1
|
Beiter J, Voth GA. Making the cut: Multiscale simulation of membrane remodeling. Curr Opin Struct Biol 2024; 87:102831. [PMID: 38740001 PMCID: PMC11283976 DOI: 10.1016/j.sbi.2024.102831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 04/17/2024] [Accepted: 04/22/2024] [Indexed: 05/16/2024]
Abstract
Biological membranes are dynamic heterogeneous materials, and their shape and organization are tightly coupled to the properties of the proteins in and around them. However, the length scales of lipid and protein dynamics are far below the size of membrane-bound organelles, much less an entire cell. Therefore, multiscale modeling approaches are often necessary to build a comprehensive picture of the interplay of these factors, and have provided critical insights into our understanding of membrane dynamics. Here, we review computational methods for studying membrane remodeling, as well as passive and active examples of protein-driven membrane remodeling. As the field advances towards the modeling of key aspects of organelles and whole cells - an increasingly accessible regime of study - we summarize here recent successes and offer comments on future trends.
Collapse
Affiliation(s)
- Jeriann Beiter
- Department of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA
| | - Gregory A Voth
- Department of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA.
| |
Collapse
|
2
|
Kephart SM, Hom N, Lee KK. Visualizing intermediate stages of viral membrane fusion by cryo-electron tomography. Trends Biochem Sci 2024:S0968-0004(24)00160-9. [PMID: 39054240 DOI: 10.1016/j.tibs.2024.06.012] [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: 03/06/2024] [Revised: 06/07/2024] [Accepted: 06/18/2024] [Indexed: 07/27/2024]
Abstract
Protein-mediated membrane fusion is the dynamic process where specialized protein machinery undergoes dramatic conformational changes that drive two membrane bilayers together, leading to lipid mixing and opening of a fusion pore between previously separate membrane-bound compartments. Membrane fusion is an essential stage of enveloped virus entry that results in viral genome delivery into host cells. Recent studies applying cryo-electron microscopy techniques in a time-resolved fashion provide unprecedented glimpses into the interaction of viral fusion proteins and membranes, revealing fusion intermediate states from the initiation of fusion to release of the viral genome. In combination with complementary structural, biophysical, and computation modeling approaches, these advances are shedding new light on the mechanics and dynamics of protein-mediated membrane fusion.
Collapse
Affiliation(s)
- Sally M Kephart
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, USA
| | - Nancy Hom
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, USA
| | - Kelly K Lee
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, USA; Biological Structure Physics and Design Graduate Program, University of Washington, Seattle, WA, USA.
| |
Collapse
|
3
|
Leitz J, Wang C, Esquivies L, Peters JJ, Gopal N, Pfuetzner RA, Wang AL, Brunger AT. Observing isolated synaptic vesicle association and fusion ex vivo. Nat Protoc 2024:10.1038/s41596-024-01014-x. [PMID: 38956381 DOI: 10.1038/s41596-024-01014-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 05/15/2024] [Indexed: 07/04/2024]
Abstract
Here, we present a protocol for isolating functionally intact glutamatergic synaptic vesicles from whole-mouse brain tissue and using them in a single-vesicle assay to examine their association and fusion with plasma membrane mimic vesicles. This is a Protocol Extension, building on our previous protocol, which used a purely synthetic system comprised of reconstituted proteins in liposomes. We also describe the generation of a peptide based on the vesicular glutamate transporter, which is essential in the isolation process of glutamatergic synaptic vesicles. This method uses easily accessible reagents to generate fusion-competent glutamatergic synaptic vesicles through immunoisolation. The generation of the vGlut peptide can be accomplished in 6 d, while the isolation of the synaptic vesicles by using the peptide can be accomplished in 2 d, with an additional day to fluorescently label the synaptic vesicles for use in a single-vesicle hybrid fusion assay. The single-vesicle fusion assay can be accomplished in 1 d and can unambiguously delineate synaptic vesicle association, dissociation, Ca2+-independent and Ca2+-dependent fusion modalities. This assay grants control of the synaptic vesicle environment while retaining the complexity of the synaptic vesicles themselves. This protocol can be adapted to studies of other types of synaptic vesicles or, more generally, different secretory or transport vesicles. The workflow described here requires expertise in biochemistry techniques, in particular, protein purification and fluorescence imaging. We assume that the laboratory has protein-purification equipment, including chromatography systems.
Collapse
Affiliation(s)
- Jeremy Leitz
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
- Department of Structural Biology, Stanford University, Stanford, CA, USA
- Department of Photon Science, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Chuchu Wang
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
- Department of Structural Biology, Stanford University, Stanford, CA, USA
- Department of Photon Science, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Luis Esquivies
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
- Department of Structural Biology, Stanford University, Stanford, CA, USA
- Department of Photon Science, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - John J Peters
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
- Department of Structural Biology, Stanford University, Stanford, CA, USA
- Department of Photon Science, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Nisha Gopal
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
- Department of Structural Biology, Stanford University, Stanford, CA, USA
- Department of Photon Science, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Richard A Pfuetzner
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
- Department of Structural Biology, Stanford University, Stanford, CA, USA
- Department of Photon Science, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Austin L Wang
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
- Department of Structural Biology, Stanford University, Stanford, CA, USA
- Department of Photon Science, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Axel T Brunger
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA.
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA.
- Department of Structural Biology, Stanford University, Stanford, CA, USA.
- Department of Photon Science, Stanford University, Stanford, CA, USA.
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA.
| |
Collapse
|
4
|
Mitra S, Chandersekhar B, Li Y, Coopershlyak M, Mahoney ME, Evans B, Koenig R, Hall SCL, Klösgen B, Heinrich F, Deslouches B, Tristram-Nagle S. Novel non-helical antimicrobial peptides insert into and fuse lipid model membranes. SOFT MATTER 2024; 20:4088-4101. [PMID: 38712559 PMCID: PMC11109824 DOI: 10.1039/d4sm00220b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 04/26/2024] [Indexed: 05/08/2024]
Abstract
This research addresses the growing menace of antibiotic resistance by exploring antimicrobial peptides (AMPs) as alternatives to conventional antibiotics. Specifically, we investigate two linear amphipathic AMPs, LE-53 (12-mer) and LE-55 (16-mer), finding that the shorter LE-53 exhibits greater bactericidal activity against both Gram-negative (G(-)) and Gram-positive (G(+)) bacteria. Remarkably, both AMPs are non-toxic to eukaryotic cells. The heightened effectiveness of LE-53 is attributed to its increased hydrophobicity (H) compared to LE-55. Circular dichroism (CD) reveals that LE-53 and LE-55 both adopt β-sheet and random coil structures in lipid model membranes (LMMs) mimicking G(-) and G(+) bacteria, so secondary structure is not the cause of the potency difference. X-ray diffuse scattering (XDS) reveals increased lipid chain order in LE-53, a potential key distinction. Additionally, XDS study uncovers a significant link between LE-53's upper hydrocarbon location in G(-) and G(+) LMMs and its efficacy. Neutron reflectometry (NR) confirms the AMP locations determined using XDS. Solution small angle X-ray scattering (SAXS) demonstrates LE-53's ability to induce vesicle fusion in bacterial LMMs without affecting eukaryotic LMMs, offering a promising strategy to combat antibiotic-resistant strains while preserving human cell integrity, whereas LE-55 has a smaller ability to induce fusion.
Collapse
Affiliation(s)
- Saheli Mitra
- Biological Physics Group, Physics Department, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
| | - Bhairavi Chandersekhar
- Biological Physics Group, Physics Department, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
| | - Yunshu Li
- Biological Physics Group, Physics Department, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
| | - Mark Coopershlyak
- Biological Physics Group, Physics Department, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
| | - Margot E Mahoney
- Biological Physics Group, Physics Department, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
| | - Brandt Evans
- Biological Physics Group, Physics Department, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
| | - Rachel Koenig
- Biological Physics Group, Physics Department, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
| | - Stephen C L Hall
- ISIS Neutron and Muon Source, Rutherford Appleton Laboratory, Harwell Campus, Didcot, Oxfordshire, OX11 0QX, UK
| | - Beate Klösgen
- University of Southern Denmark, Dept. Physics, Chemistry & Pharmacy, PhyLife, Campusvej 55, Odense M5230, Denmark
| | - Frank Heinrich
- Biological Physics Group, Physics Department, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
- Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - Berthony Deslouches
- Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Stephanie Tristram-Nagle
- Biological Physics Group, Physics Department, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
| |
Collapse
|
5
|
Li Q, Li Y, Pu Q, Yang H, Du M, Li X, Li Y, Li X. Exposure estimation and neurotoxicity inhibition of dioxins in sensitive populations near domestic waste incineration plant through adverse outcome pathway. JOURNAL OF HAZARDOUS MATERIALS 2024; 469:134066. [PMID: 38522193 DOI: 10.1016/j.jhazmat.2024.134066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 03/09/2024] [Accepted: 03/16/2024] [Indexed: 03/26/2024]
Abstract
The neurotoxicity induced by dioxins has been recognized as a serious concern to sensitive population living near waste incineration plants. However, investigating the intracellular neurotoxicity of dioxin in humans and the corresponding mitigation strategies has been barely studied. Thus, a domestic waste incineration plant was selected in this study to characterize the neurotoxicity risks of sensitive populations by estimating the ratio of dioxin in human cells using membrane structure dynamics simulation; and constructing a complete dioxin neurotoxicity adverse outcome pathway considering the binding process of AhR/ARNT dimer protein and dioxin response element (DRE). Six dioxins with high neurotoxicity risk were identified. According to the composite neurotoxicity risk analysis, the highest composite neurotoxicity risk appeared when the six dioxins were jointly exposed. Dietary schemes were designed using 1/2 partial factor experimental design to mitigate the composite neurotoxicity risk of six dioxins and No. 16 was screened as the optimum combination which can effectively alleviate the composite neurotoxicity risk by 29.52%. Mechanism analysis shows that the interaction between AhR/ARNT dimer protein and DRE was inhibited under the optimal dietary scheme. This study provides theoretical feasibility and reference significance for assessing composite toxicity risks of pollutants and safety mitigation measures for toxic effects.
Collapse
Affiliation(s)
- Qing Li
- College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, China
| | - Yunxiang Li
- College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, China
| | - Qikun Pu
- College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, China
| | - Hao Yang
- College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, China
| | - Meijin Du
- College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, China
| | - Xinao Li
- College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, China
| | - Yu Li
- College of Environmental Science and Engineering, North China Electric Power University, Beijing 102206, China
| | - Xixi Li
- State Key Laboratory of Environmental Criteria and Risk Assessment, National Engineering Laboratory for Lake Pollution Control and Ecological Restoration, State Environmental Protection Key Laboratory for Lake Pollution Control, Chinese Research Academy of Environmental Sciences, Beijing 100012, China; Northern Region Persistent Organic Pollution Control (NRPOP) Laboratory, Faculty of Engineering and Applied Science, Memorial University, St. John's, NL A1B 3×5, Canada.
| |
Collapse
|
6
|
Orlikowska-Rzeznik H, Krok E, Domanska M, Setny P, Lągowska A, Chattopadhyay M, Piatkowski L. Dehydration of Lipid Membranes Drives Redistribution of Cholesterol Between Lateral Domains. J Phys Chem Lett 2024; 15:4515-4522. [PMID: 38634827 PMCID: PMC11056968 DOI: 10.1021/acs.jpclett.4c00332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 03/30/2024] [Accepted: 04/10/2024] [Indexed: 04/19/2024]
Abstract
Cholesterol-rich lipid rafts are found to facilitate membrane fusion, central to processes like viral entry, fertilization, and neurotransmitter release. While the fusion process involves local, transient membrane dehydration, the impact of reduced hydration on cholesterol's structural organization in biological membranes remains unclear. Here, we employ confocal fluorescence microscopy and atomistic molecular dynamics simulations to investigate cholesterol behavior in phase-separated lipid bilayers under controlled hydration. We unveiled that dehydration prompts cholesterol release from raft-like domains into the surrounding fluid phase. Unsaturated phospholipids undergo more significant dehydration-induced structural changes and lose more hydrogen bonds with water than sphingomyelin. The results suggest that cholesterol redistribution is driven by the equalization of biophysical properties between phases and the need to satisfy lipid hydrogen bonds. This underscores the role of cholesterol-phospholipid-water interplay in governing cholesterol affinity for a specific lipid type, providing a new perspective on the regulatory role of cell membrane heterogeneity during membrane fusion.
Collapse
Affiliation(s)
- Hanna Orlikowska-Rzeznik
- Faculty of
Materials Engineering and Technical Physics, Poznan University of Technology, 60-965 Poznan, Poland
| | - Emilia Krok
- Faculty of
Materials Engineering and Technical Physics, Poznan University of Technology, 60-965 Poznan, Poland
| | - Maria Domanska
- Biomolecular
Modelling Group, Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland
| | - Piotr Setny
- Biomolecular
Modelling Group, Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland
| | - Anna Lągowska
- Faculty of
Materials Engineering and Technical Physics, Poznan University of Technology, 60-965 Poznan, Poland
| | - Madhurima Chattopadhyay
- Faculty of
Materials Engineering and Technical Physics, Poznan University of Technology, 60-965 Poznan, Poland
| | - Lukasz Piatkowski
- Faculty of
Materials Engineering and Technical Physics, Poznan University of Technology, 60-965 Poznan, Poland
| |
Collapse
|
7
|
Jahn R, Cafiso DC, Tamm LK. Mechanisms of SNARE proteins in membrane fusion. Nat Rev Mol Cell Biol 2024; 25:101-118. [PMID: 37848589 DOI: 10.1038/s41580-023-00668-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/06/2023] [Indexed: 10/19/2023]
Abstract
Soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs) are a family of small conserved eukaryotic proteins that mediate membrane fusion between organelles and with the plasma membrane. SNAREs are directly or indirectly anchored to membranes. Prior to fusion, complementary SNAREs assemble between membranes with the aid of accessory proteins that provide a scaffold to initiate SNARE zippering, pulling the membranes together and mediating fusion. Recent advances have enabled the construction of detailed models describing bilayer transitions and energy barriers along the fusion pathway and have elucidated the structures of SNAREs complexed in various states with regulatory proteins. In this Review, we discuss how these advances are yielding an increasingly detailed picture of the SNARE-mediated fusion pathway, leading from first contact between the membranes via metastable non-bilayer intermediates towards the opening and expansion of a fusion pore. We describe how SNARE proteins assemble into complexes, how this assembly is regulated by accessory proteins and how SNARE complexes overcome the free energy barriers that prevent spontaneous membrane fusion.
Collapse
Affiliation(s)
- Reinhard Jahn
- Laboratory of Neurobiology, Max-Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
| | - David C Cafiso
- Department of Chemistry, University of Virginia, Charlottesville, VA, USA
| | - Lukas K Tamm
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
| |
Collapse
|
8
|
Lira RB, Hammond JCF, Cavalcanti RRM, Rous M, Riske KA, Roos WH. The underlying mechanical properties of membranes tune their ability to fuse. J Biol Chem 2023; 299:105430. [PMID: 37926280 PMCID: PMC10716014 DOI: 10.1016/j.jbc.2023.105430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 10/16/2023] [Accepted: 10/23/2023] [Indexed: 11/07/2023] Open
Abstract
Membrane fusion is a ubiquitous process associated with a multitude of biological events. Although it has long been appreciated that membrane mechanics plays an important role in membrane fusion, the molecular interplay between mechanics and fusion has remained elusive. For example, although different lipids modulate membrane mechanics differently, depending on their composition, molar ratio, and complex interactions, differing lipid compositions may lead to similar mechanical properties. This raises the question of whether (i) the specific lipid composition or (ii) the average mesoscale mechanics of membranes acts as the determining factor for cellular function. Furthermore, little is known about the potential consequences of fusion on membrane disruption. Here, we use a combination of confocal microscopy, time-resolved imaging, and electroporation to shed light onto the underlying mechanical properties of membranes that regulate membrane fusion. Fusion efficiency follows a nearly universal behavior that depends on membrane fluidity parameters, such as membrane viscosity and bending rigidity, rather than on specific lipid composition. This helps explaining why the charged and fluid membranes of the inner leaflet of the plasma membrane are more fusogenic than their outer counterparts. Importantly, we show that physiological levels of cholesterol, a key component of biological membranes, has a mild effect on fusion but significantly enhances membrane mechanical stability against pore formation, suggesting that its high cellular levels buffer the membrane against disruption. The ability of membranes to efficiently fuse while preserving their integrity may have given evolutionary advantages to cells by enabling their function while preserving membrane stability.
Collapse
Affiliation(s)
- Rafael B Lira
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen, Groningen, Netherlands.
| | - Jayna C F Hammond
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen, Groningen, Netherlands
| | | | - Madelief Rous
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen, Groningen, Netherlands
| | - Karin A Riske
- Departamento de Biofísica, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Wouter H Roos
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen, Groningen, Netherlands.
| |
Collapse
|
9
|
Weichard I, Taschenberger H, Gsell F, Bornschein G, Ritzau-Jost A, Schmidt H, Kittel RJ, Eilers J, Neher E, Hallermann S, Nerlich J. Fully-primed slowly-recovering vesicles mediate presynaptic LTP at neocortical neurons. Proc Natl Acad Sci U S A 2023; 120:e2305460120. [PMID: 37856547 PMCID: PMC10614622 DOI: 10.1073/pnas.2305460120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 08/26/2023] [Indexed: 10/21/2023] Open
Abstract
Pre- and postsynaptic forms of long-term potentiation (LTP) are candidate synaptic mechanisms underlying learning and memory. At layer 5 pyramidal neurons, LTP increases the initial synaptic strength but also short-term depression during high-frequency transmission. This classical form of presynaptic LTP has been referred to as redistribution of synaptic efficacy. However, the underlying mechanisms remain unclear. We therefore performed whole-cell recordings from layer 5 pyramidal neurons in acute cortical slices of rats and analyzed presynaptic function before and after LTP induction by paired pre- and postsynaptic neuronal activity. LTP was successfully induced in about half of the synaptic connections tested and resulted in increased synaptic short-term depression during high-frequency transmission and a decelerated recovery from short-term depression due to an increased fraction of a slow recovery component. Analysis with a recently established sequential two-step vesicle priming model indicates an increase in the abundance of fully-primed and slowly-recovering vesicles. A systematic analysis of short-term plasticity and synapse-to-synapse variability of synaptic strength at various types of synapses revealed that stronger synapses generally recover more slowly from synaptic short-term depression. Finally, pharmacological stimulation of the cyclic adenosine monophosphate and diacylglycerol signaling pathways, which are both known to promote synaptic vesicle priming, mimicked LTP and slowed the recovery from short-term depression. Our data thus demonstrate that LTP at layer 5 pyramidal neurons increases synaptic strength primarily by enlarging a subpool of fully-primed slowly-recovering vesicles.
Collapse
Affiliation(s)
- Iron Weichard
- Faculty of Medicine, Carl-Ludwig-Institute for Physiology, Leipzig University, Leipzig04103, Germany
| | - Holger Taschenberger
- Department of Molecular Neurobiology, Max Planck Institute for Multidisciplinary Sciences, Göttingen37075, Germany
| | - Felix Gsell
- Faculty of Medicine, Carl-Ludwig-Institute for Physiology, Leipzig University, Leipzig04103, Germany
| | - Grit Bornschein
- Faculty of Medicine, Carl-Ludwig-Institute for Physiology, Leipzig University, Leipzig04103, Germany
| | - Andreas Ritzau-Jost
- Faculty of Medicine, Carl-Ludwig-Institute for Physiology, Leipzig University, Leipzig04103, Germany
| | - Hartmut Schmidt
- Faculty of Medicine, Carl-Ludwig-Institute for Physiology, Leipzig University, Leipzig04103, Germany
| | - Robert J. Kittel
- Department of Animal Physiology, Institute of Biology, Leipzig University, Leipzig04103, Germany
| | - Jens Eilers
- Faculty of Medicine, Carl-Ludwig-Institute for Physiology, Leipzig University, Leipzig04103, Germany
| | - Erwin Neher
- Emeritus Laboratory of Membrane Biophysics, Max Planck Institute for Multidisciplinary Sciences, Göttingen37070, Germany
- Cluster of Excellence “Multiscale Bioimaging: From Molecular Machines to Networks of Excitable Cells”, University of Göttingen, Göttingen37073, Germany
| | - Stefan Hallermann
- Faculty of Medicine, Carl-Ludwig-Institute for Physiology, Leipzig University, Leipzig04103, Germany
| | - Jana Nerlich
- Faculty of Medicine, Carl-Ludwig-Institute for Physiology, Leipzig University, Leipzig04103, Germany
| |
Collapse
|
10
|
Shendrik P, Golani G, Dharan R, Schwarz US, Sorkin R. Membrane Tension Inhibits Lipid Mixing by Increasing the Hemifusion Stalk Energy. ACS NANO 2023; 17:18942-18951. [PMID: 37669531 PMCID: PMC7615193 DOI: 10.1021/acsnano.3c04293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Accepted: 08/23/2023] [Indexed: 09/07/2023]
Abstract
Fusion of biological membranes is fundamental in various physiological events. The fusion process involves several intermediate stages with energy barriers that are tightly dependent on the mechanical and physical properties of the system, one of which is membrane tension. As previously established, the late stages of fusion, including hemifusion diaphragm and pore expansions, are favored by membrane tension. However, a current understanding of how the energy barrier of earlier fusion stages is affected by membrane tension is lacking. Here, we apply a newly developed experimental approach combining micropipette-aspirated giant unilamellar vesicles and optically trapped membrane-coated beads, revealing that membrane tension inhibits lipid mixing. We show that lipid mixing is 6 times slower under a tension of 0.12 mN/m compared with tension-free membranes. Furthermore, using continuum elastic theory, we calculate the dependence of the hemifusion stalk formation energy on membrane tension and intermembrane distance and find the increase in the corresponding energy barrier to be 1.6 kBT in our setting, which can explain the increase in lipid mixing time delay. Finally, we show that tension can be a significant factor in the stalk energy if the pre-fusion intermembrane distance is on the order of several nanometers, while for membranes that are tightly docked, tension has a negligible effect.
Collapse
Affiliation(s)
- Petr Shendrik
- School
of Chemistry, Raymond & Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, 6997801, Israel
- Center
of Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Gonen Golani
- Institute
for Theoretical Physics and BioQuant Center for Quantitative Biology, Heidelberg University, 69120, Heidelberg, Germany
| | - Raviv Dharan
- School
of Chemistry, Raymond & Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, 6997801, Israel
- Center
of Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Ulrich S. Schwarz
- Institute
for Theoretical Physics and BioQuant Center for Quantitative Biology, Heidelberg University, 69120, Heidelberg, Germany
| | - Raya Sorkin
- School
of Chemistry, Raymond & Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, 6997801, Israel
- Center
of Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv, 6997801, Israel
| |
Collapse
|
11
|
Stanton AE, Hughson FM. The machinery of vesicle fusion. Curr Opin Cell Biol 2023; 83:102191. [PMID: 37421936 PMCID: PMC10529041 DOI: 10.1016/j.ceb.2023.102191] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 06/01/2023] [Accepted: 06/07/2023] [Indexed: 07/10/2023]
Abstract
The compartmentalization of eukaryotic cells is reliant on the fidelity of vesicle-mediated intracellular transport. Vesicles deliver their cargo via membrane fusion, a process requiring membrane tethers, Sec1/Munc18 (SM) proteins, and SNAREs. These components function in concert to ensure that membrane fusion is efficient and accurate, but the mechanisms underlying their cooperative action are still in many respects mysterious. In this brief review, we highlight recent progress toward a more integrative understanding of the vesicle fusion machinery. We focus particular attention on cryo-electron microscopy structures of intact multisubunit tethers in complex with SNAREs or SM proteins, as well as a structure of an SM protein bound to multiple SNAREs. The insights gained from this work emphasize the advantages of studying the fusion machinery intact and in context.
Collapse
Affiliation(s)
- Abigail E Stanton
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Frederick M Hughson
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.
| |
Collapse
|
12
|
Miyajima A, Nakao H, Ikeda K, Nakano M. The Nanometer-Scale Proximity of Bilayers Facilitates Intermembrane Lipid Transfer. J Phys Chem Lett 2023; 14:4172-4178. [PMID: 37114850 DOI: 10.1021/acs.jpclett.3c00154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Biological membranes approach one another in various biological phenomena, such as lipid transport at membrane contact sites and membrane fusion. The proximity of two bilayers may cause environmental changes in the interbilayer space and alter the dynamics of lipid molecules. Here, we investigate the structure and dynamics of vesicles aggregated due to the depletion attraction caused by polyethylene glycol (PEG) through static and dynamic small-angle neutron scattering. Manipulation of the interbilayer distance using PEG-conjugated lipids reveals that lipid molecules rapidly transfer between vesicles when the opposing bilayers are within ∼2 nm of each other. This distance corresponds to a region in which water molecules are more structured than in bulk water. Kinetic analysis suggests that the decrease in water entropy is responsible for the progression of lipid transfer. These results provide a basis for understanding the dynamic function of biomembranes in confined regions.
Collapse
Affiliation(s)
- Ayari Miyajima
- Department of Biointerface Chemistry, Faculty of Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Hiroyuki Nakao
- Department of Biointerface Chemistry, Faculty of Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Keisuke Ikeda
- Department of Biointerface Chemistry, Faculty of Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| | - Minoru Nakano
- Department of Biointerface Chemistry, Faculty of Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
| |
Collapse
|
13
|
Beck K, Nandy J, Hoernke M. Membrane permeabilization can be crucially biased by a fusogenic lipid composition - leaky fusion caused by antimicrobial peptides in model membranes. SOFT MATTER 2023; 19:2919-2931. [PMID: 37010846 DOI: 10.1039/d2sm01691e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Induced membrane permeabilization or leakage is often taken as an indication for activity of membrane-active molecules, such as antimicrobial peptides (AMPs). The exact leakage mechanism is often unknown, but important, because certain mechanisms might actually contribute to microbial killing, while others are unselective, or potentially irrelevant in an in vivo situation. Using an antimicrobial example peptide (cR3W3), we illustrate one of the potentially misleading leakage mechanisms: leaky fusion, where leakage is coupled to membrane fusion. Like many others, we examine peptide-induced leakage in model vesicles consisting of binary mixtures of anionic and zwitterionic phospholipids. In fact, phosphatidylglycerol and phosphatidylethanolamine (PG/PE) are supposed to reflect bacterial membranes, but exhibit a high propensity for vesicle aggregation and fusion. We describe the implications of this vesicle fusion and aggregation for the reliability of model studies. The ambiguous role of the relatively fusogenic PE-lipids becomes clear as leakage decreases significantly when aggregation and fusion are prevented by sterical shielding. Furthermore, the mechanism of leakage changes if PE is exchanged for phosphatidylcholine (PC). We thus point out that the lipid composition of model membranes can be biased towards leaky fusion. This can lead to discrepancies between model studies and activity in true microbes, because leaky fusion is likely prevented by bacterial peptidoglycan layers. In conclusion, choosing the model membrane might implicate the type of effect (here leakage mechanism) that is observed. In the worst case, as with leaky fusion of PG/PE vesicles, this is not directly relevant for the intended antimicrobial application.
Collapse
Affiliation(s)
- Katharina Beck
- Chemistry and Pharmacy, Albert-Ludwigs-Universität, Freiburg i. Br., Germany.
| | - Janina Nandy
- Chemistry and Pharmacy, Albert-Ludwigs-Universität, Freiburg i. Br., Germany.
| | - Maria Hoernke
- Chemistry and Pharmacy, Albert-Ludwigs-Universität, Freiburg i. Br., Germany.
| |
Collapse
|
14
|
Karmacharya M, Kumar S, Cho YK. Tuning the Extracellular Vesicles Membrane through Fusion for Biomedical Applications. J Funct Biomater 2023; 14:jfb14020117. [PMID: 36826916 PMCID: PMC9960107 DOI: 10.3390/jfb14020117] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 02/14/2023] [Accepted: 02/16/2023] [Indexed: 02/22/2023] Open
Abstract
Membrane fusion is one of the key phenomena in the living cell for maintaining the basic function of life. Extracellular vesicles (EVs) have the ability to transfer information between cells through plasma membrane fusion, making them a promising tool in diagnostics and therapeutics. This study explores the potential applications of natural membrane vesicles, EVs, and their fusion with liposomes, EVs, and cells and introduces methodologies for enhancing the fusion process. EVs have a high loading capacity, bio-compatibility, and stability, making them ideal for producing effective drugs and diagnostics. The unique properties of fused EVs and the crucial design and development procedures that are necessary to realize their potential as drug carriers and diagnostic tools are also examined. The promise of EVs in various stages of disease management highlights their potential role in future healthcare.
Collapse
Affiliation(s)
- Mamata Karmacharya
- Center for Soft and Living Matter, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
- Department of Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Sumit Kumar
- Center for Soft and Living Matter, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Correspondence: (S.K.); (Y.-K.C.)
| | - Yoon-Kyoung Cho
- Center for Soft and Living Matter, Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Correspondence: (S.K.); (Y.-K.C.)
| |
Collapse
|
15
|
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.
Collapse
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.
| |
Collapse
|
16
|
Shi S, Fan H, Hoernke M. Leaky membrane fusion: an ambivalent effect induced by antimicrobial polycations. NANOSCALE ADVANCES 2022; 4:5109-5122. [PMID: 36504745 PMCID: PMC9680940 DOI: 10.1039/d2na00464j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 10/24/2022] [Indexed: 05/28/2023]
Abstract
Both antimicrobial peptides and their synthetic mimics are potential alternatives to classical antibiotics. They can induce several membrane perturbations including permeabilization. Especially in model studies, aggregation of vesicles by such polycations is often reported. Here, we show that unintended vesicle aggregation or indeed fusion can cause apparent leakage in model studies that is not possible in most microbes, thus potentially leading to misinterpretations. The interactions of a highly charged and highly selective membrane-active polycation with negatively charged phosphatidylethanolamine/phosphatidylglycerol (PE/PG) vesicles are studied by a combination of biophysical methods. At low polycation concentrations, apparent vesicle aggregation was found to involve exchange of lipids. Upon neutralization of the negatively charged vesicles by the polycation, full fusion and leakage occurred and leaky fusion is suspected. To elucidate the interplay of leakage and fusion, we prevented membrane contacts by decorating the vesicles with PEG-chains. This inhibited fusion and also leakage activity. Leaky fusion is further corroborated by increased leakage with increasing likeliness of vesicle-vesicle contacts. Because of its similar appearance to other leakage mechanisms, leaky fusion is difficult to identify and might be overlooked and more common amongst polycationic membrane-active compounds. Regarding biological activity, leaky fusion needs to be carefully distinguished from other membrane permeabilization mechanisms, as it may be less relevant to bacteria, but potentially relevant for fungi. Furthermore, leaky fusion is an interesting effect that could help in endosomal escape for drug delivery. A comprehensive step-by-step protocol for membrane permeabilization/vesicle leakage using calcein fluorescence lifetime is provided in the ESI.
Collapse
Affiliation(s)
- Shuai Shi
- Chemistry and Pharmacy, Albert-Ludwigs-Universität 79104 Freiburg i.Br. Germany
| | - Helen Fan
- Leslie Dan Faculty of Pharmacy, University of Toronto Toronto Canada
| | - Maria Hoernke
- Chemistry and Pharmacy, Albert-Ludwigs-Universität 79104 Freiburg i.Br. Germany
| |
Collapse
|
17
|
Coffman RE, Kraichely KN, Kreutzberger AJB, Kiessling V, Tamm LK, Woodbury DJ. Drunken lipid membranes, not drunken SNARE proteins, promote fusion in a model of neurotransmitter release. Front Mol Neurosci 2022; 15:1022756. [PMID: 36311016 PMCID: PMC9614348 DOI: 10.3389/fnmol.2022.1022756] [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: 08/18/2022] [Accepted: 09/20/2022] [Indexed: 11/29/2022] Open
Abstract
Alcohol affects many neuronal proteins that are upstream or down-stream of synaptic vesicle fusion and neurotransmitter release. Less well studied is alcohol’s effect on the fusion machinery including SNARE proteins and lipid membranes. Using a SNARE-driven fusion assay we show that fusion probability is significantly increased at 0.4% v/v (68 mM) ethanol; but not with methanol up to 10%. Ethanol appears to act directly on membrane lipids since experiments focused on protein properties [circular dichroism spectrometry, site-directed fluorescence interference contrast (sdFLIC) microscopy, and vesicle docking results] showed no significant changes up to 5% ethanol, but a protein-free fusion assay also showed increased lipid membrane fusion rates with 0.4% ethanol. These data show that the effects of high physiological doses of ethanol on SNARE-driven fusion are mediated through ethanol’s interaction with the lipid bilayer of membranes and not SNARE proteins, and that methanol affects lipid membranes and SNARE proteins only at high doses.
Collapse
Affiliation(s)
- Robert E. Coffman
- Neuroscience Center, Brigham Young University, Provo, UT, United States
| | - Katelyn N. Kraichely
- Department of Molecular Physiology and Biological Physics, University of Virginia Health System, Charlottesville, VA, United States
| | - Alex J. B. Kreutzberger
- Department of Molecular Physiology and Biological Physics, University of Virginia Health System, Charlottesville, VA, United States
| | - Volker Kiessling
- Department of Molecular Physiology and Biological Physics, University of Virginia Health System, Charlottesville, VA, United States
| | - Lukas K. Tamm
- Department of Molecular Physiology and Biological Physics, University of Virginia Health System, Charlottesville, VA, United States
| | - Dixon J. Woodbury
- Neuroscience Center, Brigham Young University, Provo, UT, United States
- Department of Cell Biology and Physiology, Brigham Young University, Provo, UT, United States
- *Correspondence: Dixon J. Woodbury,
| |
Collapse
|
18
|
Mangala Prasad V, Blijleven JS, Smit JM, Lee KK. Visualization of conformational changes and membrane remodeling leading to genome delivery by viral class-II fusion machinery. Nat Commun 2022; 13:4772. [PMID: 35970990 PMCID: PMC9378758 DOI: 10.1038/s41467-022-32431-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 07/31/2022] [Indexed: 11/09/2022] Open
Abstract
Chikungunya virus (CHIKV) is a human pathogen that delivers its genome to the host cell cytoplasm through endocytic low pH-activated membrane fusion mediated by class-II fusion proteins. Though structures of prefusion, icosahedral CHIKV are available, structural characterization of virion interaction with membranes has been limited. Here, we have used cryo-electron tomography to visualize CHIKV's complete membrane fusion pathway, identifying key intermediary glycoprotein conformations coupled to membrane remodeling events. Using sub-tomogram averaging, we elucidate features of the low pH-exposed virion, nucleocapsid and full-length E1-glycoprotein's post-fusion structure. Contrary to class-I fusion systems, CHIKV achieves membrane apposition by protrusion of extended E1-glycoprotein homotrimers into the target membrane. The fusion process also features a large hemifusion diaphragm that transitions to a wide pore for intact nucleocapsid delivery. Our analyses provide comprehensive ultrastructural insights into the class-II virus fusion system function and direct mechanistic characterization of the fundamental process of protein-mediated membrane fusion.
Collapse
Affiliation(s)
- Vidya Mangala Prasad
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, USA.,Molecular Biophysics Unit, Indian Institute of Science, Bengaluru, Karnataka, India
| | - Jelle S Blijleven
- Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands
| | - Jolanda M Smit
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Kelly K Lee
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, USA. .,Biological Physics, Structure and Design Graduate Program, University of Washington, Seattle, WA, USA. .,Department of Microbiology, University of Washington, Seattle, WA, USA.
| |
Collapse
|
19
|
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.
Collapse
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
| |
Collapse
|
20
|
Kusick GF, Ogunmowo TH, Watanabe S. Transient docking of synaptic vesicles: Implications and mechanisms. Curr Opin Neurobiol 2022; 74:102535. [PMID: 35398664 PMCID: PMC9167714 DOI: 10.1016/j.conb.2022.102535] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 02/19/2022] [Accepted: 03/06/2022] [Indexed: 02/03/2023]
Abstract
As synaptic vesicles fuse, they must continually be replaced with new docked, fusion-competent vesicles to sustain neurotransmission. It has long been appreciated that vesicles are recruited to docking sites in an activity-dependent manner. However, once entering the sites, vesicles were thought to be stably docked, awaiting calcium signals. Based on recent data from electrophysiology, electron microscopy, biochemistry, and computer simulations, a picture emerges in which vesicles can rapidly and reversibly transit between docking and undocking during activity. This "transient docking" can account for many aspects of synaptic physiology. In this review, we cover recent evidence for transient docking, physiological processes at the synapse that it may support, and progress on the underlying mechanisms. We also discuss an open question: what determines for how long and whether vesicles stay docked, or eventually undock?
Collapse
Affiliation(s)
- Grant F Kusick
- Department of Cell Biology, Johns Hopkins University, School of Medicine, 725 N Wolfe St., Baltimore, MD 21287, USA; Biochemistry, Cellular and Molecular Biology Graduate Program, Johns Hopkins University, School of Medicine, 1830 E. Monument St., Baltimore, MD 21287, USA. https://twitter.com/@ultrafastgrant
| | - Tyler H Ogunmowo
- Department of Cell Biology, Johns Hopkins University, School of Medicine, 725 N Wolfe St., Baltimore, MD 21287, USA; Biochemistry, Cellular and Molecular Biology Graduate Program, Johns Hopkins University, School of Medicine, 1830 E. Monument St., Baltimore, MD 21287, USA. https://twitter.com/@unculturedTy
| | - Shigeki Watanabe
- Department of Cell Biology, Johns Hopkins University, School of Medicine, 725 N Wolfe St., Baltimore, MD 21287, USA; Solomon H. Snyder Department of Neuroscience, Johns Hopkins University, School of Medicine, 725 N Wolfe St., Baltimore, MD 21287, USA.
| |
Collapse
|
21
|
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.
Collapse
Affiliation(s)
- Josep Rizo
- Departments of Biophysics, Biochemistry, and Pharmacology, University of Texas Southwestern Medical Center, Dallas, Texas, USA;
| |
Collapse
|
22
|
Mittal A, Chauhan A. Aspects of Biological Replication and Evolution Independent of the Central Dogma: Insights from Protein-Free Vesicular Transformations and Protein-Mediated Membrane Remodeling. J Membr Biol 2022; 255:185-209. [PMID: 35333977 PMCID: PMC8951669 DOI: 10.1007/s00232-022-00230-4] [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: 01/22/2022] [Accepted: 03/06/2022] [Indexed: 11/21/2022]
Abstract
Biological membrane remodeling is central to living systems. In spite of serving as “containers” of whole-living systems and functioning as dynamic compartments within living systems, biological membranes still find a “blue collar” treatment compared to the “white collar” nucleic acids and proteins in biology. This may be attributable to the fact that scientific literature on biological membrane remodeling is only 50 years old compared to ~ 150 years of literature on proteins and a little less than 100 years on nucleic acids. However, recently, evidence for symbiotic origins of eukaryotic cells from data only on biological membranes was reported. This, coupled with appreciation of reproducible amphiphilic self-assemblies in aqueous environments (mimicking replication), has already initiated discussions on origins of life beyond nucleic acids and proteins. This work presents a comprehensive compilation and meta-analyses of data on self-assembly and vesicular transformations in biological membranes—starting from model membranes to establishment of Influenza Hemagglutinin-mediated membrane fusion as a prototypical remodeling system to a thorough comparison between enveloped mammalian viruses and cellular vesicles. We show that viral membrane fusion proteins, in addition to obeying “stoichiometry-driven protein folding”, have tighter compositional constraints on their amino acid occurrences than general-structured proteins, regardless of type/class. From the perspective of vesicular assemblies and biological membrane remodeling (with and without proteins) we find that cellular vesicles are quite different from viruses. Finally, we propose that in addition to pre-existing thermodynamic frameworks, kinetic considerations in de novo formation of metastable membrane structures with available “third-party” constituents (including proteins) were not only crucial for origins of life but also continue to offer morphological replication and/or functional mechanisms in modern life forms, independent of the central dogma.
Collapse
Affiliation(s)
- Aditya Mittal
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi (IIT Delhi), Hauz Khas, New Delhi, 110016, India. .,Supercomputing Facility for Bioinformatics and Computational Biology (SCFBio), IIT Delhi, Hauz Khas, New Delhi, 110016, India.
| | - Akanksha Chauhan
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi (IIT Delhi), Hauz Khas, New Delhi, 110016, India
| |
Collapse
|
23
|
Tuerkova A, Kasson PM. Computational methods to study enveloped viral entry. Biochem Soc Trans 2021; 49:2527-2537. [PMID: 34783344 PMCID: PMC10184508 DOI: 10.1042/bst20210190] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 10/25/2021] [Accepted: 10/27/2021] [Indexed: 12/15/2022]
Abstract
The protein-membrane interactions that mediate viral infection occur via loosely ordered, transient assemblies, creating challenges for high-resolution structure determination. Computational methods and in particular molecular dynamics simulation have thus become important adjuncts for integrating experimental data, developing mechanistic models, and suggesting testable hypotheses regarding viral function. However, the large molecular scales of virus-host interaction also create challenges for detailed molecular simulation. For this reason, continuum membrane models have played a large historical role, although they have become less favored for high-resolution models of protein assemblies and lipid organization. Here, we review recent progress in the field, with an emphasis on the insight that has been gained using a mixture of coarse-grained and atomic-resolution molecular dynamics simulations. Based on successes and challenges to date, we suggest a multiresolution strategy that should yield the best mixture of computational efficiency and physical fidelity. This strategy may facilitate further simulations of viral entry by a broader range of viruses, helping illuminate the diversity of viral entry strategies and the essential common elements that can be targeted for antiviral therapies.
Collapse
Affiliation(s)
- Alzbeta Tuerkova
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala 75124, Sweden
| | - Peter M Kasson
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala 75124, Sweden
- Departments of Molecular Physiology and Biomedical Engineering, University of Virginia, Charlottesville, VA 22908, U.S.A
| |
Collapse
|