMCID: PMC9811660 DOI: 10.1002/2211-5463.13503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/19/2022] [Accepted: 10/27/2022] [Indexed: 01/07/2023] Open
Abstract
Characterizing interactions of Synaptotagmin-1 with the SNARE complex is crucial to understand the mechanism of neurotransmitter release. X-ray crystallography revealed how the Synaptotagmin-1 C2 B domain binds to the SNARE complex through a so-called primary interface and to a complexin-1-SNARE complex through a so-called tripartite interface. Mutagenesis and electrophysiology supported the functional relevance of both interfaces, and extensive additional data validated the primary interface. However, ITC evidence suggesting that binding via the tripartite interface occurs in solution was called into question by subsequent NMR data. Here, we describe joint efforts to address this apparent contradiction. Using the same ITC approach with the same C2 B domain mutant used previously (C2 BKA-Q ) but including ion exchange chromatography to purify it, which is crucial to remove polyacidic contaminants, we were unable to observe the substantial endothermic ITC signal that was previously attributed to binding of this mutant to the complexin-1-SNARE complex through the tripartite interface. We were also unable to detect substantial populations of the tripartite interface in NMR analyses of the ITC samples or in measurements of paramagnetic relaxation effects, despite the high sensitivity of this method to detect weak protein complexes. However, these experiments do not rule out the possibility of very low affinity (KD > 1 mm) binding through this interface. These results emphasize the need to develop methods to characterize the structure of synaptotagmin-1-SNARE complexes between two membranes and to perform further structure-function analyses to establish the physiological relevance of the tripartite interface.
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Affiliation(s)
- Klaudia Jaczynska
- Department of BiophysicsUniversity of Texas Southwestern Medical CenterDallasTXUSA
- Department of BiochemistryUniversity of Texas Southwestern Medical CenterDallasTXUSA
- Department of PharmacologyUniversity of Texas Southwestern Medical CenterDallasTXUSA
| | - Luis Esquivies
- Department of Molecular and Cellular PhysiologyStanford UniversityCAUSA
- Department of Neurology and Neurological SciencesStanford UniversityCAUSA
- Department of Structural BiologyStanford UniversityCAUSA
- Department of Photon ScienceStanford UniversityCAUSA
- Howard Hughes Medical InstituteStanford UniversityCAUSA
| | - Richard A. Pfuetzner
- Department of Molecular and Cellular PhysiologyStanford UniversityCAUSA
- Department of Neurology and Neurological SciencesStanford UniversityCAUSA
- Department of Structural BiologyStanford UniversityCAUSA
- Department of Photon ScienceStanford UniversityCAUSA
- Howard Hughes Medical InstituteStanford UniversityCAUSA
| | - Baris Alten
- Department of PharmacologyVanderbilt UniversityNashvilleTNUSA
- Vanderbilt Brain InstituteVanderbilt UniversityNashvilleTNUSA
- Present address:
Department of NeurologyMassachusetts General HospitalBostonMAUSA
- Present address:
Department of NeurologyBrigham and Women's HospitalBostonMAUSA
- Present address:
Harvard Medical SchoolBostonMAUSA
| | - Kyle D. Brewer
- Department of BiophysicsUniversity of Texas Southwestern Medical CenterDallasTXUSA
- Department of BiochemistryUniversity of Texas Southwestern Medical CenterDallasTXUSA
- Department of PharmacologyUniversity of Texas Southwestern Medical CenterDallasTXUSA
- Present address:
ETTA BiotechnologyPalo AltoCAUSA
| | - Qiangjun Zhou
- Vanderbilt Brain InstituteVanderbilt UniversityNashvilleTNUSA
- Department of Cell and Developmental BiologyVanderbilt UniversityNashvilleTNUSA
| | - Ege T. Kavalali
- Department of PharmacologyVanderbilt UniversityNashvilleTNUSA
- Vanderbilt Brain InstituteVanderbilt UniversityNashvilleTNUSA
| | - Axel T. Brunger
- Department of Molecular and Cellular PhysiologyStanford UniversityCAUSA
- Department of Neurology and Neurological SciencesStanford UniversityCAUSA
- Department of Structural BiologyStanford UniversityCAUSA
- Department of Photon ScienceStanford UniversityCAUSA
- Howard Hughes Medical InstituteStanford UniversityCAUSA
| | - Josep Rizo
- Department of BiophysicsUniversity of Texas Southwestern Medical CenterDallasTXUSA
- Department of BiochemistryUniversity of Texas Southwestern Medical CenterDallasTXUSA
- Department of PharmacologyUniversity of Texas Southwestern Medical CenterDallasTXUSA
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12
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Palfreyman MT, West SE, Jorgensen EM. SNARE Proteins in Synaptic Vesicle Fusion. ADVANCES IN NEUROBIOLOGY 2023; 33:63-118. [PMID: 37615864 DOI: 10.1007/978-3-031-34229-5_4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/25/2023]
Abstract
Neurotransmitters are stored in small membrane-bound vesicles at synapses; a subset of synaptic vesicles is docked at release sites. Fusion of docked vesicles with the plasma membrane releases neurotransmitters. Membrane fusion at synapses, as well as all trafficking steps of the secretory pathway, is mediated by SNARE proteins. The SNAREs are the minimal fusion machinery. They zipper from N-termini to membrane-anchored C-termini to form a 4-helix bundle that forces the apposed membranes to fuse. At synapses, the SNAREs comprise a single helix from syntaxin and synaptobrevin; SNAP-25 contributes the other two helices to complete the bundle. Unc13 mediates synaptic vesicle docking and converts syntaxin into the permissive "open" configuration. The SM protein, Unc18, is required to initiate and proofread SNARE assembly. The SNAREs are then held in a half-zippered state by synaptotagmin and complexin. Calcium removes the synaptotagmin and complexin block, and the SNAREs drive vesicle fusion. After fusion, NSF and alpha-SNAP unwind the SNAREs and thereby recharge the system for further rounds of fusion. In this chapter, we will describe the discovery of the SNAREs, their relevant structural features, models for their function, and the central role of Unc18. In addition, we will touch upon the regulation of SNARE complex formation by Unc13, complexin, and synaptotagmin.
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Affiliation(s)
- Mark T Palfreyman
- School of Biological Sciences, and Howard Hughes Medical Institute, University of Utah, Salt Lake City, UT, USA
| | - Sam E West
- School of Biological Sciences, and Howard Hughes Medical Institute, University of Utah, Salt Lake City, UT, USA
| | - Erik M Jorgensen
- School of Biological Sciences, and Howard Hughes Medical Institute, University of Utah, Salt Lake City, UT, USA.
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13
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López-Murcia FJ, Reim K, Taschenberger H. Complexins: Ubiquitously Expressed Presynaptic Regulators of SNARE-Mediated Synaptic Vesicle Fusion. ADVANCES IN NEUROBIOLOGY 2023; 33:255-285. [PMID: 37615870 DOI: 10.1007/978-3-031-34229-5_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/25/2023]
Abstract
Neurotransmitter release is a spatially and temporally tightly regulated process, which requires assembly and disassembly of SNARE complexes to enable the exocytosis of transmitter-loaded synaptic vesicles (SVs) at presynaptic active zones (AZs). While the requirement for the core SNARE machinery is shared by most membrane fusion processes, SNARE-mediated fusion at AZs is uniquely regulated to allow very rapid Ca2+-triggered SV exocytosis following action potential (AP) arrival. To enable a sub-millisecond time course of AP-triggered SV fusion, synapse-specific accessory SNARE-binding proteins are required in addition to the core fusion machinery. Among the known SNARE regulators specific for Ca2+-triggered SV fusion are complexins, which are almost ubiquitously expressed in neurons. This chapter summarizes the structural features of complexins, models for their molecular interactions with SNAREs, and their roles in SV fusion.
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Affiliation(s)
- Francisco José López-Murcia
- Department of Pathology and Experimental Therapy, Institute of Neurosciences, University of Barcelona, L'Hospitalet de Llobregat, Barcelona, Spain.
- Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain.
| | - Kerstin Reim
- Department of Molecular Neurobiology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
| | - Holger Taschenberger
- Department of Molecular Neurobiology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
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14
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Zhou Q. Calcium Sensors of Neurotransmitter Release. ADVANCES IN NEUROBIOLOGY 2023; 33:119-138. [PMID: 37615865 DOI: 10.1007/978-3-031-34229-5_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/25/2023]
Abstract
Calcium (Ca2+) plays a critical role in triggering all three primary modes of neurotransmitter release (synchronous, asynchronous, and spontaneous). Synaptotagmin1, a protein with two C2 domains, is the first isoform of the synaptotagmin family that was identified and demonstrated as the primary Ca2+ sensor for synchronous neurotransmitter release. Other isoforms of the synaptotagmin family as well as other C2 proteins such as the double C2 domain protein family were found to act as Ca2+ sensors for different modes of neurotransmitter release. Major recent advances and previous data suggest a new model, release-of-inhibition, for the initiation of Ca2+-triggered synchronous neurotransmitter release. Synaptotagmin1 binds Ca2+ via its two C2 domains and relieves a primed pre-fusion machinery. Before Ca2+ triggering, synaptotagmin1 interacts Ca2+ independently with partially zippered SNARE complexes, the plasma membrane, phospholipids, and other components to form a primed pre-fusion state that is ready for fast release. However, membrane fusion is inhibited until the arrival of Ca2+ reorients the Ca2+-binding loops of the C2 domain to perturb the lipid bilayers, help bridge the membranes, and/or induce membrane curvatures, which serves as a power stroke to activate fusion. This chapter reviews the evidence supporting these models and discusses the molecular interactions that may underlie these abilities.
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Affiliation(s)
- Qiangjun Zhou
- Department of Cell and Developmental Biology, Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN, USA.
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15
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Li T, Cheng Q, Wang S, Ma C. Rabphilin 3A binds the N-peptide of SNAP-25 to promote SNARE complex assembly in exocytosis. eLife 2022; 11:79926. [PMID: 36173100 PMCID: PMC9522249 DOI: 10.7554/elife.79926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 09/13/2022] [Indexed: 11/13/2022] Open
Abstract
Exocytosis of secretory vesicles requires the soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) proteins and small GTPase Rabs. As a Rab3/Rab27 effector protein on secretory vesicles, Rabphilin 3A was implicated to interact with SNAP-25 to regulate vesicle exocytosis in neurons and neuroendocrine cells, yet the underlying mechanism remains unclear. In this study, we have characterized the physiologically relevant binding sites between Rabphilin 3A and SNAP-25. We found that an intramolecular interplay between the N-terminal Rab-binding domain and C-terminal C2AB domain enables Rabphilin 3A to strongly bind the SNAP-25 N-peptide region via its C2B bottom α-helix. Disruption of this interaction significantly impaired docking and fusion of vesicles with the plasma membrane in rat PC12 cells. In addition, we found that this interaction allows Rabphilin 3A to accelerate SNARE complex assembly. Furthermore, we revealed that this interaction accelerates SNARE complex assembly via inducing a conformational switch from random coils to α-helical structure in the SNAP-25 SNARE motif. Altogether, our data suggest that the promotion of SNARE complex assembly by binding the C2B bottom α-helix of Rabphilin 3A to the N-peptide of SNAP-25 underlies a pre-fusion function of Rabphilin 3A in vesicle exocytosis.
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Affiliation(s)
- Tianzhi Li
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Qiqi Cheng
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Shen Wang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Cong Ma
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
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16
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Wang X, Yu D, Wang H, Lei Z, Zhai Y, Sun M, Chen S, Yin P. Rab3 and synaptotagmin proteins in the regulation of vesicle fusion and neurotransmitter release. Life Sci 2022; 309:120995. [PMID: 36167148 DOI: 10.1016/j.lfs.2022.120995] [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: 08/05/2022] [Revised: 09/13/2022] [Accepted: 09/21/2022] [Indexed: 10/31/2022]
Abstract
Ca2+-triggered neurotransmitter release involves complex regulatory mechanisms, including a series of protein-protein interactions. Three proteins, synaptobrevin (VAMP), synaptosomal-associated protein of 25kDa (SNAP-25) and syntaxin, constitute the soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) core complex that plays key roles in controlling vesicle fusion and exocytosis. Many other proteins participate in the regulation of the processes via direct and/or indirect interaction with the SNARE complex. Although much effort has been made, the regulatory mechanism for exocytosis is still not completely clear. Accumulated evidence indicates that the small GTPase Rab3 and synaptotagmin proteins play important regulatory roles during vesicle fusion and neurotransmitter release. This review outlines our present understanding of the two regulatory proteins, with the focus on the interaction of Rab3 with synaptotagmin in the regulatory process.
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Affiliation(s)
- Xianchun Wang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Protein Chemistry Laboratory, College of Life Sciences, Hunan Normal University, Changsha 410081, China.
| | - Dianmei Yu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Protein Chemistry Laboratory, College of Life Sciences, Hunan Normal University, Changsha 410081, China
| | - Haiyan Wang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Protein Chemistry Laboratory, College of Life Sciences, Hunan Normal University, Changsha 410081, China
| | - Zhixiang Lei
- State Key Laboratory of Developmental Biology of Freshwater Fish, Protein Chemistry Laboratory, College of Life Sciences, Hunan Normal University, Changsha 410081, China
| | - Yiwen Zhai
- State Key Laboratory of Developmental Biology of Freshwater Fish, Protein Chemistry Laboratory, College of Life Sciences, Hunan Normal University, Changsha 410081, China
| | - Minlu Sun
- State Key Laboratory of Developmental Biology of Freshwater Fish, Protein Chemistry Laboratory, College of Life Sciences, Hunan Normal University, Changsha 410081, China
| | - Si Chen
- State Key Laboratory of Developmental Biology of Freshwater Fish, Protein Chemistry Laboratory, College of Life Sciences, Hunan Normal University, Changsha 410081, China
| | - Panfeng Yin
- State Key Laboratory of Developmental Biology of Freshwater Fish, Protein Chemistry Laboratory, College of Life Sciences, Hunan Normal University, Changsha 410081, China
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17
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Cui L, Li H, Xi Y, Hu Q, Liu H, Fan J, Xiang Y, Zhang X, Shui W, Lai Y. Vesicle trafficking and vesicle fusion: mechanisms, biological functions, and their implications for potential disease therapy. MOLECULAR BIOMEDICINE 2022; 3:29. [PMID: 36129576 PMCID: PMC9492833 DOI: 10.1186/s43556-022-00090-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 07/12/2022] [Indexed: 11/10/2022] Open
Abstract
Intracellular vesicle trafficking is the fundamental process to maintain the homeostasis of membrane-enclosed organelles in eukaryotic cells. These organelles transport cargo from the donor membrane to the target membrane through the cargo containing vesicles. Vesicle trafficking pathway includes vesicle formation from the donor membrane, vesicle transport, and vesicle fusion with the target membrane. Coat protein mediated vesicle formation is a delicate membrane budding process for cargo molecules selection and package into vesicle carriers. Vesicle transport is a dynamic and specific process for the cargo containing vesicles translocation from the donor membrane to the target membrane. This process requires a group of conserved proteins such as Rab GTPases, motor adaptors, and motor proteins to ensure vesicle transport along cytoskeletal track. Soluble N-ethyl-maleimide-sensitive factor (NSF) attachment protein receptors (SNARE)-mediated vesicle fusion is the final process for vesicle unloading the cargo molecules at the target membrane. To ensure vesicle fusion occurring at a defined position and time pattern in eukaryotic cell, multiple fusogenic proteins, such as synaptotagmin (Syt), complexin (Cpx), Munc13, Munc18 and other tethering factors, cooperate together to precisely regulate the process of vesicle fusion. Dysfunctions of the fusogenic proteins in SNARE-mediated vesicle fusion are closely related to many diseases. Recent studies have suggested that stimulated membrane fusion can be manipulated pharmacologically via disruption the interface between the SNARE complex and Ca2+ sensor protein. Here, we summarize recent insights into the molecular mechanisms of vesicle trafficking, and implications for the development of new therapeutics based on the manipulation of vesicle fusion.
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18
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Zhu J, McDargh ZA, Li F, Krishnakumar SS, Rothman JE, O’Shaughnessy B. Synaptotagmin rings as high-sensitivity regulators of synaptic vesicle docking and fusion. Proc Natl Acad Sci U S A 2022; 119:e2208337119. [PMID: 36103579 PMCID: PMC9499556 DOI: 10.1073/pnas.2208337119] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 07/05/2022] [Indexed: 11/18/2022] Open
Abstract
Synchronous release at neuronal synapses is accomplished by a machinery that senses calcium influx and fuses the synaptic vesicle and plasma membranes to release neurotransmitters. Previous studies suggested the calcium sensor synaptotagmin (Syt) is a facilitator of vesicle docking and both a facilitator and inhibitor of fusion. On phospholipid monolayers, the Syt C2AB domain spontaneously oligomerized into rings that are disassembled by Ca2+, suggesting Syt rings may clamp fusion as membrane-separating "washers" until Ca2+-mediated disassembly triggers fusion and release [J. Wang et al., Proc. Natl. Acad. Sci. U.S.A. 111, 13966-13971 (2014)].). Here, we combined mathematical modeling with experiment to measure the mechanical properties of Syt rings and to test this mechanism. Consistent with experimental results, the model quantitatively recapitulates observed Syt ring-induced dome and volcano shapes on phospholipid monolayers and predicts rings are stabilized by anionic phospholipid bilayers or bulk solution with ATP. The selected ring conformation is highly sensitive to membrane composition and bulk ATP levels, a property that may regulate vesicle docking and fusion in ATP-rich synaptic terminals. We find the Syt molecules hosted by a synaptic vesicle oligomerize into a halo, unbound from the vesicle, but in proximity to sufficiently phosphatidylinositol 4,5-bisphosphate (PIP2)-rich plasma membrane (PM) domains, the PM-bound trans Syt ring conformation is preferred. Thus, the Syt halo serves as landing gear for spatially directed docking at PIP2-rich sites that define the active zones of exocytotic release, positioning the Syt ring to clamp fusion and await calcium. Our results suggest the Syt ring is both a Ca2+-sensitive fusion clamp and a high-fidelity sensor for directed docking.
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Affiliation(s)
- Jie Zhu
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06520
| | - Zachary A. McDargh
- Department of Chemical Engineering, Columbia University, New York, NY 10027
| | - Feng Li
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06520
| | | | - James E. Rothman
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06520
| | - Ben O’Shaughnessy
- Department of Chemical Engineering, Columbia University, New York, NY 10027
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19
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Rizo J, David G, Fealey ME, Jaczynska K. On the difficulties of characterizing weak protein interactions that are critical for neurotransmitter release. FEBS Open Bio 2022; 12:1912-1938. [PMID: 35986639 PMCID: PMC9623538 DOI: 10.1002/2211-5463.13473] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 08/09/2022] [Accepted: 08/18/2022] [Indexed: 01/25/2023] Open
Abstract
The mechanism of neurotransmitter release has been extensively characterized, showing that vesicle fusion is mediated by the SNARE complex formed by syntaxin-1, SNAP-25 and synaptobrevin. This complex is disassembled by N-ethylmaleimide sensitive factor (NSF) and SNAPs to recycle the SNAREs, whereas Munc18-1 and Munc13s organize SNARE complex assembly in an NSF-SNAP-resistant manner. Synaptotagmin-1 acts as the Ca2+ sensor that triggers exocytosis in a tight interplay with the SNAREs and complexins. Here, we review technical aspects associated with investigation of protein interactions underlying these steps, which is hindered because the release machinery is assembled between two membranes and is highly dynamic. Moreover, weak interactions, which are difficult to characterize, play key roles in neurotransmitter release, for instance by lowering energy barriers that need to be overcome in this highly regulated process. We illustrate the crucial role that structural biology has played in uncovering mechanisms underlying neurotransmitter release, but also discuss the importance of considering the limitations of the techniques used, including lessons learned from research in our lab and others. In particular, we emphasize: (a) the promiscuity of some protein sequences, including membrane-binding regions that can mediate irrelevant interactions with proteins in the absence of their native targets; (b) the need to ensure that weak interactions observed in crystal structures are biologically relevant; and (c) the limitations of isothermal titration calorimetry to analyze weak interactions. Finally, we stress that even studies that required re-interpretation often helped to move the field forward by improving our understanding of the system and providing testable hypotheses.
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Affiliation(s)
- Josep Rizo
- Department of BiophysicsUniversity of Texas Southwestern Medical CenterDallasTXUSA,Department of BiochemistryUniversity of Texas Southwestern Medical CenterDallasTXUSA,Department of PharmacologyUniversity of Texas Southwestern Medical CenterDallasTXUSA
| | - Guillaume David
- Department of BiophysicsUniversity of Texas Southwestern Medical CenterDallasTXUSA,Department of BiochemistryUniversity of Texas Southwestern Medical CenterDallasTXUSA,Department of PharmacologyUniversity of Texas Southwestern Medical CenterDallasTXUSA
| | - Michael E. Fealey
- Department of BiophysicsUniversity of Texas Southwestern Medical CenterDallasTXUSA,Department of BiochemistryUniversity of Texas Southwestern Medical CenterDallasTXUSA,Department of PharmacologyUniversity of Texas Southwestern Medical CenterDallasTXUSA
| | - Klaudia Jaczynska
- Department of BiophysicsUniversity of Texas Southwestern Medical CenterDallasTXUSA,Department of BiochemistryUniversity of Texas Southwestern Medical CenterDallasTXUSA,Department of PharmacologyUniversity of Texas Southwestern Medical CenterDallasTXUSA
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20
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Kobbersmed JRL, Berns MMM, Ditlevsen S, Sørensen JB, Walter AM. Allosteric stabilization of calcium and phosphoinositide dual binding engages several synaptotagmins in fast exocytosis. eLife 2022; 11:74810. [PMID: 35929728 PMCID: PMC9489213 DOI: 10.7554/elife.74810] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 08/04/2022] [Indexed: 12/04/2022] Open
Abstract
Synaptic communication relies on the fusion of synaptic vesicles with the plasma membrane, which leads to neurotransmitter release. This exocytosis is triggered by brief and local elevations of intracellular Ca2+ with remarkably high sensitivity. How this is molecularly achieved is unknown. While synaptotagmins confer the Ca2+ sensitivity of neurotransmitter exocytosis, biochemical measurements reported Ca2+ affinities too low to account for synaptic function. However, synaptotagmin’s Ca2+ affinity increases upon binding the plasma membrane phospholipid PI(4,5)P2 and, vice versa, Ca2+ binding increases synaptotagmin’s PI(4,5)P2 affinity, indicating a stabilization of the Ca2+/PI(4,5)P2 dual-bound state. Here, we devise a molecular exocytosis model based on this positive allosteric stabilization and the assumptions that (1.) synaptotagmin Ca2+/PI(4,5)P2 dual binding lowers the energy barrier for vesicle fusion and that (2.) the effect of multiple synaptotagmins on the energy barrier is additive. The model, which relies on biochemically measured Ca2+/PI(4,5)P2 affinities and protein copy numbers, reproduced the steep Ca2+ dependency of neurotransmitter release. Our results indicate that each synaptotagmin engaging in Ca2+/PI(4,5)P2 dual-binding lowers the energy barrier for vesicle fusion by ~5 kBT and that allosteric stabilization of this state enables the synchronized engagement of several (typically three) synaptotagmins for fast exocytosis. Furthermore, we show that mutations altering synaptotagmin’s allosteric properties may show dominant-negative effects, even though synaptotagmins act independently on the energy barrier, and that dynamic changes of local PI(4,5)P2 (e.g. upon vesicle movement) dramatically impact synaptic responses. We conclude that allosterically stabilized Ca2+/PI(4,5)P2 dual binding enables synaptotagmins to exert their coordinated function in neurotransmission. For our brains and nervous systems to work properly, the nerve cells within them must be able to ‘talk’ to each other. They do this by releasing chemical signals called neurotransmitters which other cells can detect and respond to. Neurotransmitters are packaged in tiny membrane-bound spheres called vesicles. When a cell of the nervous system needs to send a signal to its neighbours, the vesicles fuse with the outer membrane of the cell, discharging their chemical contents for other cells to detect. The initial trigger for neurotransmitter release is a short, fast increase in the amount of calcium ions inside the signalling cell. One of the main proteins that helps regulate this process is synaptotagmin which binds to calcium and gives vesicles the signal to start unloading their chemicals. Despite acting as a calcium sensor, synaptotagmin actually has a very low affinity for calcium ions by itself, meaning that it would not be efficient for the protein to respond alone. Synpatotagmin is more likely to bind to calcium if it is attached to a molecule called PIP2, which is found in the membranes of cells The effect also occurs in reverse, as the binding of calcium to synaptotagmin increases the protein’s affinity for PIP2. However, how these three molecules – synaptotagmin, PIP2, and calcium – work together to achieve the physiological release of neurotransmitters is poorly understood. To help answer this question, Kobbersmed, Berns et al. set up a computer simulation of ‘virtual vesicles’ using available experimental data on synaptotagmin’s affinity with calcium and PIP2. In this simulation, synaptotagmin could only trigger the release of neurotransmitters when bound to both calcium and PIP2. The model also showed that each ‘complex’ of synaptotagmin/calcium/PIP2 made the vesicles more likely to fuse with the outer membrane of the cell – to the extent that only a handful of synaptotagmin molecules were needed to start neurotransmitter release from a single vesicle. These results shed new light on a biological process central to the way nerve cells communicate with each other. In the future, Kobbersmed, Berns et al. hope that this insight will help us to understand the cause of diseases where communication in the nervous system is impaired.
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Affiliation(s)
- Janus R L Kobbersmed
- Department of Mathematical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Manon M M Berns
- Department of Neuroscience, University of Copenhagen, Copenhagen, Denmark
| | - Susanne Ditlevsen
- Department of Mathematical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Alexander M Walter
- Department of Mathematical Sciences, University of Copenhagen, Copenhagen, Denmark
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21
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Wu Z, Ma L, Courtney NA, Zhu J, Landajuela A, Zhang Y, Chapman ER, Karatekin E. Polybasic Patches in Both C2 Domains of Synaptotagmin-1 Are Required for Evoked Neurotransmitter Release. J Neurosci 2022; 42:5816-5829. [PMID: 35701163 PMCID: PMC9337609 DOI: 10.1523/jneurosci.1385-21.2022] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 02/04/2022] [Accepted: 03/13/2022] [Indexed: 01/29/2023] Open
Abstract
Synaptotagmin-1 (Syt1) is a vesicular calcium sensor required for synchronous neurotransmitter release, composed of a single-pass transmembrane domain linked to two C2 domains (C2A and C2B) that bind calcium, acidic lipids, and SNARE proteins that drive fusion of the synaptic vesicle with the plasma membrane. Despite its essential role, how Syt1 couples calcium entry to synchronous release is poorly understood. Calcium binding to C2B is critical for synchronous release, and C2B additionally binds the SNARE complex. The C2A domain is also required for Syt1 function, but it is not clear why. Here, we asked what critical feature of C2A may be responsible for its functional role and compared this to the analogous feature in C2B. We focused on highly conserved poly-lysine patches located on the sides of C2A (K189-192) and C2B (K324-327). We tested effects of charge-neutralization mutations in either region (Syt1K189-192A and Syt1K326-327A) side by side to determine their relative contributions to Syt1 function in cultured cortical neurons from mice of either sex and in single-molecule experiments. Combining electrophysiological recordings and optical tweezers measurements to probe dynamic single C2 domain-membrane interactions, we show that both C2A and C2B polybasic patches contribute to membrane binding, and both are required for evoked release. The size of the readily releasable vesicle pool and the rate of spontaneous release were unaffected, so both patches are likely required specifically for synchronization of release. We suggest these patches contribute to cooperative membrane binding, increasing the overall affinity of Syt1 for negatively charged membranes and facilitating evoked release.SIGNIFICANCE STATEMENT Synaptotagmin-1 is a vesicular calcium sensor required for synchronous neurotransmitter release. Its tandem cytosolic C2 domains (C2A and C2B) bind calcium, acidic lipids, and SNARE proteins that drive fusion of the synaptic vesicle with the plasma membrane. How calcium binding to Synaptotagmin-1 leads to release and the relative contributions of the C2 domains are unclear. Combining electrophysiological recordings from cultured neurons and optical tweezers measurements of single C2 domain-membrane interactions, we show that conserved polybasic regions in both domains contribute to membrane binding cooperatively, and both are required for evoked release, likely by increasing the overall affinity of Synaptotagmin-1 for acidic membranes.
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Affiliation(s)
- Zhenyong Wu
- Department of Cellular and Molecular Physiology, Yale School of Medicine, New Haven, Connecticut 06520
- Nanobiology Institute, Yale University, West Haven, Connecticut 06516
| | - Lu Ma
- Nanobiology Institute, Yale University, West Haven, Connecticut 06516
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520
| | - Nicholas A Courtney
- Howard Hughes Medical Institute and Department of Neuroscience, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53705
| | - Jie Zhu
- Department of Cellular and Molecular Physiology, Yale School of Medicine, New Haven, Connecticut 06520
- Nanobiology Institute, Yale University, West Haven, Connecticut 06516
| | - Ane Landajuela
- Department of Cellular and Molecular Physiology, Yale School of Medicine, New Haven, Connecticut 06520
- Nanobiology Institute, Yale University, West Haven, Connecticut 06516
| | - Yongli Zhang
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520
- Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520
| | - Edwin R Chapman
- Howard Hughes Medical Institute and Department of Neuroscience, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53705
| | - Erdem Karatekin
- Department of Cellular and Molecular Physiology, Yale School of Medicine, New Haven, Connecticut 06520
- Nanobiology Institute, Yale University, West Haven, Connecticut 06516
- Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520
- Saints-Pères Paris Institute for the Neurosciences, Université de Paris, Centre National de la Recherche Scientifique UMR 8003, 75270 Paris, France
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22
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Synaptic Secretion and Beyond: Targeting Synapse and Neurotransmitters to Treat Neurodegenerative Diseases. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:9176923. [PMID: 35923862 PMCID: PMC9343216 DOI: 10.1155/2022/9176923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 05/16/2022] [Accepted: 06/04/2022] [Indexed: 11/17/2022]
Abstract
The nervous system is important, because it regulates the physiological function of the body. Neurons are the most basic structural and functional unit of the nervous system. The synapse is an asymmetric structure that is important for neuronal function. The chemical transmission mode of the synapse is realized through neurotransmitters and electrical processes. Based on vesicle transport, the abnormal information transmission process in the synapse can lead to a series of neurorelated diseases. Numerous proteins and complexes that regulate the process of vesicle transport, such as SNARE proteins, Munc18-1, and Synaptotagmin-1, have been identified. Their regulation of synaptic vesicle secretion is complicated and delicate, and their defects can lead to a series of neurodegenerative diseases. This review will discuss the structure and functions of vesicle-based synapses and their roles in neurons. Furthermore, we will analyze neurotransmitter and synaptic functions in neurodegenerative diseases and discuss the potential of using related drugs in their treatment.
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23
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Di Bartolo AL, Tomes CN, Mayorga LS, Masone D. Enhanced Expansion and Reduced Kiss-and-Run Events in Fusion Pores Steered by Synaptotagmin-1 C2B Domains. J Chem Theory Comput 2022; 18:4544-4554. [PMID: 35759758 DOI: 10.1021/acs.jctc.2c00424] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The fusion pore controls the release of exocytotic vesicle contents through a precise orchestration of lipids from the fusing membranes and proteins. There is a major lipid reorganization during the different stages in life of the fusion pore (membrane fusion, nucleation, and expansion) that can be scrutinized thermodynamically. In this work, using umbrella sampling simulations we describe the expansion of the fusion pore. We have calculated free energy profiles to drive a nascent, just nucleated, fusion pore to its expanded configuration. We have quantified the effects on the free energy of one and two Synaptotagmin-1 C2B domains in the cytosolic space. We show that C2B domains cumulatively reduce the cost for expansion, favoring the system to evolve toward full fusion. Finally, by conducting thousands of unbiased molecular dynamics simulations, we show that C2B domains significantly decrease the probability of kiss-and-run events.
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Affiliation(s)
- Ary Lautaro Di Bartolo
- Instituto de Histología y Embriología de Mendoza (IHEM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Cuyo (UNCuyo), 5500 Mendoza, Argentina.,Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo (UNCuyo), 5500 Mendoza, Argentina
| | - Claudia N Tomes
- Instituto de Histología y Embriología de Mendoza (IHEM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Cuyo (UNCuyo), 5500 Mendoza, Argentina.,Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo (UNCuyo), 5500 Mendoza, Argentina
| | - Luis S Mayorga
- Instituto de Histología y Embriología de Mendoza (IHEM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Cuyo (UNCuyo), 5500 Mendoza, Argentina.,Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo (UNCuyo), 5500 Mendoza, Argentina
| | - Diego Masone
- Instituto de Histología y Embriología de Mendoza (IHEM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Cuyo (UNCuyo), 5500 Mendoza, Argentina.,Facultad de Ingeniería, Universidad Nacional de Cuyo (UNCuyo), 5500 Mendoza, Argentina
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24
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Brewer KD, Shi SM, Wyss-Coray T. Unraveling protein dynamics to understand the brain - the next molecular frontier. Mol Neurodegener 2022; 17:45. [PMID: 35717317 PMCID: PMC9206758 DOI: 10.1186/s13024-022-00546-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 05/25/2022] [Indexed: 11/29/2022] Open
Abstract
The technological revolution to measure global gene expression at the single-cell level is currently transforming our knowledge of the brain and neurological diseases, leading from a basic understanding of genetic regulators and risk factors to one of more complex gene interactions and biological pathways. Looking ahead, our next challenge will be the reliable measurement and understanding of proteins. We describe in this review how to apply new, powerful methods of protein labeling, tracking, and detection. Recent developments of these methods now enable researchers to uncover protein mechanisms in vivo that may previously have only been hypothesized. These methods are also useful for discovering new biology because how proteins regulate systemic interactions is not well understood in most cases, such as how they travel through the bloodstream to distal targets or cross the blood–brain barrier. Genetic sequencing of DNA and RNA have enabled many great discoveries in the past 20 years, and now, the protein methods described here are creating a more complete picture of how cells to whole organisms function. It is likely that these developments will generate another transformation in biomedical research and our understanding of the brain and will ultimately allow for patient-specific medicine on a protein level.
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Affiliation(s)
- Kyle D Brewer
- ChEM-H, Stanford University, Stanford, CA, USA.,Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA.,Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
| | - Sophia M Shi
- ChEM-H, Stanford University, Stanford, CA, USA.,Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA.,Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA.,Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Tony Wyss-Coray
- ChEM-H, Stanford University, Stanford, CA, USA. .,Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA. .,Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA. .,Phil and Penny Knight Initiative for Brain Resilience, Stanford University, Stanford, CA, USA.
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25
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Rizo J, Sari L, Qi Y, Im W, Lin MM. All-atom molecular dynamics simulations of Synaptotagmin-SNARE-complexin complexes bridging a vesicle and a flat lipid bilayer. eLife 2022; 11:76356. [PMID: 35708237 PMCID: PMC9239685 DOI: 10.7554/elife.76356] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 06/15/2022] [Indexed: 12/14/2022] Open
Abstract
Synaptic vesicles are primed into a state that is ready for fast neurotransmitter release upon Ca2+-binding to Synaptotagmin-1. This state likely includes trans-SNARE complexes between the vesicle and plasma membranes that are bound to Synaptotagmin-1 and complexins. However, the nature of this state and the steps leading to membrane fusion are unclear, in part because of the difficulty of studying this dynamic process experimentally. To shed light into these questions, we performed all-atom molecular dynamics simulations of systems containing trans-SNARE complexes between two flat bilayers or a vesicle and a flat bilayer with or without fragments of Synaptotagmin-1 and/or complexin-1. Our results need to be interpreted with caution because of the limited simulation times and the absence of key components, but suggest mechanistic features that may control release and help visualize potential states of the primed Synaptotagmin-1-SNARE-complexin-1 complex. The simulations suggest that SNAREs alone induce formation of extended membrane-membrane contact interfaces that may fuse slowly, and that the primed state contains macromolecular assemblies of trans-SNARE complexes bound to the Synaptotagmin-1 C2B domain and complexin-1 in a spring-loaded configuration that prevents premature membrane merger and formation of extended interfaces, but keeps the system ready for fast fusion upon Ca2+ influx.
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Affiliation(s)
- Josep Rizo
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, United States.,Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, United States.,Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Levent Sari
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, United States.,Green Center for Systems Biology, The University of Texas Southwestern Medical Center, Dallas, United States
| | - Yife Qi
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai, China
| | - Wonpil Im
- Department of Biological Sciences, Lehigh University, Bethlehem, United States.,Department of Chemistry, Lehigh University, Bethlehem, United States.,Department of Bioengineering, Lehigh University, Bethlehem, United States.,Department of Computer Science and Engineering, Lehigh University, Bethlehem, United States
| | - Milo M Lin
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, United States.,Green Center for Systems Biology, The University of Texas Southwestern Medical Center, Dallas, United States
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26
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Miao Q, Nitsche C, Orton H, Overhand M, Otting G, Ubbink M. Paramagnetic Chemical Probes for Studying Biological Macromolecules. Chem Rev 2022; 122:9571-9642. [PMID: 35084831 PMCID: PMC9136935 DOI: 10.1021/acs.chemrev.1c00708] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Indexed: 12/11/2022]
Abstract
Paramagnetic chemical probes have been used in electron paramagnetic resonance (EPR) and nuclear magnetic resonance (NMR) spectroscopy for more than four decades. Recent years witnessed a great increase in the variety of probes for the study of biological macromolecules (proteins, nucleic acids, and oligosaccharides). This Review aims to provide a comprehensive overview of the existing paramagnetic chemical probes, including chemical synthetic approaches, functional properties, and selected applications. Recent developments have seen, in particular, a rapid expansion of the range of lanthanoid probes with anisotropic magnetic susceptibilities for the generation of structural restraints based on residual dipolar couplings and pseudocontact shifts in solution and solid state NMR spectroscopy, mostly for protein studies. Also many new isotropic paramagnetic probes, suitable for NMR measurements of paramagnetic relaxation enhancements, as well as EPR spectroscopic studies (in particular double resonance techniques) have been developed and employed to investigate biological macromolecules. Notwithstanding the large number of reported probes, only few have found broad application and further development of probes for dedicated applications is foreseen.
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Affiliation(s)
- Qing Miao
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
- School
of Chemistry &Chemical Engineering, Shaanxi University of Science & Technology, Xi’an710021, China
| | - Christoph Nitsche
- Research
School of Chemistry, The Australian National
University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
| | - Henry Orton
- Research
School of Chemistry, The Australian National
University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
- ARC
Centre of Excellence for Innovations in Peptide & Protein Science,
Research School of Chemistry, Australian
National University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
| | - Mark Overhand
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
| | - Gottfried Otting
- Research
School of Chemistry, The Australian National
University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
- ARC
Centre of Excellence for Innovations in Peptide & Protein Science,
Research School of Chemistry, Australian
National University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
| | - Marcellus Ubbink
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
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27
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Abstract
Major recent advances and previous data have led to a plausible model of how key proteins mediate neurotransmitter release. In this model, the soluble N-ethylmaleimide-sensitive factor (NSF) attachment protein (SNAP) receptor (SNARE) proteins syntaxin-1, SNAP-25, and synaptobrevin form tight complexes that bring the membranes together and are crucial for membrane fusion. NSF and SNAPs disassemble SNARE complexes and ensure that fusion occurs through an exquisitely regulated pathway that starts with Munc18-1 bound to a closed conformation of syntaxin-1. Munc18-1 also binds to synaptobrevin, forming a template to assemble the SNARE complex when Munc13-1 opens syntaxin-1 while bridging the vesicle and plasma membranes. Synaptotagmin-1 and complexin bind to partially assembled SNARE complexes, likely stabilizing them and preventing fusion until Ca2+ binding to synaptotagmin-1 causes dissociation from the SNARE complex and induces interactions with phospholipids that help trigger release. Although fundamental questions remain about the mechanism of membrane fusion, these advances provide a framework to investigate the mechanisms underlying presynaptic plasticity.
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Affiliation(s)
- Josep Rizo
- Departments of Biophysics, Biochemistry, and Pharmacology, University of Texas Southwestern Medical Center, Dallas, Texas, USA;
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28
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Orton HW, Abdelkader EH, Topping L, Butler SJ, Otting G. Localising nuclear spins by pseudocontact shifts from a single tagging site. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2022; 3:65-76. [PMID: 37905181 PMCID: PMC10539793 DOI: 10.5194/mr-3-65-2022] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 04/18/2022] [Indexed: 11/01/2023]
Abstract
Ligating a protein at a specific site with a tag molecule containing a paramagnetic metal ion provides a versatile way of generating pseudocontact shifts (PCSs) in nuclear magnetic resonance (NMR) spectra. PCSs can be observed for nuclear spins far from the tagging site, and PCSs generated from multiple tagging sites have been shown to enable highly accurate structure determinations at specific sites of interest, even when using flexible tags, provided the fitted effective magnetic susceptibility anisotropy (Δ χ ) tensors accurately back-calculate the experimental PCSs measured in the immediate vicinity of the site of interest. The present work investigates the situation where only the local structure of a protein region or bound ligand is to be determined rather than the structure of the entire molecular system. In this case, the need for gathering structural information from tags deployed at multiple sites may be queried. Our study presents a computational simulation of the structural information available from samples produced with single tags attached at up to six different sites, up to six different tags attached to a single site, and in-between scenarios. The results indicate that the number of tags is more important than the number of tagging sites. This has important practical implications, as it is much easier to identify a single site that is suitable for tagging than multiple ones. In an initial experimental demonstration with the ubiquitin mutant S57C, PCSs generated with four different tags at a single site are shown to accurately pinpoint the location of amide protons in different segments of the protein.
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Affiliation(s)
- Henry W Orton
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Elwy H Abdelkader
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Lydia Topping
- Department of Chemistry, Loughborough University, Epinal Way, Loughborough, LE11 3TU, United Kingdom
| | - Stephen J Butler
- Department of Chemistry, Loughborough University, Epinal Way, Loughborough, LE11 3TU, United Kingdom
| | - Gottfried Otting
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
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29
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Xia X, Wang Y, Qin Y, Zhao S, Zheng JC. Exosome: A novel neurotransmission modulator or non-canonical neurotransmitter? Ageing Res Rev 2022; 74:101558. [PMID: 34990846 DOI: 10.1016/j.arr.2021.101558] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 08/13/2021] [Accepted: 12/30/2021] [Indexed: 02/08/2023]
Abstract
Neurotransmission is the electrical impulse-triggered propagation of signals between neurons or between neurons and other cell types such as skeletal muscle cells. Recent studies point out the involvement of exosomes, a type of small bilipid layer-enclosed extracellular vesicles, in regulating neurotransmission. Through horizontally transferring proteins, lipids, and nucleic acids, exosomes can modulate synaptic activities rapidly by controlling neurotransmitter release or progressively by regulating neural plasticity including synapse formation, neurite growth & removal, and axon guidance & elongation. In this review, we summarize the similarities and differences between exosomes and synaptic vesicles in their biogenesis, contents, and release. We also highlight the recent progress made in demonstrating the biological roles of exosome in regulating neurotransmission, and propose a modified model of neurotransmission, in which exosomes act as novel neurotransmitters. Lastly, we provide a comprehensive discussion of the enlightenment of the current knowledge on neurotransmission to the future directions of exosome research.
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30
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Müntener T, Joss D, Häussinger D, Hiller S. Pseudocontact Shifts in Biomolecular NMR Spectroscopy. Chem Rev 2022; 122:9422-9467. [PMID: 35005884 DOI: 10.1021/acs.chemrev.1c00796] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Paramagnetic centers in biomolecules, such as specific metal ions that are bound to a protein, affect the nuclei in their surrounding in various ways. One of these effects is the pseudocontact shift (PCS), which leads to strong chemical shift perturbations of nuclear spins, with a remarkably long range of 50 Å and beyond. The PCS in solution NMR is an effect originating from the anisotropic part of the dipole-dipole interaction between the magnetic momentum of unpaired electrons and nuclear spins. The PCS contains spatial information that can be exploited in multiple ways to characterize structure, function, and dynamics of biomacromolecules. It can be used to refine structures, magnify effects of dynamics, help resonance assignments, allows for an intermolecular positioning system, and gives structural information in sensitivity-limited situations where all other methods fail. Here, we review applications of the PCS in biomolecular solution NMR spectroscopy, starting from early works on natural metalloproteins, following the development of non-natural tags to chelate and attach lanthanoid ions to any biomolecular target to advanced applications on large biomolecular complexes and inside living cells. We thus hope to not only highlight past applications but also shed light on the tremendous potential the PCS has in structural biology.
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Affiliation(s)
- Thomas Müntener
- Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
| | - Daniel Joss
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, 4056 Basel, Switzerland
| | - Daniel Häussinger
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, 4056 Basel, Switzerland
| | - Sebastian Hiller
- Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
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31
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Orton H, Herath I, Maleckis A, Jabar S, Szabo M, Graham B, Breen C, Topping L, Butler S, Otting G. Localising individual atoms of tryptophan side chains in the metallo- β-lactamase IMP-1 by pseudocontact shifts from paramagnetic lanthanoid tags at multiple sites. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2022; 3:1-13. [PMID: 37905175 PMCID: PMC10583275 DOI: 10.5194/mr-3-1-2022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 12/21/2021] [Indexed: 11/01/2023]
Abstract
The metallo-β -lactamase IMP-1 features a flexible loop near the active site that assumes different conformations in single crystal structures, which may assist in substrate binding and enzymatic activity. To probe the position of this loop, we labelled the tryptophan residues of IMP-1 with 7-13 C-indole and the protein with lanthanoid tags at three different sites. The magnetic susceptibility anisotropy (Δ χ ) tensors were determined by measuring pseudocontact shifts (PCSs) of backbone amide protons. The Δ χ tensors were subsequently used to identify the atomic coordinates of the tryptophan side chains in the protein. The PCSs were sufficient to determine the location of Trp28, which is in the active site loop targeted by our experiments, with high accuracy. Its average atomic coordinates showed barely significant changes in response to the inhibitor captopril. It was found that localisation spaces could be defined with better accuracy by including only the PCSs of a single paramagnetic lanthanoid ion for each tag and tagging site. The effect was attributed to the shallow angle with which PCS isosurfaces tend to intersect if generated by tags and tagging sites that are identical except for the paramagnetic lanthanoid ion.
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Affiliation(s)
- Henry W. Orton
- ARC Centre of Excellence for Innovations in Peptide & Protein
Science, Research School of Chemistry, Australian National University,
Canberra, ACT 2601, Australia
| | - Iresha D. Herath
- Research School of Chemistry, The Australian National University,
Sullivans Creek Road, Canberra ACT 2601, Australia
| | - Ansis Maleckis
- Latvian Institute of Organic Synthesis, Aizkraukles 21, 1006 Riga,
Latvia
| | - Shereen Jabar
- Research School of Chemistry, The Australian National University,
Sullivans Creek Road, Canberra ACT 2601, Australia
| | - Monika Szabo
- Monash Institute of Pharmaceutical Sciences, Monash University,
Parkville, VIC 3052, Australia
| | - Bim Graham
- Monash Institute of Pharmaceutical Sciences, Monash University,
Parkville, VIC 3052, Australia
| | - Colum Breen
- Department of Chemistry, Loughborough University, Epinal Way, Loughborough, LE11 3TU, United Kingdom
| | - Lydia Topping
- Department of Chemistry, Loughborough University, Epinal Way, Loughborough, LE11 3TU, United Kingdom
| | - Stephen J. Butler
- Department of Chemistry, Loughborough University, Epinal Way, Loughborough, LE11 3TU, United Kingdom
| | - Gottfried Otting
- ARC Centre of Excellence for Innovations in Peptide & Protein
Science, Research School of Chemistry, Australian National University,
Canberra, ACT 2601, Australia
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32
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Di Bartolo AL, Masone D. Synaptotagmin-1 C2B domains cooperatively stabilize the fusion stalk via a master-servant mechanism. Chem Sci 2022; 13:3437-3446. [PMID: 35432859 PMCID: PMC8943895 DOI: 10.1039/d1sc06711g] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 02/22/2022] [Indexed: 11/21/2022] Open
Abstract
Synaptotagmin-1 is a low-affinity Ca2+ sensor that triggers synchronous vesicle fusion. It contains two similar C2 domains (C2A and C2B) that cooperate in membrane binding, being the C2B domain the...
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Affiliation(s)
- Ary Lautaro Di Bartolo
- Instituto de Histología y Embriología de Mendoza (IHEM) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Cuyo (UNCuyo) 5500 Mendoza Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo (UNCuyo) 5500 Mendoza Argentina
| | - Diego Masone
- Instituto de Histología y Embriología de Mendoza (IHEM) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Cuyo (UNCuyo) 5500 Mendoza Argentina
- Facultad de Ingeniería, Universidad Nacional de Cuyo (UNCuyo) 5500 Mendoza Argentina
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33
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Abbineni PS, Briguglio JS, Chapman ER, Holz RW, Axelrod D. VAMP2 and synaptotagmin mobility in chromaffin granule membranes: implications for regulated exocytosis. Mol Biol Cell 2021; 33:ar53. [PMID: 34851717 PMCID: PMC9265163 DOI: 10.1091/mbc.e21-10-0494] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Granule-plasma membrane docking and fusion can only occur when proteins that enable these reactions are present at the granule-plasma membrane contact. Thus, the mobility of granule membrane proteins may influence docking, and membrane fusion. We measured the mobility of vesicle associated membrane protein 2 (VAMP2), synaptotagmin 1 (Syt1), and synaptotagmin 7 (Syt7) in chromaffin granule membranes in living chromaffin cells. We used a method that is not limited by standard optical resolution. A bright flash of strongly decaying evanescent field produced by total internal reflection (TIR) was used to photobleach GFP-labeled proteins in the granule membrane. Fluorescence recovery occurs as unbleached protein in the granule membrane distal from the glass interface diffuses into the more bleached proximal regions, enabling the measurement of diffusion coefficients. We found that VAMP2-EGFP and Syt7-EGFP are mobile with a diffusion coefficient of approximately 3 × 10-10 cm2/s. Syt1-EGFP mobility was below the detection limit. Utilizing these diffusion parameters, we estimated the time required for these proteins to arrive at docking and nascent fusion sites to be many tens of milliseconds. Our analyses raise the possibility that the diffusion characteristics of VAMP2 and Syt proteins could be a factor that influences the rate of exocytosis.
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Affiliation(s)
- Prabhodh S Abbineni
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan.,Department of Pharmacology, University of Michigan, Ann Arbor, Michigan
| | - Joseph S Briguglio
- Howard Hughes Medical Institute, Department of Neuroscience, University of Wisconsin, Madison, WI
| | - Edwin R Chapman
- Howard Hughes Medical Institute, Department of Neuroscience, University of Wisconsin, Madison, WI
| | - Ronald W Holz
- Department of Pharmacology, University of Michigan, Ann Arbor, Michigan
| | - Daniel Axelrod
- Department of Pharmacology, University of Michigan, Ann Arbor, Michigan.,Department of Physics, University of Michigan, Ann Arbor, Michigan
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34
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Kumar S, Javed R, Mudd M, Pallikkuth S, Lidke KA, Jain A, Tangavelou K, Gudmundsson SR, Ye C, Rusten TE, Anonsen JH, Lystad AH, Claude-Taupin A, Simonsen A, Salemi M, Phinney B, Li J, Guo LW, Bradfute SB, Timmins GS, Eskelinen EL, Deretic V. Mammalian hybrid pre-autophagosomal structure HyPAS generates autophagosomes. Cell 2021; 184:5950-5969.e22. [PMID: 34741801 PMCID: PMC8616855 DOI: 10.1016/j.cell.2021.10.017] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 05/12/2021] [Accepted: 10/15/2021] [Indexed: 12/14/2022]
Abstract
The biogenesis of mammalian autophagosomes remains to be fully defined. Here, we used cellular and in vitro membrane fusion analyses to show that autophagosomes are formed from a hitherto unappreciated hybrid membrane compartment. The autophagic precursors emerge through fusion of FIP200 vesicles, derived from the cis-Golgi, with endosomally derived ATG16L1 membranes to generate a hybrid pre-autophagosomal structure, HyPAS. A previously unrecognized apparatus defined here controls HyPAS biogenesis and mammalian autophagosomal precursor membranes. HyPAS can be modulated by pharmacological agents whereas its formation is inhibited upon severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection or by expression of SARS-CoV-2 nsp6. These findings reveal the origin of mammalian autophagosomal membranes, which emerge via convergence of secretory and endosomal pathways, and show that this process is targeted by microbial factors such as coronaviral membrane-modulating proteins.
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Affiliation(s)
- Suresh Kumar
- Autophagy Inflammation and Metabolism Center, University of New Mexico Health Sciences Center, Albuquerque, NM, USA; Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Ruheena Javed
- Autophagy Inflammation and Metabolism Center, University of New Mexico Health Sciences Center, Albuquerque, NM, USA; Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Michal Mudd
- Autophagy Inflammation and Metabolism Center, University of New Mexico Health Sciences Center, Albuquerque, NM, USA; Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Sandeep Pallikkuth
- Department of Physics and Astronomy, University of New Mexico, Albuquerque, NM, USA
| | - Keith A Lidke
- Department of Physics and Astronomy, University of New Mexico, Albuquerque, NM, USA
| | - Ashish Jain
- Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Karthikeyan Tangavelou
- Autophagy Inflammation and Metabolism Center, University of New Mexico Health Sciences Center, Albuquerque, NM, USA; Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | | | - Chunyan Ye
- Center for Global Health, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | | | | | | | - Aurore Claude-Taupin
- Autophagy Inflammation and Metabolism Center, University of New Mexico Health Sciences Center, Albuquerque, NM, USA; Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Anne Simonsen
- Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Michelle Salemi
- Proteomics Core, University of California Davis, Davis, CA, USA
| | - Brett Phinney
- Proteomics Core, University of California Davis, Davis, CA, USA
| | - Jing Li
- Department of Surgery, University of Virginia, Charlottesville, VA, USA
| | - Lian-Wang Guo
- Department of Surgery, University of Virginia, Charlottesville, VA, USA
| | - Steven B Bradfute
- Center for Global Health, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Graham S Timmins
- Autophagy Inflammation and Metabolism Center, University of New Mexico Health Sciences Center, Albuquerque, NM, USA; School of Pharmacy, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | | | - Vojo Deretic
- Autophagy Inflammation and Metabolism Center, University of New Mexico Health Sciences Center, Albuquerque, NM, USA; Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM, USA.
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35
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Vogel R, Müntener T, Häussinger D. Intrinsic anisotropy parameters of a series of lanthanoid complexes deliver new insights into the structure-magnetism relationship. Chem 2021. [DOI: 10.1016/j.chempr.2021.08.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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36
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Voleti R, Bali S, Guerrero J, Smothers J, Springhower C, Acosta GA, Brewer KD, Albericio F, Rizo J. Evaluation of the tert-butyl group as a probe for NMR studies of macromolecular complexes. JOURNAL OF BIOMOLECULAR NMR 2021; 75:347-363. [PMID: 34505210 PMCID: PMC9482097 DOI: 10.1007/s10858-021-00380-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 08/23/2021] [Indexed: 05/04/2023]
Abstract
The development of methyl transverse relaxation optimized spectroscopy has greatly facilitated the study of macromolecular assemblies by solution NMR spectroscopy. However, limited sample solubility and stability has hindered application of this technique to ongoing studies of complexes formed on membranes by the neuronal SNAREs that mediate neurotransmitter release and synaptotagmin-1, the Ca2+ sensor that triggers release. Since the 1H NMR signal of a tBu group attached to a large protein or complex can be observed with high sensitivity if the group retains high mobility, we have explored the use of this strategy to analyze presynaptic complexes involved in neurotransmitter release. For this purpose, we attached tBu groups at single cysteines of fragments of synaptotagmin-1, complexin-1 and the neuronal SNAREs by reaction with 5-(tert-butyldisulfaneyl)-2-nitrobenzoic acid (BDSNB), tBu iodoacetamide or tBu acrylate. The tBu resonances of the tagged proteins were generally sharp and intense, although tBu groups attached with BDSNB had a tendency to exhibit somewhat broader resonances that likely result because of the shorter linkage between the tBu and the tagged cysteine. Incorporation of the tagged proteins into complexes on nanodiscs led to severe broadening of the tBu resonances in some cases. However, sharp tBu resonances could readily be observed for some complexes of more than 200 kDa at low micromolar concentrations. Our results show that tagging of proteins with tBu groups provides a powerful approach to study large biomolecular assemblies of limited stability and/or solubility that may be applicable even at nanomolar concentrations.
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Affiliation(s)
- Rashmi Voleti
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Sofia Bali
- Center for Alzheimer's and Neurodegenerative Diseases, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Jaime Guerrero
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Jared Smothers
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Charis Springhower
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
- Alicat Scientific, Tucson, AZ, 85743, USA
| | - Gerardo A Acosta
- CIBER-BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine, and Department of Organic Chemistry, University of Barcelona, 08028, Barcelona, Spain
- Institute of Advanced Chemistry of Catalonia (IQAC-CSIC), Spanish National Research Council (CSIC), Jordi Girona 18-26, 08034, Barcelona, Spain
| | - Kyle D Brewer
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Fernando Albericio
- CIBER-BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine, and Department of Organic Chemistry, University of Barcelona, 08028, Barcelona, Spain
- Institute of Advanced Chemistry of Catalonia (IQAC-CSIC), Spanish National Research Council (CSIC), Jordi Girona 18-26, 08034, Barcelona, Spain
- Peptide Science Laboratory, School of Chemistry and Physics, University of KwaZulu-Natal, Durban, 4001, South Africa
| | - Josep Rizo
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
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37
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Complexin Suppresses Spontaneous Exocytosis by Capturing the Membrane-Proximal Regions of VAMP2 and SNAP25. Cell Rep 2021; 32:107926. [PMID: 32698012 PMCID: PMC7116205 DOI: 10.1016/j.celrep.2020.107926] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Revised: 02/28/2020] [Accepted: 06/26/2020] [Indexed: 01/29/2023] Open
Abstract
The neuronal protein complexin contains multiple domains that exert clamping and facilitatory functions to tune spontaneous and action potential-triggered synaptic release. We address the clamping mechanism and show that the accessory helix of complexin arrests assembly of the soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) complex that forms the core machinery of intracellular membrane fusion. In a reconstituted fusion assay, site-and stage-specific photo-cross-linking reveals that, prior to fusion, the complexin accessory helix laterally binds the membrane-proximal C-terminal ends of SNAP25 and VAMP2. Corresponding complexin interface mutants selectively increase spontaneous release of neuro-transmitters in living neurons, implying that the accessory helix suppresses final zippering/assembly of the SNARE four-helix bundle by restraining VAMP2 and SNAP25.
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38
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Orientational Ambiguity in Septin Coiled Coils and its Structural Basis. J Mol Biol 2021; 433:166889. [PMID: 33639214 DOI: 10.1016/j.jmb.2021.166889] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 01/25/2021] [Accepted: 02/17/2021] [Indexed: 12/21/2022]
Abstract
Septins are an example of subtle molecular recognition whereby different paralogues must correctly assemble into functional filaments important for essential cellular events such as cytokinesis. Most possess C-terminal domains capable of forming coiled coils which are believed to be involved in filament formation and bundling. Here, we report an integrated structural approach which aims to unravel their architectural diversity and in so doing provide direct structural information for the coiled-coil regions of five human septins. Unexpectedly, we encounter dimeric structures presenting both parallel and antiparallel arrangements which are in consonance with molecular modelling suggesting that both are energetically accessible. These sequences therefore code for two metastable states of different orientations which employ different but overlapping interfaces. The antiparallel structures present a mixed coiled-coil interface, one side of which is dominated by a continuous chain of core hydrophilic residues. This unusual type of coiled coil could be used to expand the toolkit currently available to the protein engineer for the design of previously unforeseen coiled-coil based assemblies. Within a physiological context, our data provide the first atomic details related to the assumption that the parallel orientation is likely formed between septin monomers from the same filament whilst antiparallelism may participate in the widely described interfilament cross bridges necessary for higher order structures and thereby septin function.
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39
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Bykhovskaia M. SNARE complex alters the interactions of the Ca 2+ sensor synaptotagmin 1 with lipid bilayers. Biophys J 2021; 120:642-661. [PMID: 33453271 DOI: 10.1016/j.bpj.2020.12.025] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 12/19/2020] [Accepted: 12/24/2020] [Indexed: 12/24/2022] Open
Abstract
Release of neuronal transmitters from nerve terminals is triggered by the molecular Ca2+ sensor synaptotagmin 1 (Syt1). Syt1 is a transmembrane protein attached to the synaptic vesicle (SV), and its cytosolic region comprises two domains, C2A and C2B, which are thought to penetrate into lipid bilayers upon Ca2+ binding. Before fusion, SVs become attached to the presynaptic membrane (PM) by the four-helical SNARE complex, which is thought to bind the C2B domain in vivo. To understand how the interactions of Syt1 with lipid bilayers and the SNARE complex trigger fusion, we performed molecular dynamics (MD) simulations at a microsecond scale. We investigated how the isolated C2 modules and the C2AB tandem of Syt1 interact with membranes mimicking either SV or PM. The simulations showed that the C2AB tandem can either bridge SV and PM or insert into PM with its Ca2+-bound tips and that the latter configuration is more favorable. Surprisingly, C2 domains did not cooperate in penetrating into PM but instead mutually hindered their insertion into the bilayer. To test whether the interaction of Syt1 with lipid bilayers could be affected by the C2B-SNARE attachment, we performed systematic conformational analysis of the C2AB-SNARE complex. Notably, we found that the C2B-SNARE interface precludes the coupling of C2 domains and promotes their insertion into PM. We performed the MD simulations of the prefusion protein complex positioned between the lipid bilayers mimicking PM and SV, and our results demonstrated in silico that the presence of the Ca2+ bound C2AB tandem promotes lipid merging. Altogether, our MD simulations elucidated the role of the Syt1-SNARE interactions in the fusion process and produced the dynamic all-atom model of the prefusion protein-lipid complex.
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40
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Ginger L, Malsam J, Sonnen AFP, Morado D, Scheutzow A, Söllner TH, Briggs JAG. Arrangements of proteins at reconstituted synaptic vesicle fusion sites depend on membrane separation. FEBS Lett 2020; 594:3450-3463. [PMID: 32860428 PMCID: PMC7711843 DOI: 10.1002/1873-3468.13916] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 07/16/2020] [Accepted: 08/09/2020] [Indexed: 11/18/2022]
Abstract
Synaptic vesicle proteins, including N‐ethylmaleimide‐sensitive factor attachment protein receptors (SNAREs), Synaptotagmin‐1 and Complexin, are responsible for controlling the synchronised fusion of synaptic vesicles with the presynaptic plasma membrane in response to elevated cytosolic calcium levels. A range of structures of SNAREs and their regulatory proteins have been elucidated, but the exact organisation of these proteins at synaptic junction membranes remains elusive. Here, we have used cryoelectron tomography to investigate the arrangement of synaptic proteins in an in vitro reconstituted fusion system. We found that the separation between vesicle and target membranes strongly correlates with the organisation of protein complexes at junctions. At larger membrane separations, protein complexes assume a ‘clustered’ distribution at the docking site, inducing a protrusion in the target membrane. As the membrane separation decreases, protein complexes become displaced radially outwards and assume a ‘ring‐like’ arrangement. Our findings indicate that docked vesicles can possess a wide range of protein complex numbers and be heterogeneous in their protein arrangements.
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Affiliation(s)
- Lucy Ginger
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Joerg Malsam
- Heidelberg University Biochemistry Center, Heidelberg, Germany
| | - Andreas F-P Sonnen
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | | | | | | | - John A G Briggs
- MRC Laboratory of Molecular Biology, Cambridge, UK.,Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
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41
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Voleti R, Jaczynska K, Rizo J. Ca 2+-dependent release of synaptotagmin-1 from the SNARE complex on phosphatidylinositol 4,5-bisphosphate-containing membranes. eLife 2020; 9:57154. [PMID: 32808925 PMCID: PMC7498268 DOI: 10.7554/elife.57154] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 08/12/2020] [Indexed: 11/13/2022] Open
Abstract
The Ca2+ sensor synaptotagmin-1 and the SNARE complex cooperate to trigger neurotransmitter release. Structural studies elucidated three distinct synaptotagmin-1-SNARE complex binding modes involving 'polybasic', 'primary' and 'tripartite' interfaces of synaptotagmin-1. We investigated these interactions using NMR and fluorescence spectroscopy. Synaptotagmin-1 binds to the SNARE complex through the polybasic and primary interfaces in solution. Ca2+-free synaptotagmin-1 binds to SNARE complexes anchored on PIP2-containing nanodiscs. R398Q/R399Q and E295A/Y338W mutations at the primary interface, which strongly impair neurotransmitter release, disrupt and enhance synaptotagmin-1-SNARE complex binding, respectively. Ca2+ induces tight binding of synaptotagmin-1 to PIP2-containing nanodiscs, disrupting synaptotagmin-1-SNARE interactions. Specific effects of mutations in the polybasic region on Ca2+-dependent synaptotagmin-1-PIP2-membrane interactions correlate with their effects on release. Our data suggest that synaptotagmin-1 binds to the SNARE complex through the primary interface and that Ca2+ releases this interaction, inducing PIP2/membrane binding and allowing cooperation between synaptotagmin-1 and the SNAREs in membrane fusion to trigger release.
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Affiliation(s)
- Rashmi Voleti
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, United States.,Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, United States.,Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Klaudia Jaczynska
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, United States.,Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, United States.,Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Josep Rizo
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, United States.,Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, United States.,Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, United States
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42
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Prasad R, Zhou HX. Membrane Association and Functional Mechanism of Synaptotagmin-1 in Triggering Vesicle Fusion. Biophys J 2020; 119:1255-1265. [PMID: 32882186 DOI: 10.1016/j.bpj.2020.08.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 07/23/2020] [Accepted: 08/10/2020] [Indexed: 12/23/2022] Open
Abstract
Upon Ca2+ influx, synaptic vesicles fuse with the presynaptic plasma membrane (PM) to release neurotransmitters. Membrane fusion is triggered by synaptotagmin-1, a transmembrane protein in the vesicle membrane (VM), but the mechanism is under debate. Synaptotagmin-1 contains a single transmembrane helix (TM) and two tandem C2 domains (C2A and C2B). This study aimed to use molecular dynamics simulations to elucidate how Ca2+-bound synaptotagmin-1, by simultaneously associating with VM and PM, brings them together for fusion. Although C2A stably associates with VM via two Ca2+-binding loops, C2B has a propensity to partially dissociate. Importantly, an acidic motif in the TM-C2A linker competes with VM for interacting with C2B, thereby flipping its orientation to face PM. Subsequently, C2B readily associates with PM via a polybasic cluster and a Ca2+-binding loop. The resulting mechanistic model for the triggering of membrane fusion by synaptotagmin-1 reconciles many experimental observations.
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Affiliation(s)
- Ramesh Prasad
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois
| | - Huan-Xiang Zhou
- Department of Chemistry, University of Illinois at Chicago, Chicago, Illinois; Department of Physics, University of Illinois at Chicago, Chicago, Illinois.
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43
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Ruiter M, Kádková A, Scheutzow A, Malsam J, Söllner TH, Sørensen JB. An Electrostatic Energy Barrier for SNARE-Dependent Spontaneous and Evoked Synaptic Transmission. Cell Rep 2020; 26:2340-2352.e5. [PMID: 30811985 DOI: 10.1016/j.celrep.2019.01.103] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 11/05/2018] [Accepted: 01/28/2019] [Indexed: 12/22/2022] Open
Abstract
Information transfer across CNS synapses depends on the very low basal vesicle fusion rate and the ability to rapidly upregulate that rate upon Ca2+ influx. We show that local electrostatic repulsion participates in creating an energy barrier, which limits spontaneous synaptic transmission. The barrier amplitude is increased by negative charges and decreased by positive charges on the SNARE-complex surface. Strikingly, the effect of charges on the barrier is additive and this extends to evoked transmission, but with a shallower charge dependence. Action potential-driven synaptic release is equivalent to the abrupt addition of ∼35 positive charges to the fusion machine. Within an electrostatic model for triggering, the Ca2+ sensor synaptotagmin-1 contributes ∼18 charges by binding Ca2+, while also modulating the fusion barrier at rest. Thus, the energy barrier for synaptic vesicle fusion has a large electrostatic component, allowing synaptotagmin-1 to act as an electrostatic switch and modulator to trigger vesicle fusion.
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Affiliation(s)
- Marvin Ruiter
- Department of Neuroscience, Faculty of Health and Medical Sciences, 2200 Copenhagen N, University of Copenhagen, Copenhagen, Denmark
| | - Anna Kádková
- Department of Neuroscience, Faculty of Health and Medical Sciences, 2200 Copenhagen N, University of Copenhagen, Copenhagen, Denmark
| | - Andrea Scheutzow
- Heidelberg University Biochemistry Center, 69120 Heidelberg, Germany
| | - Jörg Malsam
- Heidelberg University Biochemistry Center, 69120 Heidelberg, Germany
| | - Thomas H Söllner
- Heidelberg University Biochemistry Center, 69120 Heidelberg, Germany
| | - Jakob B Sørensen
- Department of Neuroscience, Faculty of Health and Medical Sciences, 2200 Copenhagen N, University of Copenhagen, Copenhagen, Denmark.
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44
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Magdziarek M, Bolembach AA, Stepien KP, Quade B, Liu X, Rizo J. Re-examining how Munc13-1 facilitates opening of syntaxin-1. Protein Sci 2020; 29:1440-1458. [PMID: 32086964 DOI: 10.1002/pro.3844] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 02/19/2020] [Accepted: 02/20/2020] [Indexed: 11/06/2022]
Abstract
Munc13-1 is crucial for neurotransmitter release and, together with Munc18-1, orchestrates assembly of the neuronal SNARE complex formed by syntaxin-1, SNAP-25, and synaptobrevin. Assembly starts with syntaxin-1 folded into a self-inhibited closed conformation that binds to Munc18-1. Munc13-1 is believed to catalyze the opening of syntaxin-1 to facilitate SNARE complex formation. However, different types of Munc13-1-syntaxin-1 interactions have been reported to underlie this activity, and the critical nature of Munc13-1 for release may arise because of its key role in bridging the vesicle and plasma membranes. To shed light into the mechanism of action of Munc13-1, we have used NMR spectroscopy, SNARE complex assembly experiments, and liposome fusion assays. We show that point mutations in a linker region of syntaxin-1 that forms intrinsic part of the closed conformation strongly impair stimulation of SNARE complex assembly and liposome fusion mediated by Munc13-1 fragments, even though binding of this linker region to Munc13-1 is barely detectable. Conversely, the syntaxin-1 SNARE motif clearly binds to Munc13-1, but a mutation that disrupts this interaction does not affect SNARE complex assembly or liposome fusion. We also show that Munc13-1 cannot be replaced by an artificial tethering factor to mediate liposome fusion. Overall, these results emphasize how very weak interactions can play fundamental roles in promoting conformational transitions and strongly support a model whereby the critical nature of Munc13-1 for neurotransmitter release arises not only from its ability to bridge two membranes but also from an active role in opening syntaxin-1 via interactions with the linker.
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Affiliation(s)
- Magdalena Magdziarek
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas, USA.,Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, USA.,Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Agnieszka A Bolembach
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas, USA.,Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, USA.,Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Karolina P Stepien
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas, USA.,Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, USA.,Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Bradley Quade
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas, USA.,Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, USA.,Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Xiaoxia Liu
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas, USA.,Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, USA.,Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, Texas, USA.,Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Josep Rizo
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas, USA.,Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, USA.,Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
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45
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Pan YZ, Liu X, Rizo J. Analysis of asymmetry in lipid and content mixing assays with reconstituted proteoliposomes containing the neuronal SNAREs. Sci Rep 2020; 10:2907. [PMID: 32076023 PMCID: PMC7031292 DOI: 10.1038/s41598-020-59740-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 02/03/2020] [Indexed: 11/09/2022] Open
Abstract
Reconstitution assays with proteoliposomes provide a powerful tool to elucidate the mechanism of neurotransmitter release, but it is important to understand how these assays report on membrane fusion, and recent studies with yeast vacuolar SNAREs uncovered asymmetry in the results of lipid mixing assays. We have investigated whether such asymmetry also occurs in reconstitution assays with the neuronal SNAREs, using syntaxin-1-SNAP-25-containing liposomes and liposomes containing synaptobrevin (T and V liposomes, respectively), and fluorescent probes to monitor lipid and content mixing simultaneously. Switching the fluorescent probes placed on the T and V liposomes, we observed a striking asymmetry in both lipid and content mixing stimulated by a fragment spanning the two C2 domains of synaptotagmin-1, or by a peptide that spans the C-terminal half of the synaptobrevin SNARE motif. However, no such asymmetry was observed in assays performed in the presence of Munc18-1, Munc13-1, NSF and αSNAP, which coordinate the assembly-disassembly cycle of neuronal SNARE complexes. Our results show that switching fluorescent probes between the two types of liposomes provides a useful approach to better understand the reactions that occur between liposomes and detect heterogenous behavior in these reactions.
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Affiliation(s)
- Yun-Zu Pan
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas, United States.,Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, United States.,Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, Texas, United States
| | - Xiaoxia Liu
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Department of Pathophysiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Josep Rizo
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas, United States. .,Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, United States. .,Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, Texas, United States.
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Katti S, Nyenhuis SB, Her B, Cafiso DS, Igumenova TI. Partial Metal Ion Saturation of C2 Domains Primes Synaptotagmin 1-Membrane Interactions. Biophys J 2020; 118:1409-1423. [PMID: 32075747 DOI: 10.1016/j.bpj.2020.01.032] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 01/15/2020] [Accepted: 01/27/2020] [Indexed: 12/29/2022] Open
Abstract
Synaptotagmin 1 (Syt1) is an integral membrane protein whose phospholipid-binding tandem C2 domains, C2A and C2B, act as Ca2+ sensors of neurotransmitter release. Our objective was to understand the role of individual metal-ion binding sites of these domains in the membrane association process. We used Pb2+, a structural and functional surrogate of Ca2+, to generate the protein states with well-defined protein-metal ion stoichiometry. NMR experiments revealed that binding of one divalent metal ion per C2 domain results in loss of conformational plasticity of the loop regions, potentially pre-organizing them for additional metal-ion and membrane-binding events. In C2A, a divalent metal ion in site 1 is sufficient to drive its weak association with phosphatidylserine-containing membranes, whereas in C2B, it enhances the interactions with the signaling lipid phosphatidylinositol-4,5-bisphosphate. In full-length Syt1, both Pb2+-complexed C2 domains associate with phosphatidylserine-containing membranes. Electron paramagnetic resonance experiments show that the extent of membrane insertion correlates with the occupancy of the C2 metal ion sites. Together, our results indicate that upon partial metal ion saturation of the intra-loop region, Syt1 adopts a dynamic, partially membrane-bound state. The properties of this state, such as conformationally restricted loop regions and positioning of C2 domains in close proximity to anionic lipid headgroups, "prime" Syt1 for cooperative binding of a full complement of metal ions and deeper membrane insertion.
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Affiliation(s)
- Sachin Katti
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas
| | - Sarah B Nyenhuis
- Department of Chemistry and Biophysics Program, University of Virginia, Charlottesville, Virginia
| | - Bin Her
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas
| | - David S Cafiso
- Department of Chemistry and Biophysics Program, University of Virginia, Charlottesville, Virginia
| | - Tatyana I Igumenova
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas.
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Resolving kinetic intermediates during the regulated assembly and disassembly of fusion pores. Nat Commun 2020; 11:231. [PMID: 31932584 PMCID: PMC6957489 DOI: 10.1038/s41467-019-14072-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 12/10/2019] [Indexed: 11/08/2022] Open
Abstract
The opening of a fusion pore during exocytosis creates the first aqueous connection between the lumen of a vesicle and the extracellular space. Soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs) mediate the formation of these dynamic structures, and their kinetic transitions are tightly regulated by accessory proteins at the synapse. Here, we utilize two single molecule approaches, nanodisc-based planar bilayer electrophysiology and single-molecule FRET, to address the relationship between SNARE complex assembly and rapid (micro-millisecond) fusion pore transitions, and to define the role of accessory proteins. Synaptotagmin (syt) 1, a major Ca2+-sensor for synaptic vesicle exocytosis, drove the formation of an intermediate: committed trans-SNARE complexes that form large, stable pores. Once open, these pores could only be closed by the action of the ATPase, NSF. Time-resolved measurements revealed that NSF-mediated pore closure occurred via a complex ‘stuttering’ mechanism. This simplified system thus reveals the dynamic formation and dissolution of fusion pores. SNAREs mediate the formation of a fusion pore during exocytosis which connects the lumen of a vesicle with the extracellular space. Here, authors use single molecule approaches to define the role of synaptotagmin 1 and NSF in synaptic pore formation and dissolution.
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Joss D, Winter F, Häussinger D. A novel, rationally designed lanthanoid chelating tag delivers large paramagnetic structural restraints for biomolecular NMR. Chem Commun (Camb) 2020; 56:12861-12864. [DOI: 10.1039/d0cc04337k] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A novel, rationally designed lanthanoid chelating tag enables fast ligation to biomacromolecules and delivers long-range structural restraints by NMR.
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Affiliation(s)
- Daniel Joss
- Department of Chemistry
- University of Basel
- Basel 4056
- Switzerland
| | - Florine Winter
- Department of Chemistry
- University of Basel
- Basel 4056
- Switzerland
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Synaptotagmin-1 and Doc2b Exhibit Distinct Membrane-Remodeling Mechanisms. Biophys J 2019; 118:643-656. [PMID: 31952804 DOI: 10.1016/j.bpj.2019.12.021] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 12/13/2019] [Accepted: 12/16/2019] [Indexed: 11/24/2022] Open
Abstract
Synaptotagmin-1 (Syt1) is a calcium sensor protein that is critical for neurotransmission and is therefore extensively studied. Here, we use pairs of optically trapped beads coated with SNARE-free synthetic membranes to investigate Syt1-induced membrane remodeling. This activity is compared with that of Doc2b, which contains a conserved C2AB domain and induces membrane tethering and hemifusion in this cell-free model. We find that the soluble C2AB domain of Syt1 strongly affects the probability and strength of membrane-membrane interactions in a strictly Ca2+- and protein-dependent manner. Single-membrane loading of Syt1 yielded the highest probability and force of membrane interactions, whereas in contrast, Doc2b was more effective after loading both membranes. A lipid-mixing assay with confocal imaging reveals that both Syt1 and Doc2b are able to induce hemifusion; however, significantly higher Syt1 concentrations are required. Consistently, both C2AB fragments cause a reduction in the membrane-bending modulus, as measured by a method based on atomic force microscopy. This lowering of the energy required for membrane deformation may contribute to Ca2+-induced fusion.
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50
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Joss D, Häussinger D. Design and applications of lanthanide chelating tags for pseudocontact shift NMR spectroscopy with biomacromolecules. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2019; 114-115:284-312. [PMID: 31779884 DOI: 10.1016/j.pnmrs.2019.08.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 08/21/2019] [Accepted: 08/24/2019] [Indexed: 05/14/2023]
Abstract
In this review, lanthanide chelating tags and their applications to pseudocontact shift NMR spectroscopy as well as analysis of residual dipolar couplings are covered. A complete overview is presented of DOTA-derived and non-DOTA-derived lanthanide chelating tags, critical points in the design of lanthanide chelating tags as appropriate linker moieties, their stability under reductive conditions, e.g., for in-cell applications, the magnitude of the anisotropy transferred from the lanthanide chelating tag to the biomacromolecule under investigation and structural properties, as well as conformational bias of the lanthanide chelating tags are discussed. Furthermore, all DOTA-derived lanthanide chelating tags used for PCS NMR spectroscopy published to date are displayed in tabular form, including their anisotropy parameters, with all employed lanthanide ions, CB-Ln distances and tagging reaction conditions, i.e., the stoichiometry of lanthanide chelating tags, pH, buffer composition, temperature and reaction time. Additionally, applications of lanthanide chelating tags for pseudocontact shifts and residual dipolar couplings that have been reported for proteins, protein-protein and protein-ligand complexes, carbohydrates, carbohydrate-protein complexes, nucleic acids and nucleic acid-protein complexes are presented and critically reviewed. The vast and impressive range of applications of lanthanide chelating tags to structural investigations of biomacromolecules in solution clearly illustrates the significance of this particular field of research. The extension of the repertoire of lanthanide chelating tags from proteins to nucleic acids holds great promise for the determination of valuable structural parameters and further developments in characterizing intermolecular interactions.
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Affiliation(s)
- Daniel Joss
- University of Basel, St. Johanns-Ring 19, 4056 Basel, Switzerland.
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