1
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Mishra S, Chakraborty H. Phosphatidylethanolamine and Cholesterol Promote Hemifusion Formation: A Tug of War between Membrane Interfacial Order and Intrinsic Negative Curvature of Lipids. J Phys Chem B 2023; 127:7721-7729. [PMID: 37644708 DOI: 10.1021/acs.jpcb.3c04489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Membrane fusion is an important process for the survival of eukaryotes. The shape of lipids plays an important role in fusion by stabilizing nonlamellar fusion intermediates. Lipids with intrinsic positive curvature such as lysophosphatidylcholine and others inhibit hemifusion formation, whereas lipids having intrinsic negative curvature, e.g., phosphatidylethanolamine and cholesterol (CH), are known to promote hemifusion formation. In this work, we have measured the effect of dioleoylphosphatidylethanolamine (DOPE) and CH on the depth-dependent organization, dynamics, and fusion of dioleoylphosphatidylcholine membranes. Both DOPE and CH promote hemifusion formation despite their ability to order the interfacial and acyl chain region of the membrane and block water percolation at these regions. Generally, membrane ordering and inhibition of water percolation at the acyl chain region are detrimental to membrane fusion. This clearly emphasizes the importance of intrinsic negative curvature of lipids in membrane fusion. Interestingly, DOPE and CH show differential effects on the rate of hemifusion formation, which might be owing to their ability to induce order at the interfacial region and intrinsic negative curvature. Overall, our result is significant in understanding the role of lipidic shape in membrane fusion.
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Affiliation(s)
- Smruti Mishra
- School of Chemistry, Sambalpur University, Jyoti Vihar, Burla 768 019, Odisha, India
| | - Hirak Chakraborty
- School of Chemistry, Sambalpur University, Jyoti Vihar, Burla 768 019, Odisha, India
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2
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Li Z, Wang J, O’Hagan MP, Huang F, Xia F, Willner I. Dynamic Fusion of Nucleic Acid Functionalized Nano-/Micro-Cell-Like Containments: From Basic Concepts to Applications. ACS NANO 2023; 17:15308-15327. [PMID: 37549398 PMCID: PMC10448756 DOI: 10.1021/acsnano.3c04415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 08/01/2023] [Indexed: 08/09/2023]
Abstract
Membrane fusion processes play key roles in biological transformations, such as endocytosis/exocytosis, signal transduction, neurotransmission, or viral infections, and substantial research efforts have been directed to emulate these functions by artificial means. The recognition and dynamic reconfiguration properties of nucleic acids provide a versatile means to induce membrane fusion. Here we address recent advances in the functionalization of liposomes or membranes with structurally engineered lipidated nucleic acids guiding the fusion of cell-like containments, and the biophysical and chemical parameters controlling the fusion of the liposomes will be discussed. Intermembrane bridging by duplex or triplex nucleic acids and light-induced activation of membrane-associated nucleic acid constituents provide the means for spatiotemporal fusion of liposomes or nucleic acid modified liposome fusion with native cell membranes. The membrane fusion processes lead to exchange of loads in the fused containments and are a means to integrate functional assemblies. This is exemplified with the operation of biocatalytic cascades and dynamic DNA polymerization/nicking or transcription machineries in fused protocell systems. Membrane fusion processes of protocell assemblies are found to have important drug-delivery, therapeutic, sensing, and biocatalytic applications. The future challenges and perspectives of DNA-guided fused containments and membranes are addressed.
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Affiliation(s)
- Zhenzhen Li
- The
Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Jianbang Wang
- The
Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Michael P. O’Hagan
- The
Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Fujian Huang
- State
Key Laboratory of Biogeology and Environmental Geology, Engineering
Research Center of Nano-Geomaterials of Ministry of Education, Faculty
of Materials Science and Chemistry, China
University of Geosciences, Wuhan 430074, People’s Republic of China
| | - Fan Xia
- State
Key Laboratory of Biogeology and Environmental Geology, Engineering
Research Center of Nano-Geomaterials of Ministry of Education, Faculty
of Materials Science and Chemistry, China
University of Geosciences, Wuhan 430074, People’s Republic of China
| | - Itamar Willner
- The
Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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3
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Joardar A, Chakraborty H. Differential Behavior of Eicosapentaenoic and Docosahexaenoic Acids on the Organization, Dynamics, and Fusion of Homogeneous and Heterogeneous Membranes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:4439-4449. [PMID: 36931902 DOI: 10.1021/acs.langmuir.3c00119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Membrane fusion is a common course in innumerable biological processes that helps in the survival of eukaryotes. Enveloped viruses utilize this process to enter the host cells. Generally, the membrane lipid compositions play an important role in membrane fusion by modulating the membrane's physical properties and the behavior of membrane proteins in the cellular milieu. In this work, we have demonstrated the role of polyunsaturated fatty acids (PUFAs), such as eicosapentaenoic (EPA) and docosahexaenoic (DHA) acids, on the organization, dynamics, and fusion of homogeneous and heterogeneous membranes. We have exploited arrays of steady-state and time-resolved fluorescence spectroscopic methods and polyethylene glycol-induced membrane fusion assay to elucidate the behavior of EPA and DHA on dioleoyl phosphatidylcholine (DOPC)/cholesterol (CH) homogeneous and DOPC/sphingomyelin/CH heterogeneous membranes. Our results suggest that EPA and DHA display differential effects on two different membranes. The effects of PUFAs in homogeneous membranes are majorly attributed to their flexible chain dynamics, whereas the ability of PUFA-induced cholesterol transfer from the lo to the ld phase rules their behavior in heterogeneous membranes. Overall, our results provide detailed information on the effect of PUFAs on homogeneous and heterogeneous membranes.
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Affiliation(s)
- Ankita Joardar
- School of Chemistry, Sambalpur University, Jyoti Vihar, Burla, Odisha 768 019, India
| | - Hirak Chakraborty
- School of Chemistry, Sambalpur University, Jyoti Vihar, Burla, Odisha 768 019, India
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4
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Shekunov EV, Zlodeeva PD, Efimova SS, Muryleva AA, Zarubaev VV, Slita AV, Ostroumova OS. Cyclic lipopeptides as membrane fusion inhibitors against SARS-CoV-2: New tricks for old dogs. Antiviral Res 2023; 212:105575. [PMID: 36868316 PMCID: PMC9977712 DOI: 10.1016/j.antiviral.2023.105575] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 02/25/2023] [Accepted: 02/28/2023] [Indexed: 03/05/2023]
Abstract
With the resurgence of the coronavirus pandemic, the repositioning of FDA-approved drugs against coronovirus and finding alternative strategies for antiviral therapy are both important. We previously identified the viral lipid envelope as a potential target for the prevention and treatment of SARS-CoV-2 infection with plant alkaloids (Shekunov et al., 2021). Here, we investigated the effects of eleven cyclic lipopeptides (CLPs), including well-known antifungal and antibacterial compounds, on the liposome fusion triggered by calcium, polyethylene glycol 8000, and a fragment of SARS-CoV-2 fusion peptide (816-827) by calcein release assays. Differential scanning microcalorimetry of the gel-to-liquid-crystalline and lamellar-to-inverted hexagonal phase transitions and confocal fluorescence microscopy demonstrated the relation of the fusion inhibitory effects of CLPs to alterations in lipid packing, membrane curvature stress and domain organization. The antiviral effects of CLPs were evaluated in an in vitro Vero-based cell model, and aculeacin A, anidulafugin, iturin A, and mycosubtilin attenuated the cytopathogenicity of SARS-CoV-2 without specific toxicity.
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Affiliation(s)
- Egor V Shekunov
- Institute of Cytology of Russian Academy of Sciences, Tikhoretsky 4, 194064, Saint Petersburg, Russia
| | - Polina D Zlodeeva
- Institute of Cytology of Russian Academy of Sciences, Tikhoretsky 4, 194064, Saint Petersburg, Russia
| | - Svetlana S Efimova
- Institute of Cytology of Russian Academy of Sciences, Tikhoretsky 4, 194064, Saint Petersburg, Russia
| | - Anna A Muryleva
- Institute of Cytology of Russian Academy of Sciences, Tikhoretsky 4, 194064, Saint Petersburg, Russia; Saint-Petersburg Pasteur Institute of Epidemiology and Microbiology, Mira 14, 197101, Saint Petersburg, Russia
| | - Vladimir V Zarubaev
- Saint-Petersburg Pasteur Institute of Epidemiology and Microbiology, Mira 14, 197101, Saint Petersburg, Russia
| | - Alexander V Slita
- Saint-Petersburg Pasteur Institute of Epidemiology and Microbiology, Mira 14, 197101, Saint Petersburg, Russia
| | - Olga S Ostroumova
- Institute of Cytology of Russian Academy of Sciences, Tikhoretsky 4, 194064, Saint Petersburg, Russia.
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5
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Ko TH, Chen YF. Correlation between the In-Plane Critical Behavior and Out-of-Plane Interaction of Ternary Lipid Membranes. MEMBRANES 2022; 13:6. [PMID: 36676813 PMCID: PMC9860714 DOI: 10.3390/membranes13010006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 12/15/2022] [Accepted: 12/16/2022] [Indexed: 06/17/2023]
Abstract
Liquid-liquid phase-separating lipid membranes belong to the 2-D Ising universality class. While their in-plane critical behaviors are well studied, how the behaviors modulate out-of-plane interactions is rarely explored, despite its profound implications for biomembranes and 2-D ferromagnets. Here, we examine how the interlayer interaction, manifested as membrane fusion, is affected by the membranes' critical fluctuations. Remarkably, the critical fluctuations suppress membrane fusion, suggesting a correlation between critical behaviors and interlayer interactions for 2-D Ising systems.
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6
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Paez-Perez M, Russell IA, Cicuta P, Di Michele L. Modulating membrane fusion through the design of fusogenic DNA circuits and bilayer composition. SOFT MATTER 2022; 18:7035-7044. [PMID: 36000473 PMCID: PMC9516350 DOI: 10.1039/d2sm00863g] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 08/17/2022] [Indexed: 06/15/2023]
Abstract
Membrane fusion is a ubiquitous phenomenon linked to many biological processes, and represents a crucial step in liposome-based drug delivery strategies. The ability to control, ever more precisely, membrane fusion pathways would thus be highly valuable for next generation nano-medical solutions and, more generally, the design of advanced biomimetic systems such as synthetic cells. In this article, we present fusogenic nanostructures constructed from synthetic DNA which, different from previous solutions, unlock routes for modulating the rate of fusion and making it conditional to the presence of soluble DNA molecules, thus demonstrating how membrane fusion can be controlled through simple DNA-based molecular circuits. We then systematically explore the relationship between lipid-membrane composition, its biophysical properties, and measured fusion efficiency, linking our observations to the stability of transition states in the fusion pathway. Finally, we observe that specific lipid compositions lead to the emergence of complex bilayer architectures in the fusion products, such as nested morphologies, which are accompanied by alterations in biophysical behaviour. Our findings provide multiple, orthogonal strategies to program lipid-membrane fusion, which leverage the design of either the fusogenic DNA constructs or the physico/chemical properties of the membranes, and could thus be valuable in applications where some design parameters are constrained by other factors such as material cost and biocompatibility, as it is often the case in biotechnological applications.
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Affiliation(s)
- Miguel Paez-Perez
- Molecular Sciences Research Hub, Department of Chemistry, Imperial College London, Wood Lane, London, W12 0BZ, UK.
- fabriCELL, Imperial College London, Wood Lane, London, W12 0BZ, UK
| | - I Alasdair Russell
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | - Pietro Cicuta
- Biological and Soft Systems, Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, UK.
| | - Lorenzo Di Michele
- Molecular Sciences Research Hub, Department of Chemistry, Imperial College London, Wood Lane, London, W12 0BZ, UK.
- fabriCELL, Imperial College London, Wood Lane, London, W12 0BZ, UK
- Biological and Soft Systems, Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, UK.
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7
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Meers PR. Membrane Organization Strategies in Vesicular Antibiotic Delivery. J Membr Biol 2022; 255:523-535. [PMID: 35018488 DOI: 10.1007/s00232-021-00210-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 12/06/2021] [Indexed: 01/08/2023]
Abstract
Small molecule antibiotics are often derived from microorganisms that thrive in competitive environments. Their importance as therapeutics for infectious disease in humans has been established over many years. It has now become clear that antibiotic-producing organisms use packaging and delivery in the form of vesicles in many cases. A similar strategy has evolved in recent decades in the pharmaceutical industry for formulation of antibiotic therapies. The top-down approach that has evolved over millions of years in various micro-organisms has generated complex, efficient delivery systems that we are just now beginning to understand. The bottom-up formulation approach involves simple, safe compositions, which are being continually enhanced by trying to add features of which the natural systems inform us. A comparison is made here of these paradigms. Despite the differences, there are a number of common features in the basic physical and biological requirements that must be satisfied. In this review, illustration and comparison of some of these requirements is given, demonstrating the ongoing challenges in this area of research.
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Affiliation(s)
- Paul R Meers
- Department of Plant Biology, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, NJ, USA.
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8
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Wei C, Pohorille A. Fast bilayer-micelle fusion mediated by hydrophobic dipeptides. Biophys J 2021; 120:2330-2342. [PMID: 33887225 DOI: 10.1016/j.bpj.2021.04.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 03/15/2021] [Accepted: 04/02/2021] [Indexed: 11/30/2022] Open
Abstract
To understand the transition from inanimate matter to life, we studied a process that directly couples simple metabolism to evolution via natural selection, demonstrated experimentally by Adamala and Szostak. In this process, dipeptides synthesized inside precursors of cells promote absorption of fatty acid micelles to vesicles, inducing their preferential growth and division at the expense of other vesicles. The process is explained on the basis of coarse-grained molecular dynamics simulations, each extending for tens of microseconds, carried out to model fusion between a micelle and a membrane, both made of fatty acids in the absence and presence of hydrophobic dipeptides. In all systems with dipeptides, but not in their absence, fusion events were observed. They involve the formation of a stalk made by hydrophobic chains from the micelle and the membrane, similar to that postulated for vesicle-vesicle fusion. The emergence of a stalk is facilitated by transient clusters of dipeptides, side chains of which form hydrophobic patches at the membrane surface. Committor probability calculations indicate that the size of a patch is a suitable reaction coordinate and allows for identifying the transition state for fusion. Free-energy barrier to fusion is greatly reduced in the presence of dipeptides to only 4-5 kcal/mol, depending on the hydrophobicity of side chains. The mechanism of mediated fusion, which is expected to apply to other small peptides and hydrophobic molecules, provides a robust means by which a nascent metabolism can confer evolutionary advantage to precursors of cells.
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Affiliation(s)
- Chenyu Wei
- NASA Ames Research Center, Moffett Field, California; Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California
| | - Andrew Pohorille
- NASA Ames Research Center, Moffett Field, California; Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California.
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9
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Ripa I, Andreu S, López-Guerrero JA, Bello-Morales R. Membrane Rafts: Portals for Viral Entry. Front Microbiol 2021; 12:631274. [PMID: 33613502 PMCID: PMC7890030 DOI: 10.3389/fmicb.2021.631274] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 01/14/2021] [Indexed: 02/02/2023] Open
Abstract
Membrane rafts are dynamic, small (10-200 nm) domains enriched with cholesterol and sphingolipids that compartmentalize cellular processes. Rafts participate in roles essential to the lifecycle of different viral families including virus entry, assembly and/or budding events. Rafts seem to participate in virus attachment and recruitment to the cell surface, as well as the endocytic and non-endocytic mechanisms some viruses use to enter host cells. In this review, we will introduce the specific role of rafts in viral entry and define cellular factors implied in the choice of one entry pathway over the others. Finally, we will summarize the most relevant information about raft participation in the entry process of enveloped and non-enveloped viruses.
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Affiliation(s)
- Inés Ripa
- Departamento de Biología Molecular, Universidad Autónoma de Madrid, Madrid, Spain
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Madrid, Spain
| | - Sabina Andreu
- Departamento de Biología Molecular, Universidad Autónoma de Madrid, Madrid, Spain
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Madrid, Spain
| | - José Antonio López-Guerrero
- Departamento de Biología Molecular, Universidad Autónoma de Madrid, Madrid, Spain
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Madrid, Spain
| | - Raquel Bello-Morales
- Departamento de Biología Molecular, Universidad Autónoma de Madrid, Madrid, Spain
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Madrid, Spain
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10
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Risselada HJ, Grubmüller H. How proteins open fusion pores: insights from molecular simulations. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2020; 50:279-293. [PMID: 33340336 PMCID: PMC8071795 DOI: 10.1007/s00249-020-01484-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 11/16/2020] [Accepted: 11/24/2020] [Indexed: 02/06/2023]
Abstract
Fusion proteins can play a versatile and involved role during all stages of the fusion reaction. Their roles go far beyond forcing the opposing membranes into close proximity to drive stalk formation and fusion. Molecular simulations have played a central role in providing a molecular understanding of how fusion proteins actively overcome the free energy barriers of the fusion reaction up to the expansion of the fusion pore. Unexpectedly, molecular simulations have revealed a preference of the biological fusion reaction to proceed through asymmetric pathways resulting in the formation of, e.g., a stalk-hole complex, rim-pore, or vertex pore. Force-field based molecular simulations are now able to directly resolve the minimum free-energy path in protein-mediated fusion as well as quantifying the free energies of formed reaction intermediates. Ongoing developments in Graphics Processing Units (GPUs), free energy calculations, and coarse-grained force-fields will soon gain additional insights into the diverse roles of fusion proteins.
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Affiliation(s)
- H Jelger Risselada
- Department of Theoretical Physics, Georg-August University of Göttingen, Göttingen, Germany. .,Leiden University, Leiden Institute of Chemistry (LIC), Leiden, The Netherlands.
| | - Helmut Grubmüller
- Max Planck Institute for Biophysical Chemistry, Theoretical and Computational Biophysics Department, Göttingen, Germany
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11
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Salvador-Castell M, Demé B, Oger P, Peters J. Lipid Phase Separation Induced by the Apolar Polyisoprenoid Squalane Demonstrates Its Role in Membrane Domain Formation in Archaeal Membranes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:7375-7382. [PMID: 32515591 DOI: 10.1021/acs.langmuir.0c00901] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Archaea synthesize methyl-branched, ether phospholipids, which confer the archaeal membrane exceptional physicochemical properties. A novel membrane organization was proposed recently to explain the thermal and high pressure tolerance of the polyextremophilic archaeon Thermococcus barophilus. According to this theoretical model, apolar molecules could populate the midplane of the bilayer and could alter the physicochemical properties of the membrane, among which is the possibility to form membrane domains. We tested this hypothesis using neutron diffraction on a model archaeal membrane composed of two archaeal diether lipids with phosphocholine and phosphoethanolamine headgroups in the presence of the apolar polyisoprenoid squalane. We show that squalane is inserted in the midplane at a maximal concentration between 5 and 10 mol % and that squalane can modify the lateral organization of the membrane and induces the coexistence of separate phases. The lateral reorganization is temperature- and squalane concentration-dependent and could be due to the release of lipid chain frustration and the induction of a negative curvature in the lipids.
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Affiliation(s)
| | - Bruno Demé
- Institut Laue Langevin, Grenoble Cedex 9 F-38042, France
| | - Phil Oger
- INSA Lyon, Université de Lyon, CNRS, UMR5240, Villeurbanne 69621, France
| | - Judith Peters
- Institut Laue Langevin, Grenoble Cedex 9 F-38042, France
- Univ. Grenoble Alpes, CNRS, LIPhy, Grenoble 38000, France
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12
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Jefferies D, Khalid S. To infect or not to infect: molecular determinants of bacterial outer membrane vesicle internalization by host membranes. J Mol Biol 2020; 432:1251-1264. [DOI: 10.1016/j.jmb.2020.01.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Revised: 12/13/2019] [Accepted: 01/06/2020] [Indexed: 02/08/2023]
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13
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Peruzzi JA, Jacobs ML, Vu TQ, Wang KS, Kamat NP. Barcoding Biological Reactions with DNA-Functionalized Vesicles. Angew Chem Int Ed Engl 2019; 58:18683-18690. [PMID: 31596992 PMCID: PMC6901749 DOI: 10.1002/anie.201911544] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Indexed: 11/08/2022]
Abstract
Targeted vesicle fusion is a promising approach to selectively control interactions between vesicle compartments and would enable the initiation of biological reactions in complex aqueous environments. Here, we explore how two features of vesicle membranes, DNA tethers and phase-segregated membranes, promote fusion between specific vesicle populations. Membrane phase-segregation provides an energetic driver for membrane fusion that increases the efficiency of DNA-mediated fusion events. The orthogonality provided by DNA tethers allows us to direct fusion and delivery of DNA cargo to specific vesicle populations. Vesicle fusion between DNA-tethered vesicles can be used to initiate in vitro protein expression to produce model soluble and membrane proteins. Engineering orthogonal fusion events between DNA-tethered vesicles provides a new strategy to control the spatiotemporal dynamics of cell-free reactions, expanding opportunities to engineer artificial cellular systems.
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Affiliation(s)
- Justin A Peruzzi
- Department of Chemical and Biological Engineering, Northwestern University, USA
| | - Miranda L Jacobs
- Department of Biomedical Engineering, Northwestern University, McCormick School of Engineering, Technological Institute, 2145 Sheridan Road, Evanston, Il, 60208, USA
| | - Timothy Q Vu
- Department of Biomedical Engineering, Northwestern University, McCormick School of Engineering, Technological Institute, 2145 Sheridan Road, Evanston, Il, 60208, USA
| | - Kenneth S Wang
- Department of Biomedical Engineering, Northwestern University, McCormick School of Engineering, Technological Institute, 2145 Sheridan Road, Evanston, Il, 60208, USA
| | - Neha P Kamat
- Department of Biomedical Engineering, Northwestern University, McCormick School of Engineering, Technological Institute, 2145 Sheridan Road, Evanston, Il, 60208, USA
- Center for Synthetic Biology, Northwestern University, USA
- Chemistry of Life Processes Institute, Northwestern University, USA
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14
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Peruzzi JA, Jacobs ML, Vu TQ, Wang KS, Kamat NP. Barcoding Biological Reactions with DNA‐Functionalized Vesicles. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201911544] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Justin A. Peruzzi
- Department of Chemical and Biological Engineering Northwestern University USA
| | - Miranda L. Jacobs
- Department of Biomedical Engineering Northwestern University McCormick School of Engineering Technological Institute 2145 Sheridan Road Evanston Il 60208 USA
| | - Timothy Q. Vu
- Department of Biomedical Engineering Northwestern University McCormick School of Engineering Technological Institute 2145 Sheridan Road Evanston Il 60208 USA
| | - Kenneth S. Wang
- Department of Biomedical Engineering Northwestern University McCormick School of Engineering Technological Institute 2145 Sheridan Road Evanston Il 60208 USA
| | - Neha P. Kamat
- Department of Biomedical Engineering Northwestern University McCormick School of Engineering Technological Institute 2145 Sheridan Road Evanston Il 60208 USA
- Center for Synthetic Biology Northwestern University USA
- Chemistry of Life Processes Institute Northwestern University USA
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15
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Marrink SJ, Corradi V, Souza PC, Ingólfsson HI, Tieleman DP, Sansom MS. Computational Modeling of Realistic Cell Membranes. Chem Rev 2019; 119:6184-6226. [PMID: 30623647 PMCID: PMC6509646 DOI: 10.1021/acs.chemrev.8b00460] [Citation(s) in RCA: 410] [Impact Index Per Article: 82.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Indexed: 12/15/2022]
Abstract
Cell membranes contain a large variety of lipid types and are crowded with proteins, endowing them with the plasticity needed to fulfill their key roles in cell functioning. The compositional complexity of cellular membranes gives rise to a heterogeneous lateral organization, which is still poorly understood. Computational models, in particular molecular dynamics simulations and related techniques, have provided important insight into the organizational principles of cell membranes over the past decades. Now, we are witnessing a transition from simulations of simpler membrane models to multicomponent systems, culminating in realistic models of an increasing variety of cell types and organelles. Here, we review the state of the art in the field of realistic membrane simulations and discuss the current limitations and challenges ahead.
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Affiliation(s)
- Siewert J. Marrink
- Groningen
Biomolecular Sciences and Biotechnology Institute & Zernike Institute
for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Valentina Corradi
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Paulo C.T. Souza
- Groningen
Biomolecular Sciences and Biotechnology Institute & Zernike Institute
for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Helgi I. Ingólfsson
- Biosciences
and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, United States
| | - D. Peter Tieleman
- Centre
for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Mark S.P. Sansom
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K.
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16
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Corradi V, Sejdiu BI, Mesa-Galloso H, Abdizadeh H, Noskov SY, Marrink SJ, Tieleman DP. Emerging Diversity in Lipid-Protein Interactions. Chem Rev 2019; 119:5775-5848. [PMID: 30758191 PMCID: PMC6509647 DOI: 10.1021/acs.chemrev.8b00451] [Citation(s) in RCA: 245] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
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Membrane
lipids interact with proteins in a variety of ways, ranging
from providing a stable membrane environment for proteins to being
embedded in to detailed roles in complicated and well-regulated protein
functions. Experimental and computational advances are converging
in a rapidly expanding research area of lipid–protein interactions.
Experimentally, the database of high-resolution membrane protein structures
is growing, as are capabilities to identify the complex lipid composition
of different membranes, to probe the challenging time and length scales
of lipid–protein interactions, and to link lipid–protein
interactions to protein function in a variety of proteins. Computationally,
more accurate membrane models and more powerful computers now enable
a detailed look at lipid–protein interactions and increasing
overlap with experimental observations for validation and joint interpretation
of simulation and experiment. Here we review papers that use computational
approaches to study detailed lipid–protein interactions, together
with brief experimental and physiological contexts, aiming at comprehensive
coverage of simulation papers in the last five years. Overall, a complex
picture of lipid–protein interactions emerges, through a range
of mechanisms including modulation of the physical properties of the
lipid environment, detailed chemical interactions between lipids and
proteins, and key functional roles of very specific lipids binding
to well-defined binding sites on proteins. Computationally, despite
important limitations, molecular dynamics simulations with current
computer power and theoretical models are now in an excellent position
to answer detailed questions about lipid–protein interactions.
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Affiliation(s)
- Valentina Corradi
- Centre for Molecular Simulation and Department of Biological Sciences , University of Calgary , 2500 University Drive NW , Calgary , Alberta T2N 1N4 , Canada
| | - Besian I Sejdiu
- Centre for Molecular Simulation and Department of Biological Sciences , University of Calgary , 2500 University Drive NW , Calgary , Alberta T2N 1N4 , Canada
| | - Haydee Mesa-Galloso
- Centre for Molecular Simulation and Department of Biological Sciences , University of Calgary , 2500 University Drive NW , Calgary , Alberta T2N 1N4 , Canada
| | - Haleh Abdizadeh
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials , University of Groningen , Nijenborgh 7 , 9747 AG Groningen , The Netherlands
| | - Sergei Yu Noskov
- Centre for Molecular Simulation and Department of Biological Sciences , University of Calgary , 2500 University Drive NW , Calgary , Alberta T2N 1N4 , Canada
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials , University of Groningen , Nijenborgh 7 , 9747 AG Groningen , The Netherlands
| | - D Peter Tieleman
- Centre for Molecular Simulation and Department of Biological Sciences , University of Calgary , 2500 University Drive NW , Calgary , Alberta T2N 1N4 , Canada
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17
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Fantini J, Epand RM, Barrantes FJ. Cholesterol-Recognition Motifs in Membrane Proteins. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1135:3-25. [PMID: 31098808 DOI: 10.1007/978-3-030-14265-0_1] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The impact of cholesterol on the structure and function of membrane proteins was recognized several decades ago, but the molecular mechanisms underlying these effects have remained elusive. There appear to be multiple mechanisms by which cholesterol interacts with proteins. A complete understanding of cholesterol-sensing motifs is still undergoing refinement. Initially, cholesterol was thought to exert only non-specific effects on membrane fluidity. It was later shown that this lipid could specifically interact with membrane proteins and affect both their structure and function. In this article, we have summarized and critically analyzed our evolving understanding of the affinity, specificity and stereoselectivity of the interactions of cholesterol with membrane proteins. We review the different computational approaches that are currently used to identify cholesterol binding sites in membrane proteins and the biochemical logic that governs each type of site, including CRAC, CARC, SSD and amphipathic helix motifs. There are physiological implications of these cholesterol-recognition motifs for G-protein coupled receptors (GPCR) and ion channels, in membrane trafficking and membrane fusion (SNARE) proteins. There are also pathological implications of cholesterol binding to proteins involved in neurological disorders (Alzheimer, Parkinson, Creutzfeldt-Jakob) and HIV fusion. In each case, our discussion is focused on the key molecular aspects of the cholesterol and amino acid motifs in membrane-embedded regions of membrane proteins that define the physiologically relevant crosstalk between the two. Our understanding of the factors that determine if these motifs are functional in cholesterol binding will allow us enhanced predictive capabilities.
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Affiliation(s)
- Jacques Fantini
- INSERM UMR_S 1072, Marseille, France. .,Aix-Marseille Université, Marseille, France.
| | - Richard M Epand
- Department of Biochemistry and Biomedical Sciences, McMaster University, Health Sciences Centre, Hamilton, ON, Canada
| | - Francisco J Barrantes
- Laboratory of Molecular Neurobiology, Biomedical Research Institute (BIOMED), UCA-CONICET, Buenos Aires, Argentina
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18
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Kreutzberger AJB, Kiessling V, Liang B, Yang ST, Castle JD, Tamm LK. Asymmetric Phosphatidylethanolamine Distribution Controls Fusion Pore Lifetime and Probability. Biophys J 2017; 113:1912-1915. [PMID: 29037600 DOI: 10.1016/j.bpj.2017.09.014] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 09/11/2017] [Accepted: 09/13/2017] [Indexed: 01/18/2023] Open
Abstract
Little attention has been given to how the asymmetric lipid distribution of the plasma membrane might facilitate fusion pore formation during exocytosis. Phosphatidylethanolamine (PE), a cone-shaped phospholipid, is predominantly located in the inner leaflet of the plasma membrane and has been proposed to promote membrane deformation and stabilize fusion pores during exocytotic events. To explore this possibility, we modeled exocytosis using plasma membrane SNARE-containing planar-supported bilayers and purified neuroendocrine dense core vesicles (DCVs) as fusion partners, and we examined how different PE distributions between the two leaflets of the supported bilayers affected SNARE-mediated fusion. Using total internal reflection fluorescence microscopy, the fusion of single DCVs with the planar-supported bilayer was monitored by observing DCV-associated neuropeptide Y tagged with a fluorescent protein. The time-dependent line shape of the fluorescent signal enables detection of DCV docking, fusion-pore opening, and vesicle collapse into the planar membrane. Four different distributions of PE in the planar bilayer mimicking the plasma membrane were examined: exclusively in the leaflet facing the DCVs; exclusively in the opposite leaflet; equally distributed in both leaflets; and absent from both leaflets. With PE in the leaflet facing the DCVs, overall fusion was most efficient and the extended fusion pore lifetime (0.7 s) enabled notable detection of content release preceding vesicle collapse. All other PE distributions decreased fusion efficiency, altered pore lifetime, and reduced content release. With PE exclusively in the opposite leaflet, resolution of pore opening and content release was lost.
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Affiliation(s)
- Alex J B Kreutzberger
- Department of Molecular Physiology and Biological Physics, Center for Cell and Membrane Physiology at the University of Virginia, Charlottesville, Virginia
| | - Volker Kiessling
- Department of Molecular Physiology and Biological Physics, Center for Cell and Membrane Physiology at the University of Virginia, Charlottesville, Virginia
| | - Binyong Liang
- Department of Molecular Physiology and Biological Physics, Center for Cell and Membrane Physiology at the University of Virginia, Charlottesville, Virginia
| | - Sung-Tae Yang
- Department of Molecular Physiology and Biological Physics, Center for Cell and Membrane Physiology at the University of Virginia, Charlottesville, Virginia
| | - J David Castle
- Department of Cell Biology, Center for Cell and Membrane Physiology at the University of Virginia, Charlottesville, Virginia
| | - Lukas K Tamm
- Department of Molecular Physiology and Biological Physics, Center for Cell and Membrane Physiology at the University of Virginia, Charlottesville, Virginia.
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