1
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Kephart SM, Hom N, Lee KK. Visualizing intermediate stages of viral membrane fusion by cryo-electron tomography. Trends Biochem Sci 2024; 49:916-931. [PMID: 39054240 PMCID: PMC11455608 DOI: 10.1016/j.tibs.2024.06.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 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.
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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.
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2
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Maleš P, Nikšić-Franjić I, Wang A, Pem B, Bakarić D. Optical and molecular features of negatively curved surfaces created by POPE lipids: A crucial role of the initial conditions. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 317:124462. [PMID: 38754204 DOI: 10.1016/j.saa.2024.124462] [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: 02/13/2024] [Revised: 05/10/2024] [Accepted: 05/11/2024] [Indexed: 05/18/2024]
Abstract
Membrane fusion is closely related to plasma membrane domains rich in cone-shaped phosphatidylethanolamine (PE) lipids that can reverse membrane curvature under certain conditions. The phase transition of PE-based lipid membranes from the lamellar fluid phase (Lα) to the inverse hexagonal phase (HII) is commonly taken as a general model in reconstructing the membrane fusion pathway, and whose structural features have been mostly described so far using structural and microscopic techniques. The aim of this paper is to decipher the optical and molecular features of Lβ → Lα and especially of Lα → HII transition of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine (POPE) lipids at pH = 7.0 when they are initially prepared in the form of both multi- and unilamellar liposomes (MLVs and LUVs). The distinction between optical properties of MLS- and LUVs-derived HII phase, provided from turbidity-sensitive temperature-dependent UV-Vis spectra, was attributed to different formation mechanisms of HII phase. Most importantly, from FTIR spectroscopic data of POPE lipids in Lβ (15 °C), Lα (50 °C) and HII (85 °C) phases we identified the changes in molecular features of POPE lipids during phase transitions. Among the latter, by far the most significant is different hydration pattern of POPE lipids in MLVs- and LUVs-derived HII phase which extends from the polar-apolar interface all the way to the terminal amino group of the POPE lipid, along with the changes in the conformation of glycerol backbone as evidenced by the signature of α-methylene groups. Molecular dynamics simulations confirmed higher water penetration in HII phase and provided insight into hydrogen bonding patterns.
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Affiliation(s)
- Petra Maleš
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia
| | - Ivana Nikšić-Franjić
- School of Science, Constructor University, Bremen GmbH, Campus Ring 1, 28759 Bremen, Germany
| | - Anna Wang
- School of Chemistry, Australian Centre for Astrobiology, and ARC Centre of Excellence in Synthetic Biology, University of New South Wales Sydney, Bedegal Country, Sydney, NSW 2052, Australia
| | - Barbara Pem
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia
| | - Danijela Bakarić
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia.
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3
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Pires IS, Suggs JR, Carlo IS, Yun D, Hammond PT, Irvine DJ. Surfactant-Mediated Assembly of Precision-Size Liposomes. CHEMISTRY OF MATERIALS : A PUBLICATION OF THE AMERICAN CHEMICAL SOCIETY 2024; 36:7263-7273. [PMID: 39156714 PMCID: PMC11325547 DOI: 10.1021/acs.chemmater.4c01127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 06/12/2024] [Accepted: 06/13/2024] [Indexed: 08/20/2024]
Abstract
Liposomes can greatly improve the pharmacokinetics of therapeutic agents due to their ability to encapsulate drugs and accumulate in target tissues. Considerable effort has been focused on methods to synthesize these nanocarriers in the past decades. However, most methods fail to controllably generate lipid vesicles at specific sizes and with low polydispersity, especially via scalable approaches suitable for clinical product manufacturing. Here, we report a surfactant-assisted liposome assembly method enabling the precise production of monodisperse liposomes with diameters ranging from 50 nm to 1 μm. To overcome scalability limitations, we used tangential flow filtration, a scalable size-based separation technique, to readily concentrate and purify the liposomal samples from more than 99.9% of detergent. Further, we propose two modes of liposome self-assembly following detergent dilution to explain the wide range of liposome size control, one in which phase separation into lipid-rich and detergent-rich phases drives the formation of large bilayer liposomes and a second where the rate of detergent monomer partitioning into solution controls bilayer leaflet imbalances that promote fusion into larger vesicles. We demonstrate the utility of controlled size assembly of liposomes by evaluating nanoparticle uptake in macrophages, where we observe a clear linear relationship between vesicle size and total nanoparticle uptake.
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Affiliation(s)
- Ivan S. Pires
- Koch
Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, Massachusetts 02139, United States
- Department
of Chemical Engineering, Massachusetts Institute
of Technology, 21 Ames Street, Cambridge, Massachusetts 02139, United States
| | - Jack R. Suggs
- Koch
Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, Massachusetts 02139, United States
| | - Isabella S. Carlo
- Koch
Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, Massachusetts 02139, United States
| | - DongSoo Yun
- Koch
Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, Massachusetts 02139, United States
| | - Paula T. Hammond
- Koch
Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, Massachusetts 02139, United States
- Department
of Chemical Engineering, Massachusetts Institute
of Technology, 21 Ames Street, Cambridge, Massachusetts 02139, United States
| | - Darrell J. Irvine
- Koch
Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, Massachusetts 02139, United States
- Department
of Biological Engineering, Massachusetts
Institute of Technology, 25 Ames Street, Cambridge, Massachusetts 02139, United States
- Department
of Materials Science and Engineering, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02139, United States
- Ragon
Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02139, United States
- Howard
Hughes
Medical Institute, Chevy Chase, Maryland 20815, United States
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4
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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.
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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.
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5
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Brown CM, Marrink SJ. Modeling membranes in situ. Curr Opin Struct Biol 2024; 87:102837. [PMID: 38744147 DOI: 10.1016/j.sbi.2024.102837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 03/26/2024] [Accepted: 04/23/2024] [Indexed: 05/16/2024]
Abstract
Molecular dynamics simulations of cellular membranes have come a long way-from simple model lipid bilayers to multicomponent systems capturing the crowded and complex nature of real cell membranes. In this opinionated minireview, we discuss the current challenge to simulate the dynamics of membranes in their native environment, in situ, with the prospect of reaching the level of whole cells and cell organelles using an integrative modeling framework.
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Affiliation(s)
- Chelsea M Brown
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands. https://twitter.com/chelseabrowncg
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands. s.j.marrinkrug.nl
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6
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Bottacchiari M, Gallo M, Bussoletti M, Casciola CM. The diffuse interface description of fluid lipid membranes captures key features of the hemifusion pathway and lateral stress profile. PNAS NEXUS 2024; 3:pgae300. [PMID: 39114574 PMCID: PMC11304589 DOI: 10.1093/pnasnexus/pgae300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 07/09/2024] [Indexed: 08/10/2024]
Abstract
Topological transitions of lipid membranes are ubiquitous in key biological processes for cell life, like neurotransmission, fertilization, morphogenesis, and viral infections. Despite this, they are not well understood due to their multiscale nature, which limits the use of molecular models and calls for a mesoscopic approach such as the celebrated Canham-Helfrich one. Unfortunately, such a model cannot handle topological transitions, hiding the crucial involved forces and the appearance of the experimentally observed hemifused intermediates. In this work, we describe the membrane as a diffuse interface preserving the Canham-Helfrich elasticity. We show that pivotal features of the hemifusion pathway are captured by this mesoscopic approach, e.g. a (meta)stable hemifusion state and the fusogenic behavior of negative monolayer spontaneous curvatures. The membrane lateral stress profile is calculated as a function of the elastic rigidities, yielding a coarse-grained version of molecular models findings. Insights into the fusogenic mechanism are reported and discussed.
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Affiliation(s)
- Matteo Bottacchiari
- Department of Basic and Applied Sciences for Engineering, Sapienza University of Rome, via Antonio Scarpa 16, Rome 00161, Italy
- Department of Mechanical and Aerospace Engineering, Sapienza University of Rome, via Eudossiana 18, Rome 00184, Italy
| | - Mirko Gallo
- Department of Mechanical and Aerospace Engineering, Sapienza University of Rome, via Eudossiana 18, Rome 00184, Italy
| | - Marco Bussoletti
- Department of Mechanical and Aerospace Engineering, Sapienza University of Rome, via Eudossiana 18, Rome 00184, Italy
| | - Carlo M Casciola
- Department of Mechanical and Aerospace Engineering, Sapienza University of Rome, via Eudossiana 18, Rome 00184, Italy
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7
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Kataoka-Hamai C. Triacylglycerol-droplet-induced bilayer spontaneous curvature in giant unilamellar vesicles. Biophys J 2024; 123:1857-1868. [PMID: 38822522 PMCID: PMC11267425 DOI: 10.1016/j.bpj.2024.05.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 04/05/2024] [Accepted: 05/29/2024] [Indexed: 06/03/2024] Open
Abstract
This study investigated the incorporation of triacylglycerol droplets in the bilayers of giant unilamellar vesicles (GUVs) using four triacylglycerols and four phosphatidylcholines by confocal laser scanning microscopy. The triacylglycerol droplets were incorporated between the monolayer leaflets of the GUVs. Among the spherical droplets protruding on only one side of the bilayers, the droplets bound to the outer leaflets outnumbered those bound to the inner leaflets. The more frequent droplet binding to the outer leaflet caused transbilayer asymmetry in the droplet surface density. A vesicle consisting of a single-bilayer spherical segment and a double-bilayer spherical segment was also observed. The yield of these vesicles was comparable with or higher than that of the droplet-incorporating GUVs for many of the phosphatidylcholine-triacylglycerol combinations. In a vesicle consisting of single-bilayer and double-bilayer segments, most of the triacylglycerol droplets were localized on the outermost membrane surface along the segment boundary and in the double-bilayer segment. To rationalize the formation of these vesicle structures, we propose that the transbilayer asymmetry in the droplet surface density induces spontaneous curvature of the bilayer, with the bilayer spontaneously bending away from the droplets. Energy calculations performed assuming the existence of spontaneous curvature of the bilayer corroborated the experimentally determined membrane shapes for the vesicles consisting of unilamellar and bilamellar regions.
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Affiliation(s)
- Chiho Kataoka-Hamai
- Research Center for Macromolecules and Biomaterials, National Institute for Materials Science, Tsukuba, Ibaraki, Japan.
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8
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Parrow A, Kabedev A, Larsson P, Johansson P, Abrahamsson B, Bergström CAS. Drug solubilization in dog intestinal fluids with and without administration of lipid-based formulations. J Control Release 2024; 371:555-569. [PMID: 38844179 DOI: 10.1016/j.jconrel.2024.06.008] [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: 06/02/2023] [Revised: 05/23/2024] [Accepted: 06/03/2024] [Indexed: 06/15/2024]
Abstract
The use of animal experiments can be minimized with computational models capable of reflecting the simulated environments. One such environment is intestinal fluid and the colloids formed in it. In this study we used molecular dynamics simulations to investigate solubilization patterns for three model drugs (carvedilol, felodipine and probucol) in dog intestinal fluid, a lipid-based formulation, and a mixture of both. We observed morphological transformations that lipids undergo due to the digestion process in the intestinal environment. Further, we evaluated the effect of bile salt concentration and observed the importance of interindividual variability. We applied two methods of estimating solubility enhancement based on the simulated data, of which one was in good qualitative agreement with the experimentally observed solubility enhancement. In addition to the computational simulations, we also measured solubility in i) aspirated dog intestinal fluid samples and ii) simulated canine intestinal fluid in the fasted state, and found there was no statistical difference between the two. Hence, a simplified dissolution medium suitable for in vitro studies provided physiologically relevant data for the systems explored. The computational protocol used in this study, coupled with in vitro studies using simulated intestinal fluids, can serve as a useful prescreening tool in the process of drug delivery strategies development.
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Affiliation(s)
- Albin Parrow
- Department of Pharmacy, Uppsala University, Uppsala Biomedical Center, P.O. Box 580, SE-751 23 Uppsala, Sweden
| | - Aleksei Kabedev
- Department of Pharmacy, Uppsala University, Uppsala Biomedical Center, P.O. Box 580, SE-751 23 Uppsala, Sweden
| | - Per Larsson
- Department of Pharmacy, Uppsala University, Uppsala Biomedical Center, P.O. Box 580, SE-751 23 Uppsala, Sweden; The Swedish Drug Delivery Center, Department of Pharmacy, Uppsala University, Biomedical Center, P.O. Box 580, SE-751 23 Uppsala, Sweden
| | | | | | - Christel A S Bergström
- Department of Pharmacy, Uppsala University, Uppsala Biomedical Center, P.O. Box 580, SE-751 23 Uppsala, Sweden; The Swedish Drug Delivery Center, Department of Pharmacy, Uppsala University, Biomedical Center, P.O. Box 580, SE-751 23 Uppsala, Sweden.
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9
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Nicolella Z, Okamoto Y, Watanabe NM, Thompson GL, Umakoshi H. Significance of in situ quantitative membrane property-morphology relation (QmPMR) analysis. SOFT MATTER 2024; 20:4935-4949. [PMID: 38873752 DOI: 10.1039/d4sm00253a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2024]
Abstract
Deformation of the cell membrane is well understood from the viewpoint of protein interactions and free energy balance. However, the various dynamic properties of the membrane, such as lipid packing and hydrophobicity, and their relationship with cell membrane deformation are unknown. Therefore, the deformation of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) and oleic acid (OA) giant unilamellar vesicles (GUVs) was induced by heating and cooling cycles, and time-lapse analysis was conducted based on the membrane hydrophobicity and physical parameters of "single-parent" and "daughter" vesicles. Fluorescence ratiometric analysis by simultaneous dual-wavelength detection revealed the variation of different hydrophilic GUVs and enabled inferences of the "daughter" vesicle composition and the "parent" membrane's local composition during deformation; the "daughter" vesicle composition of OA was lower than that of the "parents", and lateral movement of OA was the primary contributor to the formation of the "daughter" vesicles. Thus, our findings and the newly developed methodology, named in situ quantitative membrane property-morphology relation (QmPMR) analysis, would provide new insights into cell deformation and accelerate research on both deformation and its related events, such as budding and birthing.
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Affiliation(s)
- Zachary Nicolella
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama-cho, Toyonaka, Osaka 560-8531, Japan.
| | - Yukihiro Okamoto
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama-cho, Toyonaka, Osaka 560-8531, Japan.
| | - Nozomi Morishita Watanabe
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama-cho, Toyonaka, Osaka 560-8531, Japan.
| | - Gary Lee Thompson
- Rowan University, Rowan Hall, Room 333 70 Sewell St., Ste. E Glassboro, NJ 08028, USA
| | - Hiroshi Umakoshi
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama-cho, Toyonaka, Osaka 560-8531, Japan.
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10
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Zhang Y, Jin D, Tivony R, Kampf N, Klein J. Cell-inspired, massive electromodulation of friction via transmembrane fields across lipid bilayers. NATURE MATERIALS 2024:10.1038/s41563-024-01926-9. [PMID: 38914644 DOI: 10.1038/s41563-024-01926-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 05/16/2024] [Indexed: 06/26/2024]
Abstract
Transient electric fields across cell bilayer membranes can lead to electroporation and cell fusion, effects crucial to cell viability whose biological implications have been extensively studied. However, little is known about these behaviours in a materials context. Here we find that transmembrane electric fields can lead to a massive, reversible modulation of the sliding friction between surfaces coated with lipid-bilayer membranes-a 200-fold variation, up to two orders of magnitude greater than that achieved to date. Atomistic simulations reveal that the transverse fields, resembling those at cell membranes, lead to fully reversible electroporation of the confined bilayers and the formation of inter-bilayer bridges analogous to the stalks preceding intermembrane fusion. These increase the interfacial dissipation through reduced hydration at the slip plane, forcing it to revert in part from the low-dissipation, hydrated lipid-headgroup plane to the intra-bilayer, high-dissipation acyl tail interface. Our results demonstrate that lipid bilayers under transmembrane electric fields can have striking materials modification properties.
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Affiliation(s)
- Yu Zhang
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot, Israel
| | - Di Jin
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot, Israel.
| | - Ran Tivony
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot, Israel
- Department of Chemical Engineering, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Nir Kampf
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot, Israel
| | - Jacob Klein
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot, Israel.
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11
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Dwivedi A, Mazumder A, Pullmannová P, Paraskevopoulou A, Opálka L, Kováčik A, Macháček M, Jančálková P, Svačinová P, Peterlik H, Maixner J, Vávrová K. Lipid Monolayer on Cell Surface Protein Templates Functional Extracellular Lipid Assembly. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2307793. [PMID: 38243890 DOI: 10.1002/smll.202307793] [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: 09/06/2023] [Revised: 12/18/2023] [Indexed: 01/22/2024]
Abstract
When the ancestors of men moved from aquatic habitats to the drylands, their evolutionary strategy to restrict water loss is to seal the skin surface with lipids. It is unknown how these rigid ceramide-dominated lipids with densely packed chains squeeze through narrow extracellular spaces and how they assemble into their complex multilamellar architecture. Here it is shown that the human corneocyte lipid envelope, a monolayer of ultralong covalently bound lipids on the cell surface protein, templates the functional barrier assembly by partly fluidizing and rearranging the free extracellular lipids in its vicinity during the sculpting of a functional skin lipid barrier. The lipid envelope also maintains the fluidity of the extracellular lipids during mechanical stress. This local lipid fluidization does not compromise the permeability barrier. The results provide new testable hypotheses about epidermal homeostasis and the pathophysiology underlying diseases with impaired lipid binding to corneocytes, such as congenital ichthyosis. In a broader sense, this lipoprotein-mediated fluidization of rigid (sphingo)lipid patches may also be relevant to lipid rafts and cellular signaling events and inspire new functional materials.
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Affiliation(s)
- Anupma Dwivedi
- Skin Barrier Research Group, Faculty of Pharmacy, Charles University, Heyrovského 1203, Hradec Králové, 50005, Czech Republic
| | - Anisha Mazumder
- Skin Barrier Research Group, Faculty of Pharmacy, Charles University, Heyrovského 1203, Hradec Králové, 50005, Czech Republic
| | - Petra Pullmannová
- Skin Barrier Research Group, Faculty of Pharmacy, Charles University, Heyrovského 1203, Hradec Králové, 50005, Czech Republic
| | - Anna Paraskevopoulou
- Skin Barrier Research Group, Faculty of Pharmacy, Charles University, Heyrovského 1203, Hradec Králové, 50005, Czech Republic
- Department of Pharmaceutical Technology, Faculty of Pharmacy, Charles University, Heyrovského 1203, Hradec Králové, 50005, Czech Republic
| | - Lukáš Opálka
- Skin Barrier Research Group, Faculty of Pharmacy, Charles University, Heyrovského 1203, Hradec Králové, 50005, Czech Republic
| | - Andrej Kováčik
- Skin Barrier Research Group, Faculty of Pharmacy, Charles University, Heyrovského 1203, Hradec Králové, 50005, Czech Republic
- Department of Pharmaceutical Technology, Faculty of Pharmacy, Charles University, Heyrovského 1203, Hradec Králové, 50005, Czech Republic
| | - Miloslav Macháček
- Department of Biochemical Sciences, Faculty of Pharmacy, Charles University, Heyrovského 1203, Hradec Králové, 50005, Czech Republic
| | - Pavla Jančálková
- Skin Barrier Research Group, Faculty of Pharmacy, Charles University, Heyrovského 1203, Hradec Králové, 50005, Czech Republic
| | - Petra Svačinová
- Department of Pharmaceutical Technology, Faculty of Pharmacy, Charles University, Heyrovského 1203, Hradec Králové, 50005, Czech Republic
| | - Herwig Peterlik
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, Vienna, 1090, Austria
| | - Jaroslav Maixner
- Faculty of Chemical Technology, University of Chemistry and Technology Prague, Technická 5, Prague, 16628, Czech Republic
| | - Kateřina Vávrová
- Skin Barrier Research Group, Faculty of Pharmacy, Charles University, Heyrovského 1203, Hradec Králové, 50005, Czech Republic
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12
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Blasco S, Sukeník L, Vácha R. Nanoparticle induced fusion of lipid membranes. NANOSCALE 2024; 16:10221-10229. [PMID: 38679949 PMCID: PMC11138393 DOI: 10.1039/d4nr00591k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 04/23/2024] [Indexed: 05/01/2024]
Abstract
Membrane fusion is crucial for infection of enveloped viruses, cellular transport, and drug delivery via liposomes. Nanoparticles can serve as fusogenic agents facilitating such membrane fusion for direct transmembrane transport. However, the underlying mechanisms of nanoparticle-induced fusion and the ideal properties of such nanoparticles remain largely unknown. Here, we used molecular dynamics simulations to investigate the efficacy of spheroidal nanoparticles with different size, prolateness, and ligand interaction strengths to enhance fusion between vesicles. By systematically varying nanoparticle properties, we identified how each parameter affects the fusion process and determined the optimal parameter range that promotes fusion. These findings provide valuable insights for the design and optimization of fusogenic nanoparticles with potential biotechnological and biomedical applications.
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Affiliation(s)
- Sofía Blasco
- CEITEC - Central European Institute of Technology, Kamenice 5, 625 00 Brno, Czech Republic.
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Lukáš Sukeník
- CEITEC - Central European Institute of Technology, Kamenice 5, 625 00 Brno, Czech Republic.
- Department of Condensed Matter Physics, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Robert Vácha
- CEITEC - Central European Institute of Technology, Kamenice 5, 625 00 Brno, Czech Republic.
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
- Department of Condensed Matter Physics, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
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13
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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.
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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.
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14
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Kasparyan G, Hub JS. Molecular Simulations Reveal the Free Energy Landscape and Transition State of Membrane Electroporation. PHYSICAL REVIEW LETTERS 2024; 132:148401. [PMID: 38640376 DOI: 10.1103/physrevlett.132.148401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 02/29/2024] [Indexed: 04/21/2024]
Abstract
The formation of pores over lipid membranes by the application of electric fields, termed membrane electroporation, is widely used in biotechnology and medicine to deliver drugs, vaccines, or genes into living cells. Continuum models for describing the free energy landscape of membrane electroporation were proposed decades ago, but they have never been tested against spatially detailed atomistic models. Using molecular dynamics (MD) simulations with a recently proposed reaction coordinate, we computed potentials of mean force of pore nucleation and pore expansion in lipid membranes at various transmembrane potentials. Whereas the free energies of pore expansion are compatible with previous continuum models, the experimentally important free energy barrier of pore nucleation is at variance with established models. The discrepancy originates from different geometries of the transition state; previous continuum models assumed the presence of a membrane-spanning defect throughout the process, whereas, according to the MD simulations, the transition state of pore nucleation is typically passed before a transmembrane defect has formed. A modified continuum model is presented that qualitatively agrees with the MD simulations. Using kinetics of pore opening together with transition state theory, our free energies of pore nucleation are in excellent agreement with previous experimental data.
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Affiliation(s)
- Gari Kasparyan
- Theoretical Physics and Center for Biophysics, Saarland University, 66123 Saarbrücken, Germany
| | - Jochen S Hub
- Theoretical Physics and Center for Biophysics, Saarland University, 66123 Saarbrücken, Germany
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15
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Yang C, Lin ZI, Zhang X, Xu Z, Xu G, Wang YM, Tsai TH, Cheng PW, Law WC, Yong KT, Chen CK. Recent Advances in Engineering Carriers for siRNA Delivery. Macromol Biosci 2024; 24:e2300362. [PMID: 38150293 DOI: 10.1002/mabi.202300362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 11/29/2023] [Indexed: 12/28/2023]
Abstract
RNA interference (RNAi) technology has been a promising treatment strategy for combating intractable diseases. However, the applications of RNAi in clinical are hampered by extracellular and intracellular barriers. To overcome these barriers, various siRNA delivery systems have been developed in the past two decades. The first approved RNAi therapeutic, Patisiran (ONPATTRO) using lipids as the carrier, for the treatment of amyloidosis is one of the most important milestones. This has greatly encouraged researchers to work on creating new functional siRNA carriers. In this review, the recent advances in siRNA carriers consisting of lipids, polymers, and polymer-modified inorganic particles for cancer therapy are summarized. Representative examples are presented to show the structural design of the carriers in order to overcome the delivery hurdles associated with RNAi therapies. Finally, the existing challenges and future perspective for developing RNAi as a clinical modality will be discussed and proposed. It is believed that the addressed contributions in this review will promote the development of siRNA delivery systems for future clinical applications.
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Affiliation(s)
- Chengbin Yang
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen University, Shenzhen, 518060, P. R. China
| | - Zheng-Ian Lin
- Polymeric Biomaterials Laboratory, Department of Materials and Optoelectronic Science, National Sun Yat-Sen University, Kaohsiung, 80424, Taiwan
| | - Xinmeng Zhang
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen University, Shenzhen, 518060, P. R. China
| | - Zhourui Xu
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen University, Shenzhen, 518060, P. R. China
| | - Gaixia Xu
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen University, Shenzhen, 518060, P. R. China
| | - Yu-Min Wang
- Polymeric Biomaterials Laboratory, Department of Materials and Optoelectronic Science, National Sun Yat-Sen University, Kaohsiung, 80424, Taiwan
| | - Tzu-Hsien Tsai
- Division of Cardiology and Department of Internal Medicine, Ditmanson Medical Foundation Chiayi Christian Hospital, Chiayi, 60002, Taiwan
| | - Pei-Wen Cheng
- Department of Medical Education and Research, Kaohsiung Veterans General Hospital, Kaohsiung, 81362, Taiwan
- Department of Biomedical Sciences, National Sun Yat-Sen University, Kaohsiung, 80424, Taiwan
| | - Wing-Cheung Law
- Department of Industrial and Systems Engineering, The Hong Kong Polytechnic University, Hung Hom, Hong Kong, 999077, P. R. China
| | - Ken-Tye Yong
- School of Biomedical Engineering, The University of Sydney, Sydney, New South Wales, 2006, Australia
| | - Chih-Kuang Chen
- Polymeric Biomaterials Laboratory, Department of Materials and Optoelectronic Science, National Sun Yat-Sen University, Kaohsiung, 80424, Taiwan
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16
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Di Bartolo AL, Caparotta M, Polo LM, Masone D. Myomerger Induces Membrane Hemifusion and Regulates Fusion Pore Expansion. Biochemistry 2024; 63:815-826. [PMID: 38349279 DOI: 10.1021/acs.biochem.3c00682] [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: 03/20/2024]
Abstract
Membrane fusion is a crucial mechanism in a wide variety of important events in cell biology from viral infection to exocytosis. However, despite many efforts and much progress, cell-cell fusion has remained elusive to our understanding. Along the life of the fusion pore, large conformational changes take place from the initial lipid bilayer bending, passing through the hemifusion intermediates, and ending with the formation of the first nascent fusion pore. In this sense, computer simulations are an ideal technique for describing such complex lipid remodeling at the molecular level. In this work, we studied the role played by the muscle-specific membrane protein Myomerger during the formation of the fusion pore. We have conducted μs length atomistic and coarse-grained molecular dynamics, together with free-energy calculations using ad hoc collective variables. Our results show that Myomerger favors the hemifusion diaphragm-stalk transition, reduces the nucleation-expansion energy difference, and promotes the formation of nonenlarging fusion pores.
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Affiliation(s)
- Ary Lautaro Di Bartolo
- Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo (UNCuyo), 5500 Mendoza, Argentina
| | - Marcelo Caparotta
- Quantum Theory Project, Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Luis Mariano Polo
- Instituto de Histología y Embriología de Mendoza (IHEM)─Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Cuyo, 5500 Mendoza, Argentina
| | - Diego Masone
- Instituto de Histología y Embriología de Mendoza (IHEM)─Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Cuyo, 5500 Mendoza, Argentina
- Facultad de Ingeniería, Universidad Nacional de Cuyo, 5500 Mendoza, Argentina
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17
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Perpiñá-Clérigues C, Mellado S, Galiana-Roselló C, Fernández-Regueras M, Marcos M, García-García F, Pascual M. Novel insight into the lipid network of plasma extracellular vesicles reveal sex-based differences in the lipidomic profile of alcohol use disorder patients. Biol Sex Differ 2024; 15:10. [PMID: 38273378 PMCID: PMC10809459 DOI: 10.1186/s13293-024-00584-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 01/11/2024] [Indexed: 01/27/2024] Open
Abstract
BACKGROUND Alcohol use disorder (AUD) is one of the most common psychiatric disorders, with the consumption of alcohol considered a leading cause of preventable deaths worldwide. Lipids play a crucial functional role in cell membranes; however, we know little about the role of lipids in extracellular vesicles (EVs) as regulatory molecules and disease biomarkers. METHODS We employed a sensitive lipidomic strategy to characterize lipid species from the plasma EVs of AUD patients to evaluate functional roles and enzymatic activity networks to improve the knowledge of lipid metabolism after alcohol consumption. We analyzed plasma EV lipids from AUD females and males and healthy individuals to highlight lipids with differential abundance and biologically interpreted lipidomics data using LINEX2, which evaluates enzymatic dysregulation using an enrichment algorithm. RESULTS Our results show, for the first time, that AUD females exhibited more significant substrate-product changes in lysophosphatidylcholine/phosphatidylcholine lipids and phospholipase/acyltransferase activity, which are potentially linked to cancer progression and neuroinflammation. Conversely, AUD males suffer from dysregulated ceramide and sphingomyelin lipids involving sphingomyelinase, sphingomyelin phosphodiesterase, and sphingomyelin synthase activity, which relates to hepatotoxicity. Notably, the analysis of plasma EVs from AUD females and males demonstrates enrichment of lipid ontology terms associated with "negative intrinsic curvature" and "positive intrinsic curvature", respectively. CONCLUSIONS Our methodological developments support an improved understanding of lipid metabolism and regulatory mechanisms, which contribute to the identification of novel lipid targets and the discovery of sex-specific clinical biomarkers in AUD.
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Affiliation(s)
- Carla Perpiñá-Clérigues
- Computational Biomedicine Laboratory, Príncipe Felipe Research Center, C/Eduardo Primo Yúfera, 3, 46012, Valencia, Spain
- Department of Physiology, School of Medicine and Dentistry, University of Valencia, Avda. Blasco Ibáñez, 15, 46010, Valencia, Spain
| | - Susana Mellado
- Department of Physiology, School of Medicine and Dentistry, University of Valencia, Avda. Blasco Ibáñez, 15, 46010, Valencia, Spain
| | - Cristina Galiana-Roselló
- Department of Inorganic Chemistry, Institute of Molecular Science, University of Valencia, 46980, Paterna, Spain
| | - María Fernández-Regueras
- Hospital Universitario de Burgos, 09006, Burgos, Spain
- Hospital Universitario de Salamanca, 37007, Salamanca, Spain
| | - Miguel Marcos
- Department of Internal Medicine, University Hospital of Salamanca, University of Salamanca, Institute of Biomedical Research of Salamanca (IBSAL), 37007, Salamanca, Spain
| | - Francisco García-García
- Computational Biomedicine Laboratory, Príncipe Felipe Research Center, C/Eduardo Primo Yúfera, 3, 46012, Valencia, Spain.
| | - María Pascual
- Department of Physiology, School of Medicine and Dentistry, University of Valencia, Avda. Blasco Ibáñez, 15, 46010, Valencia, Spain.
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18
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Bottacchiari M, Gallo M, Bussoletti M, Casciola CM. The local variation of the Gaussian modulus enables different pathways for fluid lipid vesicle fusion. Sci Rep 2024; 14:23. [PMID: 38168475 PMCID: PMC10762093 DOI: 10.1038/s41598-023-50922-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 12/28/2023] [Indexed: 01/05/2024] Open
Abstract
Viral infections, fertilization, neurotransmission, and many other fundamental biological processes rely on membrane fusion. Straightforward calculations based on the celebrated Canham-Helfrich elastic model predict a large topological energy barrier that prevents the fusion process from being thermally activated. While such high energy is in accordance with the physical barrier function of lipid membranes, it is difficult to reconcile with the biological mechanisms involved in fusion processes. In this work, we use a Ginzburg-Landau type of free energy that recovers the Canham-Helfrich model in the limit of small width-to-vesicle-extension ratio, with the additional ability to handle topological transitions. We show that a local modification of the Gaussian modulus in the merging region both dramatically lowers the elastic energy barrier and substantially changes the minimal energy pathway for fusion, in accordance with experimental evidence. Therefore, we discuss biological examples in which such a modification might play a crucial role.
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Affiliation(s)
- Matteo Bottacchiari
- Department of Mechanical and Aerospace Engineering, Sapienza Università di Roma, Rome, Italy
| | - Mirko Gallo
- Department of Mechanical and Aerospace Engineering, Sapienza Università di Roma, Rome, Italy
| | - Marco Bussoletti
- Department of Mechanical and Aerospace Engineering, Sapienza Università di Roma, Rome, Italy
| | - Carlo Massimo Casciola
- Department of Mechanical and Aerospace Engineering, Sapienza Università di Roma, Rome, Italy.
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19
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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: 2] [Impact Index Per Article: 2.0] [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.
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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.
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20
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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.
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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
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21
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Brosio G, Rossi G, Bochicchio D. Nanoparticle-induced biomembrane fusion: unraveling the effect of core size on stalk formation. NANOSCALE ADVANCES 2023; 5:4675-4680. [PMID: 37705778 PMCID: PMC10496904 DOI: 10.1039/d3na00430a] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 08/01/2023] [Indexed: 09/15/2023]
Abstract
Membrane fusion in vitro is a strategy to load model or cell-derived vesicles with proteins, drugs, and genetic materials for theranostic applications. It is thus crucial to develop strategies to control the fusion process, also through synthetic fusogenic agents. Ligand-protected, membrane-penetrating gold nanoparticles (Au NPs) can facilitate membrane fusion, but the molecular mechanisms remain unresolved. Here, we tackle NP-induced stalk formation using a coarse-grained molecular dynamics approach and enhanced sampling techniques. We show that smaller (2 nm in diameter) NPs lead to a lower free energy barrier and higher stalk stability than larger NPs (4 nm). We demonstrate that this difference is due to a different ligand conformational freedom, which in turn depends on the Au core curvature. Our study provides precious insights into the mechanisms underlying NP-mediated membrane fusion, while our computational approach is general and applicable to studying stalk formation caused by other fusogenic agents.
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Affiliation(s)
- Giorgia Brosio
- Department of Physics, University of Genoa Via Dodecaneso 33 16146 Genoa Italy
| | - Giulia Rossi
- Department of Physics, University of Genoa Via Dodecaneso 33 16146 Genoa Italy
| | - Davide Bochicchio
- Department of Physics, University of Genoa Via Dodecaneso 33 16146 Genoa Italy
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22
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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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23
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Álvarez D, Sapia J, Vanni S. Computational modeling of membrane trafficking processes: From large molecular assemblies to chemical specificity. Curr Opin Cell Biol 2023; 83:102205. [PMID: 37451175 DOI: 10.1016/j.ceb.2023.102205] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 06/16/2023] [Accepted: 06/16/2023] [Indexed: 07/18/2023]
Abstract
In the last decade, molecular dynamics (MD) simulations have become an essential tool to investigate the molecular properties of membrane trafficking processes, often in conjunction with experimental approaches. The combination of MD simulations with recent developments in structural biology, such as cryo-electron microscopy and artificial intelligence-based structure determination, opens new, exciting possibilities for future investigations. However, the full potential of MD simulations to provide a molecular view of the complex and dynamic processes involving membrane trafficking can only be realized if certain limitations are addressed, and especially those concerning the quality of coarse-grain models, which, despite recent successes in describing large-scale systems, still suffer from far-from-ideal chemical accuracy. In this review, we will highlight recent success stories of MD simulations in the investigation of membrane trafficking processes, their implications for future research, and the challenges that lie ahead in this specific research domain.
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Affiliation(s)
- Daniel Álvarez
- Department of Biology, University of Fribourg, Switzerland; Departamento de Química Física y Analítica, Universidad de Oviedo, Spain
| | - Jennifer Sapia
- Department of Biology, University of Fribourg, Switzerland
| | - Stefano Vanni
- Department of Biology, University of Fribourg, Switzerland; Université Côte d'Azur, Inserm, CNRS, Institut de Pharmacologie Moléculaire et Cellulaire, Valbonne, France.
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24
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Canepa E, Bochicchio D, Brosio G, Silva PHJ, Stellacci F, Dante S, Rossi G, Relini A. Cholesterol-Containing Liposomes Decorated With Au Nanoparticles as Minimal Tunable Fusion Machinery. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2207125. [PMID: 36899445 DOI: 10.1002/smll.202207125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 01/30/2023] [Indexed: 06/08/2023]
Abstract
Membrane fusion is essential for the basal functionality of eukaryotic cells. In physiological conditions, fusion events are regulated by a wide range of specialized proteins, operating with finely tuned local lipid composition and ionic environment. Fusogenic proteins, assisted by membrane cholesterol and calcium ions, provide the mechanical energy necessary to achieve vesicle fusion in neuromediator release. Similar cooperative effects must be explored when considering synthetic approaches for controlled membrane fusion. We show that liposomes decorated with amphiphilic Au nanoparticles (AuLips) can act as minimal tunable fusion machinery. AuLips fusion is triggered by divalent ions, while the number of fusion events dramatically changes with, and can be finely tuned by, the liposome cholesterol content. We combine quartz-crystal-microbalance with dissipation monitoring (QCM-D), fluorescence assays, and small-angle X-ray scattering (SAXS) with molecular dynamics (MD) at coarse-grained (CG) resolution, revealing new mechanistic details on the fusogenic activity of amphiphilic Au nanoparticles (AuNPs) and demonstrating the ability of these synthetic nanomaterials to induce fusion regardless of the divalent ion used (Ca2+ or Mg2+ ). The results provide a novel contribution to developing new artificial fusogenic agents for next-generation biomedical applications that require tight control of the rate of fusion events (e.g., targeted drug delivery).
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Affiliation(s)
- Ester Canepa
- Department of Physics, University of Genoa, Genoa, 16146, Italy
- Institute of Materials Science & Engineering, EPFL, Lausanne, 1015, Switzerland
| | | | - Giorgia Brosio
- Department of Physics, University of Genoa, Genoa, 16146, Italy
| | | | - Francesco Stellacci
- Materials Characterization Facility, Istituto Italiano di Tecnologia, Genoa, 16163, Italy
| | - Silvia Dante
- Institute of Materials Science & Engineering, EPFL, Lausanne, 1015, Switzerland
| | - Giulia Rossi
- Department of Physics, University of Genoa, Genoa, 16146, Italy
| | - Annalisa Relini
- Department of Physics, University of Genoa, Genoa, 16146, Italy
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25
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Michalski M, Setny P. Two modes of fusogenic action for influenza virus fusion peptide. PLoS Comput Biol 2023; 19:e1011174. [PMID: 37235589 DOI: 10.1371/journal.pcbi.1011174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 05/11/2023] [Indexed: 05/28/2023] Open
Abstract
The entry of influenza virus into the host cell requires fusion of its lipid envelope with the host membrane. It is catalysed by viral hemagglutinin protein, whose fragments called fusion peptides become inserted into the target bilayer and initiate its merging with the viral membrane. Isolated fusion peptides are already capable of inducing lipid mixing between liposomes. Years of studies indicate that upon membrane binding they form bend helical structure whose degree of opening fluctuates between tightly closed hairpin and an extended boomerang. The actual way in which they initiate fusion remains elusive. In this work we employ atomistic simulations of wild type and fusion inactive W14A mutant of influenza fusion peptides confined between two closely apposed lipid bilayers. We characterise peptide induced membrane perturbation and determine the potential of mean force for the formation of the first fusion intermediate, an interbilayer lipid bridge called stalk. Our results demonstrate two routes through which the peptides can lower free energy barrier towards fusion. The first one assumes peptides capability to adopt transmembrane configuration which subsequently promotes the creation of a stalk-hole complex. The second involves surface bound peptide configuration and proceeds owing to its ability to stabilise stalk by fitting into the region of extreme negative membrane curvature resulting from its formation. In both cases, the active peptide conformation corresponds to tight helical hairpin, whereas extended boomerang geometry appears to be unable to provide favourable thermodynamic effect. The latter observation offers plausible explanation for long known inactivity of boomerang-stabilising W14A mutation.
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Affiliation(s)
- Michal Michalski
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Piotr Setny
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
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26
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Di Bartolo AL, Caparotta M, Masone D. Intrinsic Disorder in α-Synuclein Regulates the Exocytotic Fusion Pore Transition. ACS Chem Neurosci 2023. [PMID: 37192400 DOI: 10.1021/acschemneuro.3c00040] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2023] Open
Abstract
Today, it is widely accepted that intrinsic disorder is strongly related to the cell cycle, during mitosis, differentiation, and apoptosis. Of particular interest are hybrid proteins possessing both structured and unstructured domains that are critical in human health and disease, such as α-synuclein. In this work, we describe how α-synuclein interacts with the nascent fusion pore as it evolves toward expansion. We unveil the key role played by its intrinsically disordered region as a thermodynamic regulator of the nucleation-expansion energy barrier. By analyzing a truncated variant of α-synuclein that lacks the disordered region, we find that the landscape of protein interactions with PIP2 and POPS lipids is highly altered, ultimately increasing the energy cost for the fusion pore to transit from nucleation to expansion. We conclude that the intrinsically disordered region in full-length α-synuclein recognizes and allocates pivotal protein:lipid interactions during membrane remodeling in the first stages of the fusion pore.
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Affiliation(s)
- Ary Lautaro Di Bartolo
- Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo (UNCuyo), 5500 Mendoza, Argentina
| | - Marcelo Caparotta
- Quantum Theory Project, Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Diego Masone
- Instituto de Histología y Embriología de Mendoza (IHEM) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Cuyo (UNCuyo), 5500 Mendoza, Argentina
- Facultad de Ingeniería, Universidad Nacional de Cuyo (UNCuyo), 5500 Mendoza, Argentina
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27
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Golani G, Schwarz US. High curvature promotes fusion of lipid membranes: Predictions from continuum elastic theory. Biophys J 2023; 122:1868-1882. [PMID: 37077047 PMCID: PMC10209146 DOI: 10.1016/j.bpj.2023.04.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 03/19/2023] [Accepted: 04/14/2023] [Indexed: 04/21/2023] Open
Abstract
The fusion of lipid membranes progresses through a series of hemifusion intermediates with two significant energy barriers related to the formation of stalk and fusion pore, respectively. These energy barriers determine the speed and success rate of many critical biological processes, including the fusion of highly curved membranes, for example synaptic vesicles and enveloped viruses. Here we use continuum elastic theory of lipid monolayers to determine the relationship between membrane shape and energy barriers to fusion. We find that the stalk formation energy decreases with curvature by up to 31 kBT in a 20-nm-radius vesicle compared with planar membranes and by up to 8 kBT in the fusion of highly curved, long, tubular membranes. In contrast, the fusion pore formation energy barrier shows a more complicated behavior. Immediately after stalk expansion to the hemifusion diaphragm, the fusion pore formation energy barrier is low (15-25 kBT) due to lipid stretching in the distal monolayers and increased tension in highly curved vesicles. Therefore, the opening of the fusion pore is faster. However, these stresses relax over time due to lipid flip-flop from the proximal monolayer, resulting in a larger hemifusion diaphragm and a higher fusion pore formation energy barrier, up to 35 kBT. Therefore, if the fusion pore fails to open before significant lipid flip-flop takes place, the reaction proceeds to an extended hemifusion diaphragm state, which is a dead-end configuration in the fusion process and can be used to prevent viral infections. In contrast, in the fusion of long tubular compartments, the surface tension does not accumulate due to the formation of the diaphragm, and the energy barrier for pore expansion increases with curvature by up to 11 kBT. This suggests that inhibition of polymorphic virus infection could particularly target this feature of the second barrier.
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Affiliation(s)
- Gonen Golani
- Institute for Theoretical Physics and BioQuant Center for Quantitative Biology, Heidelberg University, Heidelberg, Germany
| | - Ulrich S Schwarz
- Institute for Theoretical Physics and BioQuant Center for Quantitative Biology, Heidelberg University, Heidelberg, Germany.
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28
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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.
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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.
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29
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Kasparyan G, Hub JS. Equivalence of Charge Imbalance and External Electric Fields during Free Energy Calculations of Membrane Electroporation. J Chem Theory Comput 2023; 19:2676-2683. [PMID: 37052575 DOI: 10.1021/acs.jctc.3c00065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
Electric fields across lipid membranes play important roles in physiology, medicine, and biotechnology, rationalizing the wide interest in modeling transmembrane potentials in molecular dynamics simulations. Transmembrane potentials have been implemented with external electric fields or by imposing charge imbalance between the two water compartments of a stacked double-membrane system. We compare the two methods in the context of membrane electroporation, which involves a large change of membrane structure and capacitance. We show that, given that Ewald electrostatics are defined with tinfoil boundary conditions, the two methods lead to (i) identical potentials of mean force (PMFs) of pore formation and expansion at various potentials, demonstrating that the two methods impose equivalent driving forces for large-scale transitions at membranes, and (ii) to identical polarization of water within thin water wires or open pores, suggesting that the two methods furthermore impose equivalent local electric fields. Without tinfoil boundary conditions, effects from external fields on pore formation are spuriously suppressed or even removed. Together, our study shows that both methods, external fields and charge imbalance, are well suitable for studying large-scale transitions of lipid membranes that involve changes of membrane capacitance. However, using charge imbalance is technically more challenging for maintaining a constant transmembrane potential since it requires updating of the charge imbalance as the membrane capacitance changes.
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Affiliation(s)
- Gari Kasparyan
- Theoretical Physics and Center for Biophysics, Saarland University, 66123 Saarbrücken, Germany
| | - Jochen S Hub
- Theoretical Physics and Center for Biophysics, Saarland University, 66123 Saarbrücken, Germany
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30
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Eremchev M, Roesel D, Poojari CS, Roux A, Hub JS, Roke S. Passive transport of Ca 2+ ions through lipid bilayers imaged by widefield second harmonic microscopy. Biophys J 2023; 122:624-631. [PMID: 36659849 PMCID: PMC9989880 DOI: 10.1016/j.bpj.2023.01.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 01/04/2023] [Accepted: 01/17/2023] [Indexed: 01/21/2023] Open
Abstract
In biology, release of Ca2+ ions in the cytosol is essential to trigger or control many cell functions. Calcium signaling acutely depends on lipid membrane permeability to Ca2+. For proper understanding of membrane permeability to Ca2+, both membrane hydration and the structure of the hydrophobic core must be taken into account. Here, we vary the hydrophobic core of bilayer membranes and observe different types of behavior in high-throughput wide-field second harmonic imaging. Ca2+ translocation is observed through mono-unsaturated (DOPC:DOPA) membranes, reduced upon the addition of cholesterol, and completely inhibited for branched (DPhPC:DPhPA) and poly-unsaturated (SLPC:SLPA) lipid membranes. We propose, using molecular dynamics simulations, that ion transport occurs through ion-induced transient pores, which requires nonequilibrium membrane restructuring. This results in different rates at different locations and suggests that the hydrophobic structure of lipids plays a much more sophisticated regulating role than previously thought.
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Affiliation(s)
- Maksim Eremchev
- Laboratory for Fundamental BioPhotonics (LBP), Institute of Bioengineering (IBI), School of Engineering (STI), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - David Roesel
- Laboratory for Fundamental BioPhotonics (LBP), Institute of Bioengineering (IBI), School of Engineering (STI), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Chetan S Poojari
- Theoretical Physics and Center for Biophysics, Saarland University, Saarbrücken, Germany
| | - Aurélien Roux
- Biochemistry Department, University of Geneva, Geneva, Switzerland; Swiss National Centre for Competence in Research Programme Chemical Biology, Geneva, Switzerland; School of Chemistry and Biochemistry, University of Geneva, Geneva, Switzerland
| | - Jochen S Hub
- Theoretical Physics and Center for Biophysics, Saarland University, Saarbrücken, Germany
| | - Sylvie Roke
- Laboratory for Fundamental BioPhotonics (LBP), Institute of Bioengineering (IBI), School of Engineering (STI), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland; Institute of Materials Science and Engineering (IMX), School of Engineering (STI), École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland; Lausanne Centre for Ultrafast Science, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
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31
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Xue M, Cao Y, Shen C, Guo W. Computational Advances of Protein/Neurotransmitter-membrane Interactions Involved in Vesicle Fusion and Neurotransmitter Release. J Mol Biol 2023; 435:167818. [PMID: 36089056 DOI: 10.1016/j.jmb.2022.167818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 08/22/2022] [Accepted: 09/04/2022] [Indexed: 02/04/2023]
Abstract
Vesicle fusion is of crucial importance to neuronal communication at neuron terminals. The exquisite but complex fusion machinery for neurotransmitter release is tightly controlled and regulated by protein/neurotransmitter-membrane interactions. Computational 'microscopies', in particular molecular dynamics simulations and related techniques, have provided notable insight into the physiological process over the past decades, and have made enormous contributions to fields such as neurology, pharmacology and pathophysiology. Here we review the computational advances of protein/neurotransmitter-membrane interactions related to presynaptic vesicle-membrane fusion and neurotransmitter release, and outline the in silico challenges ahead for understanding this important physiological process.
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Affiliation(s)
- Minmin Xue
- Key Laboratory for Intelligent Nano Materials and Devices of Ministry of Education, State Key Laboratory of Mechanics and Control of Mechanical Structures, and Institute for Frontier Science, Nanjing University of Aeronautics and Astronautics, Nanjing 210016, China
| | - Yuwei Cao
- State Key Laboratory of Tribology, Department of Mechanical Engineering, Tsinghua University, Beijing, China
| | - Chun Shen
- Key Laboratory for Intelligent Nano Materials and Devices of Ministry of Education, State Key Laboratory of Mechanics and Control of Mechanical Structures, and Institute for Frontier Science, Nanjing University of Aeronautics and Astronautics, Nanjing 210016, China.
| | - Wanlin Guo
- Key Laboratory for Intelligent Nano Materials and Devices of Ministry of Education, State Key Laboratory of Mechanics and Control of Mechanical Structures, and Institute for Frontier Science, Nanjing University of Aeronautics and Astronautics, Nanjing 210016, China; State Key Laboratory of Tribology, Department of Mechanical Engineering, Tsinghua University, Beijing, China.
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32
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Pašalić L, Pem B, Bakarić D. Lamellarity-Driven Differences in Surface Structural Features of DPPS Lipids: Spectroscopic, Calorimetric and Computational Study. MEMBRANES 2023; 13:83. [PMID: 36676890 PMCID: PMC9865892 DOI: 10.3390/membranes13010083] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 12/27/2022] [Accepted: 01/05/2023] [Indexed: 06/17/2023]
Abstract
Although single-lipid bilayers are usually considered models of eukaryotic plasma membranes, their research drops drastically when it comes to exclusively anionic lipid membranes. Being a major anionic phospholipid in the inner leaflet of eukaryote membranes, phosphatidylserine-constituted lipid membranes were occasionally explored in the form of multilamellar liposomes (MLV), but their inherent instability caused a serious lack of efforts undertaken on large unilamellar liposomes (LUVs) as more realistic model membrane systems. In order to compensate the existing shortcomings, we performed a comprehensive calorimetric, spectroscopic and MD simulation study of time-varying structural features of LUV made from 1,2-dipalmitoyl-sn-glycero-3-phospho-L-serine (DPPS), whereas the corresponding MLV were examined as a reference. A substantial uncertainty of UV/Vis data of LUV from which only Tm was unambiguously determined (53.9 ± 0.8 °C), along with rather high uncertainty on the high-temperature range of DPPS melting profile obtained from DSC (≈50-59 °C), presumably reflect distinguished surface structural features in LUV. The FTIR signatures of glycerol moiety and those originated from carboxyl group serve as a strong support that in LUV, unlike in MLV, highly curved surfaces occur continuously, whereas the details on the attenuation of surface features in MLV were unraveled by molecular dynamics.
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33
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Bottacchiari M, Gallo M, Bussoletti M, Casciola CM. Activation energy and force fields during topological transitions of fluid lipid vesicles. COMMUNICATIONS PHYSICS 2022; 5:283. [PMID: 36405503 PMCID: PMC9660165 DOI: 10.1038/s42005-022-01055-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 10/24/2022] [Indexed: 06/16/2023]
Abstract
Topological transitions of fluid lipid membranes are fundamental processes for cell life. For example, they are required for endo- and exocytosis or to enable neurotransmitters to cross the neural synapses. Here, inspired by the idea that fusion and fission proteins could have evolved in Nature in order to carry out a minimal work expenditure, we evaluate the minimal free energy pathway for the transition between two spherical large unilamellar vesicles and a dumbbell-shaped one. To address the problem, we propose and successfully use a Ginzburg-Landau type of free energy, which allows us to uniquely describe without interruption the whole, full-scale topological change. We also compute the force fields needed to overcome the involved energy barriers. The obtained forces are in excellent agreement, in terms of intensity, scale, and spatial localization with experimental data on typical fission protein systems, whereas they suggest the presence of additional features in fusion proteins.
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Affiliation(s)
- Matteo Bottacchiari
- Department of Mechanical and Aerospace Engineering, Sapienza Università di Roma, Rome, Italy
| | - Mirko Gallo
- Department of Mechanical and Aerospace Engineering, Sapienza Università di Roma, Rome, Italy
- Present Address: School of Architecture, Technology and Engineering, University of Brighton, Brighton, United Kingdom
| | - Marco Bussoletti
- Department of Mechanical and Aerospace Engineering, Sapienza Università di Roma, Rome, Italy
| | - Carlo Massimo Casciola
- Department of Mechanical and Aerospace Engineering, Sapienza Università di Roma, Rome, Italy
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34
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Kalutsky MA, Galimzyanov TR, Molotkovsky RJ. A Model of Lipid Monolayer-Bilayer Fusion of Lipid Droplets and Peroxisomes. MEMBRANES 2022; 12:membranes12100992. [PMID: 36295751 PMCID: PMC9612070 DOI: 10.3390/membranes12100992] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 10/06/2022] [Accepted: 10/10/2022] [Indexed: 06/01/2023]
Abstract
Lipid droplets are unique organelles that store neutral lipids encapsulated by the lipid monolayer. In some processes of cellular metabolism, lipid droplets interact with peroxisomes resulting in the fusion of their envelopes and the formation of protrusions of the peroxisome monolayer, called pexopodia. The formation of pexopodia is facilitated by free fatty acids generated during lipolysis within lipid droplets. In this work, we studied the fusion of monolayer and bilayer membranes during the interaction between lipid droplets and peroxisomes. To this end, we built the energy trajectory of this process using the continuum elasticity theory and investigated the molecular details of the fusion structures utilizing molecular dynamics. We divided the fusion process into two stages: formation of a stalk and its consequent expansion into pexopodia. We found that in the considered system, the stalk was energetically more stable and had a lower energy barrier of formation compared to the case of bilayer fusion. The further evolution of the stalk depended on the value of the spontaneous curvature of the membrane in a threshold manner. We attributed the possible expansion of the stalk to the incorporation of free fatty acids into the stalk region. The developed model allowed describing quantitatively the process of monolayer-bilayer fusion.
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Affiliation(s)
- Maksim A. Kalutsky
- A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, 31/5 Leninskiy Prospekt, 119071 Moscow, Russia
- Department of Theoretical Physics and Quantum Technologies, National University of Science and Technology “MISiS”, 4 Leninskiy Prospekt, 119049 Moscow, Russia
| | - Timur R. Galimzyanov
- A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, 31/5 Leninskiy Prospekt, 119071 Moscow, Russia
| | - Rodion J. Molotkovsky
- A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, 31/5 Leninskiy Prospekt, 119071 Moscow, Russia
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35
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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: 9] [Impact Index Per Article: 4.5] [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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36
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Di Bartolo AL, Tomes CN, Mayorga LS, Masone D. Enhanced Expansion and Reduced Kiss-and-Run Events in Fusion Pores Steered by Synaptotagmin-1 C2B Domains. J Chem Theory Comput 2022; 18:4544-4554. [PMID: 35759758 DOI: 10.1021/acs.jctc.2c00424] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The fusion pore controls the release of exocytotic vesicle contents through a precise orchestration of lipids from the fusing membranes and proteins. There is a major lipid reorganization during the different stages in life of the fusion pore (membrane fusion, nucleation, and expansion) that can be scrutinized thermodynamically. In this work, using umbrella sampling simulations we describe the expansion of the fusion pore. We have calculated free energy profiles to drive a nascent, just nucleated, fusion pore to its expanded configuration. We have quantified the effects on the free energy of one and two Synaptotagmin-1 C2B domains in the cytosolic space. We show that C2B domains cumulatively reduce the cost for expansion, favoring the system to evolve toward full fusion. Finally, by conducting thousands of unbiased molecular dynamics simulations, we show that C2B domains significantly decrease the probability of kiss-and-run events.
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Affiliation(s)
- Ary Lautaro Di Bartolo
- Instituto de Histología y Embriología de Mendoza (IHEM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Cuyo (UNCuyo), 5500 Mendoza, Argentina.,Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo (UNCuyo), 5500 Mendoza, Argentina
| | - Claudia N Tomes
- Instituto de Histología y Embriología de Mendoza (IHEM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Cuyo (UNCuyo), 5500 Mendoza, Argentina.,Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo (UNCuyo), 5500 Mendoza, Argentina
| | - Luis S Mayorga
- Instituto de Histología y Embriología de Mendoza (IHEM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Cuyo (UNCuyo), 5500 Mendoza, Argentina.,Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo (UNCuyo), 5500 Mendoza, Argentina
| | - Diego Masone
- Instituto de Histología y Embriología de Mendoza (IHEM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Cuyo (UNCuyo), 5500 Mendoza, Argentina.,Facultad de Ingeniería, Universidad Nacional de Cuyo (UNCuyo), 5500 Mendoza, Argentina
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37
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Marrink SJ, Monticelli L, Melo MN, Alessandri R, Tieleman DP, Souza PCT. Two decades of Martini: Better beads, broader scope. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2022. [DOI: 10.1002/wcms.1620] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Siewert J. Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials University of Groningen Groningen The Netherlands
| | - Luca Monticelli
- Molecular Microbiology and Structural Biochemistry (MMSB ‐ UMR 5086) CNRS & University of Lyon Lyon France
| | - Manuel N. Melo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa Oeiras Portugal
| | - Riccardo Alessandri
- Pritzker School of Molecular Engineering University of Chicago Chicago Illinois USA
| | - D. Peter Tieleman
- Centre for Molecular Simulation and Department of Biological Sciences University of Calgary Alberta Canada
| | - Paulo C. T. Souza
- Molecular Microbiology and Structural Biochemistry (MMSB ‐ UMR 5086) CNRS & University of Lyon Lyon France
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Joardar A, Pattnaik GP, Chakraborty H. Mechanism of Membrane Fusion: Interplay of Lipid and Peptide. J Membr Biol 2022; 255:211-224. [PMID: 35435451 PMCID: PMC9014786 DOI: 10.1007/s00232-022-00233-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 03/25/2022] [Indexed: 11/26/2022]
Abstract
Membrane fusion is an essential process for the survival of eukaryotes and the entry of enveloped viruses into host cells. A proper understanding of the mechanism of membrane fusion would provide us a handle to manipulate several biological pathways, and design efficient vaccines against emerging and re-emerging viral infections. Although fusion proteins take the central stage in catalyzing the process, role of lipid composition is also of paramount importance. Lipid composition modulates membrane organization and dynamics and impacts the lipid–protein (peptide) interaction. Moreover, the intrinsic curvature of lipids has strong impact on the formation of stalk and hemifusion diaphragm. Detection of transiently stable intermediates remains the bottleneck in the understanding of fusion mechanism. In order to circumvent this challenge, analytical methods can be employed to determine the kinetic parameters from ensemble average measurements of observables, such as lipid mixing, content mixing, and content leakage. The current review aims to present an analytical method that would aid our understanding of the fusion mechanism, provides a better insight into the role of lipid shape, and discusses the interplay of lipid and peptide in membrane fusion.
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Affiliation(s)
- Ankita Joardar
- School of Chemistry, Sambalpur University, Jyoti Vihar, Burla, Odisha, 768019, India
| | | | - Hirak Chakraborty
- School of Chemistry, Sambalpur University, Jyoti Vihar, Burla, Odisha, 768019, India.
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Yang L. Scattering measurements on lipid membrane structures. Methods Enzymol 2022; 677:385-415. [DOI: 10.1016/bs.mie.2022.08.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Di Bartolo AL, Masone D. Synaptotagmin-1 C2B domains cooperatively stabilize the fusion stalk via a master-servant mechanism. Chem Sci 2022; 13:3437-3446. [PMID: 35432859 PMCID: PMC8943895 DOI: 10.1039/d1sc06711g] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 02/22/2022] [Indexed: 11/21/2022] Open
Abstract
Synaptotagmin-1 is a low-affinity Ca2+ sensor that triggers synchronous vesicle fusion. It contains two similar C2 domains (C2A and C2B) that cooperate in membrane binding, being the C2B domain the...
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Affiliation(s)
- Ary Lautaro Di Bartolo
- Instituto de Histología y Embriología de Mendoza (IHEM) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Cuyo (UNCuyo) 5500 Mendoza Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo (UNCuyo) 5500 Mendoza Argentina
| | - Diego Masone
- Instituto de Histología y Embriología de Mendoza (IHEM) - Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Cuyo (UNCuyo) 5500 Mendoza Argentina
- Facultad de Ingeniería, Universidad Nacional de Cuyo (UNCuyo) 5500 Mendoza Argentina
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